1. biolab
  2. Untitled project
  3. orange-bioinformatics


mitar  committed cefeb35

Moving files around.

  • Participants
  • Parent commits 145bc5b
  • Branches default

Comments (0)

Files changed (232)


View file
  • Ignore whitespace
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+                            Preamble
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+  The precise terms and conditions for copying, distribution and
+modification follow.
+                       TERMS AND CONDITIONS
+  0. Definitions.
+  "This License" refers to version 3 of the GNU General Public License.
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+  An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License.  If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+  1. Source Code.
+  The "source code" for a work means the preferred form of the work
+for making modifications to it.  "Object code" means any non-source
+form of a work.
+  A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+  The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form.  A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+  The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities.  However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work.  For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+  The Corresponding Source need not include anything that users
+can regenerate automatically from other parts of the Corresponding
+  The Corresponding Source for a work in source code form is that
+same work.
+  2. Basic Permissions.
+  All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met.  This License explicitly affirms your unlimited
+permission to run the unmodified Program.  The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work.  This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+  You may make, run and propagate covered works that you do not
+convey, without conditions so long as your license otherwise remains
+in force.  You may convey covered works to others for the sole purpose
+of having them make modifications exclusively for you, or provide you
+with facilities for running those works, provided that you comply with
+the terms of this License in conveying all material for which you do
+not control copyright.  Those thus making or running the covered works
+for you must do so exclusively on your behalf, under your direction
+and control, on terms that prohibit them from making any copies of
+your copyrighted material outside their relationship with you.
+  Conveying under any other circumstances is permitted solely under
+the conditions stated below.  Sublicensing is not allowed; section 10
+makes it unnecessary.
+  3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+  No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+  When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such circumvention
+is effected by exercising rights under this License with respect to
+the covered work, and you disclaim any intention to limit operation or
+modification of the work as a means of enforcing, against the work's
+users, your or third parties' legal rights to forbid circumvention of
+technological measures.
+  4. Conveying Verbatim Copies.
+  You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+  You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+  5. Conveying Modified Source Versions.
+  You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these conditions:
+    a) The work must carry prominent notices stating that you modified
+    it, and giving a relevant date.
+    b) The work must carry prominent notices stating that it is
+    released under this License and any conditions added under section
+    7.  This requirement modifies the requirement in section 4 to
+    "keep intact all notices".
+    c) You must license the entire work, as a whole, under this
+    License to anyone who comes into possession of a copy.  This
+    License will therefore apply, along with any applicable section 7
+    additional terms, to the whole of the work, and all its parts,
+    regardless of how they are packaged.  This License gives no
+    permission to license the work in any other way, but it does not
+    invalidate such permission if you have separately received it.
+    d) If the work has interactive user interfaces, each must display
+    Appropriate Legal Notices; however, if the Program has interactive
+    interfaces that do not display Appropriate Legal Notices, your
+    work need not make them do so.
+  A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit.  Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+  6. Conveying Non-Source Forms.
+  You may convey a covered work in object code form under the terms
+of sections 4 and 5, provided that you also convey the
+machine-readable Corresponding Source under the terms of this License,
+in one of these ways:
+    a) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by the
+    Corresponding Source fixed on a durable physical medium
+    customarily used for software interchange.
+    b) Convey the object code in, or embodied in, a physical product
+    (including a physical distribution medium), accompanied by a
+    written offer, valid for at least three years and valid for as
+    long as you offer spare parts or customer support for that product
+    model, to give anyone who possesses the object code either (1) a
+    copy of the Corresponding Source for all the software in the
+    product that is covered by this License, on a durable physical
+    medium customarily used for software interchange, for a price no
+    more than your reasonable cost of physically performing this
+    conveying of source, or (2) access to copy the
+    Corresponding Source from a network server at no charge.
+    c) Convey individual copies of the object code with a copy of the
+    written offer to provide the Corresponding Source.  This
+    alternative is allowed only occasionally and noncommercially, and
+    only if you received the object code with such an offer, in accord
+    with subsection 6b.
+    d) Convey the object code by offering access from a designated
+    place (gratis or for a charge), and offer equivalent access to the
+    Corresponding Source in the same way through the same place at no
+    further charge.  You need not require recipients to copy the
+    Corresponding Source along with the object code.  If the place to
+    copy the object code is a network server, the Corresponding Source
+    may be on a different server (operated by you or a third party)
+    that supports equivalent copying facilities, provided you maintain
+    clear directions next to the object code saying where to find the
+    Corresponding Source.  Regardless of what server hosts the
+    Corresponding Source, you remain obligated to ensure that it is
+    available for as long as needed to satisfy these requirements.
+    e) Convey the object code using peer-to-peer transmission, provided
+    you inform other peers where the object code and Corresponding
+    Source of the work are being offered to the general public at no
+    charge under subsection 6d.
+  A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+  A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal, family,
+or household purposes, or (2) anything designed or sold for incorporation
+into a dwelling.  In determining whether a product is a consumer product,
+doubtful cases shall be resolved in favor of coverage.  For a particular
+product received by a particular user, "normally used" refers to a
+typical or common use of that class of product, regardless of the status
+of the particular user or of the way in which the particular user
+actually uses, or expects or is expected to use, the product.  A product
+is a consumer product regardless of whether the product has substantial
+commercial, industrial or non-consumer uses, unless such uses represent
+the only significant mode of use of the product.
