Issue #49 new

Indexing-Components must have same text length

Anonymous avatarAnonymous created an issue

When I try to build index for my maf file, i got errors, Is their any requirements for the maf files?

the maf file come from multiz alignment results, which has four genomes. Some alignment records has sequences from all four species, while some other records has sequences from three species, does this matters?

Error messages:

Traceback (most recent call last): File "/PROJ/GR/share/Software/python_lib/bin/maf_build_index.py", line 5, in <module> pkg_resources.run_script('bx-python==0.7.1', 'maf_build_index.py') File "/PROJ/GR/share/Software/python_lib/lib64/python/distribute-0.6.35-py2.6.egg/pkg_resources.py", line 505, in run_script self.require(requires)[0].run_script(script_name, ns) File "/PROJ/GR/share/Software/python_lib/lib64/python/distribute-0.6.35-py2.6.egg/pkg_resources.py", line 1245, in run_script execfile(script_filename, namespace, namespace) File "/PROJ/GR/share/Software/python_lib/lib64/python/bx_python-0.7.1-py2.6-linux-x86_64.egg/EGG-INFO/scripts/maf_build_index.py", line 83, in <module> if name == "main": main() File "/PROJ/GR/share/Software/python_lib/lib64/python/bx_python-0.7.1-py2.6-linux-x86_64.egg/EGG-INFO/scripts/maf_build_index.py", line 72, in main block = maf_reader.next() File "/PROJ/GR/share/Software/python_lib/lib64/python/bx_python-0.7.1-py2.6-linux-x86_64.egg/bx/align/maf.py", line 64, in next return read_next_maf( self.file, **self.maf_kwargs ) File "/PROJ/GR/share/Software/python_lib/lib64/python/bx_python-0.7.1-py2.6-linux-x86_64.egg/bx/align/maf.py", line 165, in read_next_maf alignment.add_component( component ) File "/PROJ/GR/share/Software/python_lib/lib64/python/bx_python-0.7.1-py2.6-linux-x86_64.egg/bx/align/core.py", line 42, in add_component raise Exception( "Components must have same text length" ) Exception: Components must have same text length

Comments (1)

  1. Bob Harris

    ( using terminology from mAF spec at http://genome.ucsc.edu/FAQ/FAQformat#format5 )

    This exception is raised when two components ('s' lines) in the same alignment block have dissimilar text lengths (6th and last field in any 's' line). This could be a bug in bx-python or a bug in whatever produced the maf file, or I think it could also be caused if a maf file is truncated.

    You'll need to check your maf file to determine whether it is malformed. It would be helpful if the exception were to indicate the line number in the file being parsed. I would check the end of your maf file first to see if perhaps it has been truncated. That could result in short alignment text on the last line in the file.

    My best guess is the maf file is the problem, since this is such a simple sanity test in bx-python.

  2. Log in to comment
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.