Commits

Clint Howarth committed 7aaabd8

update docs and version

Comments (0)

Files changed (6)

 801057bc12d612a2ed94dfce354af3a04bab3de7 1.1.1
+7c3b53cee55b75ac494371a901a9063b12e8eb62 1.2
 Changes
 =======
 
+1.2
+  added option for source-specific cutoffs when culling blast hits (thanks, @jdewar)
+
 1.1
   revised initial release, better python structure, packaging, and documentation
 
 Credits
 -------
 
-Genepidgin was written by Clint Howarth and Matthew Pearson. Many people have contributed to the project:
+Genepidgin was written by Clint Howarth and Matthew Pearson, with recent updates made by Janet Gainer-Dewar. Many people have contributed to the project:
 
 cleaner
 =======
 select
 ======
 
-``genepidgin select`` was designed by Sharvari Gujja, Brian Haas, Clint Howarth, Matthew Pearson, and Qiandong Zeng. Clint Howarth implemented it.
+``genepidgin select`` was designed by Sharvari Gujja, Brian Haas, Clint Howarth, Matthew Pearson, and Qiandong Zeng. Clint Howarth implemented it, and Janet Gainer-Dewar has added features.
 
 Special Thanks
 ==============
 :doc:`select`
     selects the most appropriate product name from a vareity of homology evidence
 
-``genepidgin`` is developed and maintained by engineers and biologists at the `Broad Institute <http://www.broadinstitute.org>`_. Suggestions are welcome; we can be reached at ``pidgin-support at broadinstitute dot org``.
+``genepidgin`` is developed and lightly maintained by engineers and biologists at the `Broad Institute <http://www.broadinstitute.org>`_.
 
 Development Status
 ------------------
 
-.. warning:: *This code is not under active development, and there are better ways of doing this.* When we started this project, well-defined ontology sets were uncertain, but there are enough around that this approach is relatively antiquated. Nowadays, you're almost certainly better off with EC lookups, go-terms and similar, more direct methods.
+.. warning:: *This code is in maintenance mode only, and there are better ways of doing this.* When we started this project, well-defined ontology sets were uncertain. There are enough around now that this approach is relatively antiquated. Nowadays, you're almost certainly better off with EC lookups, go-terms and similar, more direct methods.
 
 Contents
 --------
       -o --output    : where to save files, defaults to ./pidgin_names.txt
       -e --etymology : where to save etymology (debug), defaults to ./pidgin_etymology.txt
       -h --help      : this information
+      --use_custom_blast_cutoffs : use different cutoffs for different sources
 
 The format of Input and Output files are described below.
 
     No name was ultimately selected from any of the supplied sources.
     Final name: hypothetical protein
 
+use_custom_blast_cutoffs
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+As hardcoded in pidgin.select, widens the cutoff margin for blast hits (currently KEGG-only, check source for details).
+
 .. note:: Please see :doc:`credits` for contributor information.
 

genepidgin/__init__.py

-version_info = (1, 1, 1)
+version_info = (1, 2, 0)
 version = '.'.join(str(n) for n in version_info[:3])
 release = version + ''.join(str(n) for n in version_info[3:])