+  "Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to install
+and execute modified versions of a covered work in that User Product from
+a modified version of its Corresponding Source.  The information must
+suffice to ensure that the continued functioning of the modified object
+code is in no case prevented or interfered with solely because
+modification has been made.
+  If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information.  But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+  The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or updates
+for a work that has been modified or installed by the recipient, or for
+the User Product in which it has been modified or installed.  Access to a
+network may be denied when the modification itself materially and
+adversely affects the operation of the network or violates the rules and
+protocols for communication across the network.
+  Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+  7. Additional Terms.
+  "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law.  If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+  When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it.  (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.)  You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+  Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+    a) Disclaiming warranty or limiting liability differently from the
+    terms of sections 15 and 16 of this License; or
+    b) Requiring preservation of specified reasonable legal notices or
+    author attributions in that material or in the Appropriate Legal
+    Notices displayed by works containing it; or
+    c) Prohibiting misrepresentation of the origin of that material, or
+    requiring that modified versions of such material be marked in
+    reasonable ways as different from the original version; or
+    d) Limiting the use for publicity purposes of names of licensors or
+    authors of the material; or
+    e) Declining to grant rights under trademark law for use of some
+    trade names, trademarks, or service marks; or
+    f) Requiring indemnification of licensors and authors of that
+    material by anyone who conveys the material (or modified versions of
+    it) with contractual assumptions of liability to the recipient, for
+    any liability that these contractual assumptions directly impose on
+    those licensors and authors.
+  All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10.  If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term.  If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+  If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+  Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+  8. Termination.
+  You may not propagate or modify a covered work except as expressly
+provided under this License.  Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+  However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+  Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+  Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License.  If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+  9. Acceptance Not Required for Having Copies.
+  You are not required to accept this License in order to receive or
+run a copy of the Program.  Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance.  However,
+nothing other than this License grants you permission to propagate or
+modify any covered work.  These actions infringe copyright if you do
+not accept this License.  Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+  10. Automatic Licensing of Downstream Recipients.
+  Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License.  You are not responsible
+for enforcing compliance by third parties with this License.
+  An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations.  If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+  You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License.  For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+  11. Patents.
+  A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based.  The
+work thus licensed is called the contributor's "contributor version".
+  A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version.  For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+  Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+  In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement).  To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+  If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients.  "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+  If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+  12. No Surrender of Others' Freedom.
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+  13. Use with the GNU Affero General Public License.
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+  14. Revised Versions of this License.
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+  15. Disclaimer of Warranty.
+  16. Limitation of Liability.
+  17. Interpretation of Sections 15 and 16.
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+                     END OF TERMS AND CONDITIONS
+            How to Apply These Terms to Your New Programs
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    GNU General Public License for more details.
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+Also add information on how to contact you by electronic and paper mail.
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read

File Orange/__init__.py

View file
  • Ignore whitespace

File Orange/bioinformatics/__init__.py

  • Ignore whitespace
Empty file added.

File Orange/bioinformatics/obiArrayExpress.py

View file
  • Ignore whitespace
+A python module for accessing the ArrayExpress web services and database.
+`Array Express Archive <http://www.ebi.ac.uk/arrayexpress/>`_ is a database of gene expression experiments that you
+can query and download.
+Example ::
+    >>> # Retrieve the object representing experiment with accession E-TABM-25 
+    >>> experiment = ArrayExpressExperiment("E-TABM-25")
+    >>> print experiment.accession
+    E-TABM-25
+    >>> print experiment.name
+    Transcription profiling of aging in the primate brain
+    >>> print experiment.species
+    ['Pan troglodytes']
+    >>> print experiment.files
+    [{'kind': ...
+    >>> # Retrieve the data matrix for experiment 'E-MEXP-2917'
+    >>> experiment = ArrayExpressExperiment("E-MEXP-2917")
+    >>> table = experiment.fgem_to_table() 
+Low level Array Express query using REST services::
+    >>> import obiArrayExpress
+    >>> obiArrayExpress.query_experiments(accession='E-MEXP-31')
+    {u'experiments': ...
+    >>> obiArrayExpress.query_experiments(keywords='gliobastoma')
+    {u'experiments': ...
+    >>> obiArrayExpress.query_files(accession='E-MEXP-32', format="xml")
+    <xml.etree.ElementTree.ElementTree object ...
+.. note:: Currently querying ArrayExpress files only works with the xml format.
+.. note:: See the documentation of `query_experiments` for a full set of
+          parameters that these functions accept.
+import os, sys
+import urllib2
+import orngServerFiles
+import warnings
+import posixpath
+import shelve
+import shutil
+import posixpath
+import json
+from xml.etree.ElementTree import ElementTree
+from StringIO import StringIO
+from collections import defaultdict
+from functools import partial
+from contextlib import closing
+parse_json = json.load
+def parse_xml(stream):
+    """ Parse an xml stream into an instance of xml.etree.ElementTree.ElementTree.
+    """
+    return ElementTree(file=stream) 
+# All searchable fields of ArrayExpress (see query_experiments docstring
+# for a description of the fields)
+    ["keywords",
+     "accession",
+     "array",
+     "ef",
+     "efv",
+     "expdesign",
+     "exptype",
+     "gxa",
+     "pmid",
+     "sa",
+     "species",
+     "expandefo",
+     "directsub",
+     "assaycount",
+     "efcount",
+     "samplecount",
+     "sacount",
+     "rawcount",
+     "fgemcount",
+     "miamescore",
+     "date",
+     "wholewords",
+    ]
+class ArrayExpressConnection(object):
+    """ A connection to the ArrayExpress. Used to construct a REST query
+    and run it.
+    .. todo:: Implement user login.
+    """
+    DEFAULT_ADDRESS = "http://www.ebi.ac.uk/arrayexpress/{format}/v2/"
+    DEFAULT_FORMAT = "json"
+    DEFAULT_CACHE = orngServerFiles.localpath("ArrayExpress", "ArrayExpressCache.shelve")
+    # Order of arguments in the query
+    _ARGS_ORDER = ["keywords", "species", "array"]
+    def __init__(self, address=None, timeout=30, cache=None,
+                 username=None, password=None):
+        """ Initialize the connection object.
+        :param address: Address of the ArrayExpress API
+        :param timeout: Timeout for the socket connection
+        .. todo:: Implement user login (see Accessing Private Data in API docs)
+        """
+        self.address = address if address is not None else self.DEFAULT_ADDRESS
+        self.timeout = timeout
+        self.cache = cache if cache is not None else self.DEFAULT_CACHE
+        self.username = username
+        self.password = password
+    def format_query(self, **kwargs):
+        """ Format the query arguments.
+        Example ::
+            >>> conn.format_query(gxa=True, efcount=(1, 5))
+            'efcount=[1 TO 5]&gxa=true'
+        """
+        # Formaters:
+        def format_default(val):
+            if isinstance(val, basestring):
+                return val
+            else:
+                return "+".join(val)
+        def format_species(val):
+            return '"%s"' % val.lower()
+        def format_gxa(val):
+            if val:
+                return "true"
+            else:
+                raise ValueError("gxa={0}".format(val))
+        def format_expandefo(val):
+            if val:
+                return "on"
+            else:
+                raise ValueError("expandefo={0}".format(val))
+        def format_true_false(val):
+            return "true" if val else "false"
+        def format_interval(val):
+            if isinstance(val, tuple):
+                return "[{0} TO {1}]".format(*val)
+            else:
+                raise ValueError("Must be an interval argument (min, max)!")
+        def format_date(val):
+            # TODO check if val contains a datetime.date object, assert proper format
+            return format_interval(val)
+        def format_wholewords(val):
+            if val:
+                return "on"
+            else:
+                raise ValueError("wholewords={0}".format(val))
+        formaters = {"species": format_species,
+                     "gxa": format_gxa,
+                     "expandefo": format_expandefo,
+                     "directsub": format_true_false,
+                     "assaycount": format_interval,
+                     "efcount": format_interval,
+                     "samplecount": format_interval,
+                     "sacount": format_interval,
+                     "rawcount": format_interval,
+                     "fgemcount": format_interval,
+                     "miamescore": format_interval,
+                     "date": format_date,
+                     "wholewords": format_wholewords,
+                     }
+        parts = []
+        arg_items = kwargs.items()
+        ordered = sorted(arg_items, key=lambda arg: self._ARGS_ORDER.index(arg[0]) \
+                         if arg[0] in self._ARGS_ORDER else 100)
+        for key, value in kwargs.iteritems():
+            if key == "format":
+                continue # format is handled in query_url
+            if key not in ARRAYEXPRESS_FIELDS:
+                raise ValueError("Invalid argument name: '{0}'".format(key))
+            if value is not None and value != []:
+                fmt = formaters.get(key, format_default)
+                value = fmt(value)
+                parts.append("{0}={1}".format(key, value))
+        return "&".join(parts)
+    def query_url(self, what="experiments", **kwargs):
+        """ Return a formated query URL for the query arguments
+        Example ::
+            >>> conn.query_url(accession="E-MEXP-31")
+            'http://www.ebi.ac.uk/arrayexpress/json/v2/experiments?accession=E-MEXP-31'
+        """
+        query = self.format_query(**kwargs)
+        url = posixpath.join(self.address, what)
+        url = url.format(format=kwargs.get("format", self.DEFAULT_FORMAT))
+        url = url + ("?" + query if query else "")
+        url = url.replace(" ", "%20")
+        return url
+    def query_url_experiments(self, **kwargs):
+        """ Return a formated experiments query url for the calls arguments
+        """
+        return self.query_url("experiments", **kwargs)
+    def query_url_files(self, **kwargs):
+        """ Return a formated experiments query url for the calls arguments
+        """
+        return self.query_url("files", **kwargs)
+    def query_experiment(self, **kwargs):
+        """ Return an open stream to the experiments query results.
+        .. note:: This member function takes the same arguments as the module
+                  level `query_experiemnts` function.
+        """
+        url = self.query_url_experiments(**kwargs)
+        stream = self._cache_urlopen(url, timeout=self.timeout)
+        return stream
+    def query_files(self, **kwargs):
+        """ Return an open stream to the files query results.
+        .. note:: This member function takes the same arguments as the module
+                  level `query_files` function.
+        """
+        url = self.query_url_files(**kwargs)
+        stream = self._cache_urlopen(url, timeout=self.timeout)
+        return stream
+    def open_file(self, accession, kind="raw", ext=None):
+        """ Return a file handle to experiment data.
+        Possible values for kind:
+            - raw: return the raw data if available
+            - fgem: return the processed data if available
+            - biosamples: a png or svg design image
+            - idf: investigation description
+            - adf: array design description
+            - mageml: MAGE-ML file
+        Example ::
+            >>> raw_file = conn.open_file("E-TABM-1087", kind="raw")
+            >>> processed_file = conn.open_file("E-TABM-1087", kind="fgem")
+        """
+        stream = self.query_files(accession=accession, format="xml")
+        tree = ElementTree(file=stream)
+        files = tree.findall("experiment/file")
+        for file in files:
+            filekind = file.find("kind").text
+            fileext = file.find("extension").text
+            if filekind.strip() == kind and (fileext.strip() == ext or ext is None): 
+                url = file.find("url").text
+                return self._cache_urlopen(url.strip(), timeout=self.timeout)
+    def _cache_urlopen(self, url, timeout=30):
+        if self.cache is not None:
+            with self.open_cache() as cache:
+                cached = url in cache
+            if not cached:
+                stream = urllib2.urlopen(url, timeout=timeout)
+                data = stream.read()
+                with self.open_cache() as cache:
+                    cache[url] = data
+            else:
+                with self.open_cache() as cache:
+                    data = cache[url]
+            return StringIO(data)
+        else:
+            return urllib2.urlopen(url, timeout=timeout)
+    def open_cache(self):
+        if isinstance(self.cache, basestring):
+            return closing(shelve.open(self.cache))
+        elif hasattr(self.cache, "close"):
+            return closing(self.cache)
+        elif self.cache is None:
+            return fake_closing({})
+        else:
+            return fake_closing(self.cache)
+from contextlib import contextmanager
+def fake_closing(obj):
+    yield obj
+def query_experiments(keywords=None, accession=None, array=None, ef=None,
+                      efv=None, expdesign=None, exptype=None,
+                      gxa=None, pmid=None, sa=None, species=None,
+                      expandefo=None, directsub=None, assaycount=None,
+                      efcount=None, samplecount=None, rawcount=None,
+                      fgemcount=None, miamescore=None, date=None, 
+                      format="json", wholewords=None, connection=None):
+    """ Query Array Express experiments.
+    :param keywords: A list of keywords to search (e.g. ['gliobastoma']
+    :param accession: Search by experiment accession (e.g. 'E-MEXP-31')
+    :param array: Search by array design name or accession (e.g. 'A-AFFY-33')
+    :param ef: Experimental factor (names of main variables of experiments)
+    :param efv: Experimental factor value (Has EFO expansion)
+    :param expdesign: Experiment design type. (e.g. ["dose", "response"])
+    :param exptype: Experiment type (e.g. 'RNA-Seq', has EFO expansion)
+    :param gxa: If True limit the results to experiments from the Gene
+        Expreission Atlas only.
+    :param pmid: Search by PubMed identifier
+    :param sa: Sample attribute values (e.g. 'fibroblast', has EFO expansion)
+    :param species: Search by species (e.g. 'Homo sapiens', has EFO expansion)
+    :param expandefo: If True expand the search terms with all its child terms
+        in the Experimental Factor Ontology (EFO_) (e.g. keywords="cancer"
+        will be expanded to include for synonyms and sub types of cancer).
+    :param directsub: If True return only experiments submited directly to
+        Array Express else if False return only experiments imported from GEO
+        database (default None, return both)
+    :param assaycount: A two tuple (min, max) for filter on the number of
+        assays (e.g. (1, 5) will return only experiments with at least one
+        and no more then 5 assays).
+    :param efcount: Filter on the number of experimental factors (e.g. (1, 5))
+    :param sacount: Filter on the number of sample attribute categories
+    :param rawcount: Filter on the number or raw files
+    :param fgemcount: Filter on the number of final gene expression matrix
+        (processed data) files
+    :param miamescore: Filter on the MIAME complience score (max 5)
+    :param date: Filter by release date
+    Example ::
+        >>> query_experiments(species="Homo sapiens", ef="organism_part", efv="liver")
+        {u'experiments': ...
+    .. _EFO: http://www.ebi.ac.uk/efo/
+    """
+    if connection is None:
+        connection = ArrayExpressConnection()
+    stream = connection.query_experiment(keywords=keywords, accession=accession,
+                array=array, ef=ef, efv=efv, expdesign=expdesign, exptype=exptype,
+                gxa=gxa, pmid=pmid, sa=sa, species=species, expandefo=expandefo,
+                directsub=directsub, assaycount=assaycount, efcount=efcount,
+                samplecount=samplecount, rawcount=rawcount, fgemcount=fgemcount,
+                miamescore=miamescore, date=date,  format=format,
+                wholewords=wholewords)
+    if format == "json":
+        return parse_json(stream)
+    else:
+        return parse_xml(stream)
+def query_files(keywords=None, accession=None, array=None, ef=None,
+               efv=None, expdesign=None, exptype=None,
+               gxa=None, pmid=None, sa=None, species=None,
+               expandefo=None, directsub=None, assaycount=None,
+               efcount=None, samplecount=None, rawcount=None,
+               fgemcount=None, miamescore=None, date=None, 
+               format="json", wholewords=None, connection=None):
+    """ Query Array Express files.
+    This function accepts the same arguments as `query_experiments`.
+    Example ::
+        >>> query_files(species="Mus musculus", ef="developmental_stage", efv="embryo", format="xml")
+        <xml.etree.ElementTree.ElementTree object ...
+    .. todo:: why does the json interface not work.
+    """
+    if connection is None:
+        connection = ArrayExpressConnection()
+    stream = connection.query_files(keywords=keywords, accession=accession,
+                array=array, ef=ef, efv=efv, expdesign=expdesign, exptype=exptype,
+                gxa=gxa, pmid=pmid, sa=sa, species=species, expandefo=expandefo,
+                directsub=directsub, assaycount=assaycount, efcount=efcount,
+                samplecount=samplecount, rawcount=rawcount, fgemcount=fgemcount,
+                miamescore=miamescore, date=date,  format=format,
+                wholewords=wholewords)
+    if format == "json":
+        return parse_json(stream)
+    else:
+        return parse_xml(stream)
+def open_file(accession, kind="raw", ext=None, repo_dir=None):
+    """ Open a file for the experiment. 
+    Example ::
+        >>> file = open_file("E-MTAB-369", kind="raw", repo_dir="~/.arrayexpress/")
+    """
+    raise NotImplementedError
+MAGE-TAB convinence functions, classes
+    ["Investigation Title",
+     "Date of Experiment",
+     "Public Release Date",
+     "Experiment Description",
+    ]
+def parse_idf(file):
+    """ Parse an idf.txt (Investigation Description  Format) formated file.
+    Return a list of tuples where the first element is the tag (first column)
+    and the second element is a list of all tag values.
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line and not line.startswith("#")]
+    parsed = [(line[0], line[1:]) for line in lines]
+    return parsed
+def parse_sdrf(file):
+    """ Parse an sdfr formated file. Return a tuple with the first element
+    a list of header values and the second element is a list of all rows
+    (a row is a list of string values).
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line.strip() and not line.startswith("#")]
+    header = [h for h in lines[0] if h]
+    rows = [line[:len(header)] for line in lines[1:]]
+    assert(all([len(r) == len(header) for r in rows]))
+    return header, rows
+def parse_adf(file):
+    pass
+def parse_data_matrix(file):
+    """ Parse the MAGE-TAB processed data matrix. Return a tuple where the
+    elements are:
+        - a (header REF, header values) tuple (e.g. ("Hybridization REF", ["Stage1", "Stage2", ...]) )
+        - a list of quantitations for header values (e.g. ["log2 ratio", "log2 ratio", ...])
+        - a (row REF, row names list) tuple ("e.g. ("Reporter REF", ["Probe 1", "Probe 2", ...]) )
+        - a list of list matrix with values (as strings)
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line.strip()]
+    header = lines[0]
+    header_ref, header = header[0], header[1:]
+    line2 = lines[1]
+    row_ref, quanifications = line2[0], line2[1:]
+    row_names, rows = [], []
+    for line in lines[2:]:
+        r_name, row = line[0], line[1:]
+        row_names.append(r_name)
+        rows.append(row)
+    return ((header_ref, header),
+            quanifications,
+            (row_ref, row_names),
+            rows) 
+class InvestigationDesign(dict):
+    """ Investigation design (contains the contents of the .idf).
+    Example ::
+        >>> idf = InvestigationDesign("foobar.idf")
+        >>> print idf.investigation_title
+        foo investigation
+        >>> print idf.experimental_design
+        ['fubar', 'snafu']
+        >>> print idf.sdrf_file
+        ['foobar.sdrf']
+    """
+    def __init__(self, idf_file=None):
+        idf = parse_idf(idf_file)
+        self._idf = idf
+        self.update(dict(idf))
+        for tag, values in idf:
+            if tag in IDF_SINGLE_TAGS:
+                values = values[0] if values else None
+            ttag = self.transform_tag(tag)
+            setattr(self, ttag, values)
+    def transform_tag(self, tag):
+        """ Transform the tag into a proper python attribute name by
+        replacing all spaces and special characters (e.g '[', ']' into
+        underscores).
+        """
+        toreplace = [" ", "-", "[", "]"]
+        for s in toreplace:
+            tag = tag.replace(s, "_")
+        return tag.lower()
+    def __getitem__(self, tag):
+        """ Return the tag values
+        Example ::
+            >>> idf["Investigation Title"]
+            'foo investigation'
+        """
+        try:
+            return self._idf_dict[tag]
+        except KeyError:
+            pass
+        ttag = self.transform_tag(tag)
+        if hasattr(self, ttag):
+            return getattr(self, ttag)
+        else:
+            raise KeyError(tag)
+class SampleDataRelationship(object):
+    """ Sample-Data Relationship (contains the contents of the .sdrf file).
+    Example ::
+        >>> sdr = SampleDataRelationship("foobar.sdrf")
+        >>> sdr.source_name
+        ['foo', ...
+        >>> sdr.sample_name
+        ['sampled foo', ...
+        >>> sdr.extract_protocol_ref
+        ['bar the foo', ...
+        >>> sdr.derived_array_data_matrix_file
+        ['foobar.data.txt', ...
+        >>>
+    """
+    # Nodes an edges
+    NODES_EDGES = ["Source Name", "Sample Name", "Extract Name",
+                   "Labeled Extract Name", "Hybridization Name",
+                   "Assay Name", "Scan Name", "Normalization Name",
+                   "Array Data File", "Derived Array Data File",
+                   "Array Data Matrix File", "Derived Array Data Matrix File",
+                   "Image File", "Protocol REF"]
+    # Attributes for nodes and edges
+    {"Source Name": ["Characteristics", "Provider", "Material Type", "Description", "Comment"],
+     "Sample Name": ["Characteristics", "Material Type", "Description", "Comment"],
+     "Extract Name":["Characteristics", "Material Type", "Description", "Comment"],
+     "Labeled Extract Name": ["Characteristics", "Material Type", "Description", "Label", "Comment"],
+     "Hybridization Name": ["Array Design File", "Array Design REF", "Comment"],
+     "Assay Name": ["Technology Type", "Comment"],
+     "Scan Name": ["Comment"],
+     "Normalization Name": ["Comment"],
+     "Array Data File": ["Comment"],
+     "Derived Array Data File": ["Comment"],
+     "Array Data Matrix File": ["Comment"],
+     "Derived Array Data Matrix File": ["Comment"],
+     "Image File": ["Comment"],
+     "Protocol REF": ["Term Source REF", "Parameter", "Performer", "Date", "Comment"]
+     }
+    # Attributes
+    {"Characteristics []": ["Unit", "Term Source REF"],
+     "Provider": ["Comment"],
+     "Material Type": ["Term Source REF"],
+     "Label": ["Term Source REF"],
+     "Array Design File": ["Comment"],
+     "Array Design REF": ["Term Source REF", "Comment"],    
+     "Technology Type": ["Term Source REF"],
+     "Factor Value [] ()": ["Unit", "Term Source REF"],
+     "Performer": ["Comment"],
+     "Date": [],
+     "Parameter Value []": ["Unit", "Comment"],
+     "Unit []": ["Term Source REF"],
+     "Description": [],
+     "Term Source REF": ["Term Accession Number"],
+     "Term Accession Number": [],
+     "Comment []": []
+     }
+    def __init__(self, sdrf_file=None):
+        header, rows = parse_sdrf(sdrf_file)
+        self.header = header
+        self.rows = rows 
+    def transform_tag(self, tag):
+        """ Transform the tag into a proper python attribute name by
+        replacing all spaces and special characters (e.g '[', ']' into
+        underscores).
+        """
+        toreplace = [" ", "-", "[", "]"]
+        for s in toreplace:
+            tag = tag.replace(s, "_")
+        return tag.lower()
+    def _subsection(self, name):
+        """ Return the named subsection (name must be from the
+        NODES_EDGES list).
+        """
+        idx = self.NODES_EDGES.index(name)
+        start = self.header.index(name)
+        end = -1
+        for name in self.NODES_EDGES[idx + 1:]:
+            if name in self.header[start + 1:]:
+                end = self.header.index(name, start + 1)
+                break
+        return self.header[start:end], [r[start:end] for r in self.rows]
+    def _column(self, name):
+        """ Return the named column.
+        """
+        index = self.header.index(name)
+        return [r[index] for r in self.rows]
+    def source(self):
+        """ Return the Source subsection
+        """
+        return self._subsection("Source Name")
+    def source_name(self):
+        """ Return the Source Name subsection
+        """
+        return self._column("Source Name")
+    def sample(self):
+        """ Return the Sample subsection
+        """
+        return self._subsection("Sample Name")
+    def sample_name(self):
+        """ Return the Sample Name subsection
+        """
+        return self._column("Sample Name")
+    def extract(self):
+        """ Return the Extract subsection
+        """
+        return self._subsection("Extract Name")
+    def extract_name(self):
+        """ Return the Extract Name subsection
+        """
+        return self._column("Extract Name")
+    def labeled_extract(self):
+        """ Return the Labeled Extract subsection
+        """
+        return self._subsection("Labeled Extract Name")
+    def labeled_extract_name(self):
+        """ Return the Labeled Extract Name subsection
+        """
+        return self._column("Labeled Extract Name")
+    def hybridization(self):
+        """ Return the Hibridization subsection.
+        """
+        return self._subsection("Hibridization Name")
+    def hybridization_name(self):
+        """ Return the Hibridization Name subsection.
+        """
+        return self._column("Hibridization Name")
+    def assay(self):
+        """ Return the Assay subsection
+        """
+        return self._subsection("Assay Name")
+    def assay_name(self):
+        """ Return the Assay Name subsection
+        """
+        return self._column("Assay Name")
+    def scan(self):
+        """ Return the Scan subsection
+        """
+        return self._subsection("Scan Name")
+    def scan_name(self):
+        """ Return the Scan name subsection
+        """
+        return self._column("Scan Name")
+    def normalization(self):
+        """ Return the Normalization subsection.
+        """
+        return self._subsection("Normalization Name")
+    def normalization_name(self):
+        """ Return the Normalization Name subsection.
+        """
+        return self._column("Normalization Name")
+    def array_data(self):
+        """ Return the Array Data subsection
+        """
+        return self._subsection("Array Data File")
+    def array_data_file(self):
+        """ Return the Array Data File subsection
+        """
+        return self._column("Array Data File")
+    def derived_array_data(self):
+        """ Return the Derived Array Data subsection
+        """
+        return self._subsection("Derived Array Data File")
+    def derived_array_data_file(self):
+        """ Return the Derived Array Data File subsection
+        """
+        return self._column("Derived Array Data File")
+    def array_data_matrix(self):
+        """ Return the Array Data Matrix subsection.
+        """
+        return self._subsection("Array Data Matrix File")
+    def array_data_matrix_file(self):
+        """ Return the Array Data Matrix File subsection.
+        """
+        return self._column("Array Data Matrix File")
+    def derived_array_data_matrix(self):
+        """ Return the Derived Array Data Matrix subsection.
+        """
+        return self._subsection("Derived Array Data Matrix File")
+    def derived_array_data_matrix_file(self):
+        """ Return the Derived Array Data Matrix File subsection.
+        """
+        return self._column("Derived Array Data Matrix File")
+    def image(self):
+        """ Return the Image subsection
+        """
+        return self._subsection("Image File")
+    def image_file(self):
+        """ Return the Image File subsection.
+        """
+        return self._column("Image File")
+class ArrayDesign(object):
+    """ Arary design (contains the contents of the .adf file).
+    """
+    def __init__(self, adf_file=None):
+        adf = parse_adf(adf_file)
+        self._adf = adf
+def _is_float(str):
+    try:
+        float(str)
+        return True
+    except ValueError:
+        return False
+def _is_continuous(items, check_count=100):
+    """ Are the strings in items continous numbers. 
+    """
+    count = 0
+    i = 0
+    for i, item in enumerate(items):
+        if _is_float(item):
+            count += 1
+        if i >= check_count:
+            break
+    return count >= i * 0.5
+def processed_matrix_to_orange(matrix_file):
+    """ Load a single processed matrix file in to an Orange.data.Table
+    instance. 
+    """
+    import numpy
+    import Orange
+    if isinstance(matrix_file, basestring):
+        matrix_file = open(matrix_file, "rb")
+#    data_matrix = matrix_file.read()
+    header, quantification, rows, matrix = parse_data_matrix(matrix_file)
+    header_ref, header = header
+    row_ref, rows = rows
+    matrix = numpy.array(matrix, dtype=object)
+    features = []
+    is_float = numpy.frompyfunc(_is_float, 1, 1) # an numpy ufunc
+    for header_name, quant, column in zip(header, quantification, matrix.T):
+        if _is_continuous(column):
+            feature = Orange.feature.Continuous(header_name)
+            column[numpy.where(1 - is_float(column))] = "?" # relace all non parsable floats with '?'
+        else:
+            values = set(column)
+            feature = Orange.feature.Discrete(header_name, values=sorted(values))
+        feature.attributes["quantification"] = quant
+        features.append(feature)
+    row_ref_feature = Orange.feature.String(row_ref)
+    domain = Orange.data.Domain(features, None)
+    domain.addmeta(Orange.feature.Descriptor.new_meta_id(), row_ref_feature)
+    table = Orange.data.Table(domain, [list(row) for row in matrix])
+    # Add row identifiers
+    for instance, row in zip(table, rows):
+        instance[row_ref_feature] = row
+    return table
+def mage_tab_to_orange(idf_filename):
+    """ Convert an MAGE-TAB annotated experiment into an Orange.data.Table
+    instance (assumes all the associated MAGE-TAB files are in the same
+    directory.
+    .. todo:: Add Characteristics, Factor Values ... to the feature.attributes dict
+    """
+    import Orange
+    dirname = os.path.dirname(idf_filename)
+    idf = InvestigationDesign(idf_filename)
+    sdrf_filename = os.path.join(dirname, idf.sdrf_file[0])
+    sdrf = SampleDataRelationship(sdrf_filename)
+    data_matrices = set(sdrf.derived_array_data_matrix_file())
+    data_matrices = [name for name in data_matrices if name.strip()]
+    tables = []
+    for filename in data_matrices:
+        matrix_file = os.path.join(dirname, filename)
+        table = processed_matrix_to_orange(matrix_file)
+        tables.append(table)
+    return hstack_tables(tables)
+def hstack_tables(tables):
+    """ Stack the tables horizontaly.
+    """
+    import Orange
+    max_len = max([len(table) for table in tables])
+    stacked_features = []
+    stacked_values = [[] for i in range(max_len)]
+    stacked_meta_features = []
+    stacked_meta_values = [{} for i in range(max_len)]
+    for table in tables:
+        stacked_features.extend(table.domain.variables)
+        stacked_meta_features.extend(table.domain.getmetas().items())
+        for i, instance in enumerate(table):
+            stacked_values[i].extend(list(instance))
+            stacked_meta_values[i].update(instance.getmetas())
+        # Fill extra lines with unknowns
+        for i in range(len(table), max_len):
+            stacked_values[i].extend(["?"] * len(table.domain.variables))
+    domain = Orange.data.Domain(stacked_features, tables[-1].domain.class_var)
+    domain.addmetas(dict(set(stacked_meta_features)))
+    table = Orange.data.Table(domain, stacked_values)
+    # Add meta attributes
+    for instance, metas in zip(table, stacked_meta_values):
+        for m, val in metas.iteritems():
+            instance[m] = val
+    return table
+def _dictify(element):
+    """ 'Dictify' and xml.etree.Element.Element instance by taking all
+    subnode tags as keys and the corresponding text values as items i.e. turn
+    `<node><bla>foo</bla><a>b</b></node>` into a {"bla":"foo", "a":b"}
+    """
+    if element is None:
+        element = []
+    dict = {}
+    strip = lambda s: s.strip() if s else s
+    for node in element:
+        dict[node.tag] = strip(getattr(node, "text", None))
+    return dict
+class SearchableList(list):
+    """ A list with a `search` method
+    """
+    def search(self, **kwargs):
+        """ Search the list for elements with members that correspond the
+        supplied keyword arguments.
+            >>> foo.bar = "foo"
+            >>> list = SearchableList([foo, bar])
+            >>> list.search(bar="foo") # Search for objects which have a member named "bar" and that member equals "foo"
+            [<__main__.foo object ...
+        """
+        ret = []
+        for obj in self:
+            for member, value in kwargs.items():
+                if hasattr(obj, member) and getattr(obj, member) == value:
+                    ret.append(obj)
+        return ret
+class ArrayExpressExperiment(object):
+    """ An convinience class representing an Array Express Experiment.
+    Example ::
+        >>> ae = ArrayExpressExperiment("E-MEXP-2917")
+        >>> print ae.name
+        Characterization of Data Variation in Gene Expression Profiling of Human Peripheral Blood Samples
+        >>> for file in ae.files:
+        ...     print file["name"], file["url"]
+        E-MEXP-2917.sdrf.txt http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2917/E-MEXP-2917.sdrf.txt
+        ...
+        >>> table = ae.fgem_to_table() # Retieve the experiment data table 
+    """
+    def __init__(self, accession, connection=None):
+        self.accession = accession
+        self.connection = connection
+        self._etree = tree = query_experiments(accession=accession, connection=self.connection, format="xml")
+        experiments = tree.findall("experiment")
+        # find the exact match (more then one experiment can be listed in the query result)
+        experiments = [e for e in experiments if e.find("accession").text.strip() == accession]
+        self._experiment = experiment = experiments[0]
+        self.species = [e.text for e in experiment.findall("species")]
+        bool_values = {"true": True, "false": False}
+        self.rawdatafiles = bool_values[experiment.find("rawdatafiles").get("available","false")]
+        self.fgemdatafiles = bool_values[experiment.find("fgemdatafiles").get("available", "false")]
+        self.sampleattributes = []
+        for sa in experiment.findall("sampleattribute"):
+            category = sa.find("category").text.strip()
+            values = [val.text for val in sa.findall("value")]
+            self.sampleattributes.append((category, values))
+        self.experimentalfactors = []
+        for ef in experiment.findall("experimentalfactor"):
+            name = ef.find("name").text.strip()
+            values = [val.text.strip() for val in ef.findall("values")]
+            self.experimentalfactors.append((name, values))
+        self.miamescores = _dictify(experiment.find("miamescores"))
+        self.id = experiment.find("id").text
+        self.secondaryaccession = getattr(experiment.find("secondaryaccession"), "text", None)
+        self.name = experiment.find("name").text
+        self.experimenttype = experiment.find("experimenttype").text.strip()
+        self.releasedate = experiment.find("releasedate").text
+        self.lastupdatedate = getattr(experiment.find("lastupdatedate"), "text", None)
+        self.samples = int(experiment.find("samples").text)
+        self.assays = int(experiment.find("assays").text)
+        self.arraydesign = [_dictify(e) for e in experiment.findall("arraydesign")]
+        self.bioassaydatagroups = [_dictify(group) for group in experiment.findall("bioassaydatagroup")]
+        self.bibliography = [_dictify(e) for e in experiment.findall("bibliography")]
+        self.provider = [_dictify(e) for e in experiment.findall("provider")]
+        self.experimentdesign = []
+        for expd in experiment.findall("experimentdesign"):
+            self.experimentdesign.append(expd.text)
+        self.description = [_dictify(e) for e in experiment.findall("description")]
+        tree = query_files(accession=self.accession, format="xml", connection=self.connection)
+        experiments = tree.findall("experiment")
+        experiments = [e for e in experiments if e.find("accession").text.strip() == accession]
+        experiment = experiments[0]
+        files = experiment.findall("file")
+        self.files = [_dictify(file) for file in files]
+    def _download_processed(self):
+        """ Download the processed matrix file, and associated MAGE-TAB files (idf, sdrf, adf)
+        .. todo:: What about the raw data files (we need converters for other file types) 
+        """
+        assert(self.fgemdatafiles)
+        exp_files = [(f["kind"], f) for f in self.files if f.get("kind") in ["idf", "sdrf"] and f.get("extension") == "txt"]
+        exp_files += [(f["kind"], f) for f in self.files if f.get("kind") == "fgem"]
+        array_files = [(f["kind"], f) for f in self.files if f.get("kind") == "adf" and f.get("extension") == "txt"]
+        assert(len(files) == 3)
+        for type, file in files.iteritems():
+            url = file["url"].strip()
+            rest, basename = os.path.split(url)
+            _, dirname = os.path.split(rest)
+            repo_dir = orngServerFiles.localpath("ArrayExpress", dirname)
+            try:
+                os.makedirs(repo_dir)
+            except OSError:
+                pass
+            local_filename = os.path.join(repo_dir, basename)
+            stream = urllib2.urlopen(url)
+            shutil.copyfileobj(stream, open(local_filename, "wb"))
+            if file["extension"] == "zip":
+                import zipfile
+                zfile = zlib.ZipFile(local_filename)
+                zfile.extractall(repo_dir)
+            elif file["extension"] == "gz":
+                import gzip
+                gzfile = gzip.open(local_filename)