I would definitely like to help test this code. How can I do it?
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I installed biopython 1.58 on my MAC Pro.
Then I tried running the following code from here:
from Bio import AlignIO
for multiple_alignment in AlignIO.parse("chr10.maf", "maf"):
print "printing a new multiple alignment"
for seqrec in multiple_alignment:
print "starts at %s on the %s strand of a sequence %s in length, and runs for %s bp" % \
(seqrec.annotations["start"],
seqrec.annotations["strand"],
seqrec.annotations["srcSize"],
seqrec.annotations["size"])
(I changed "chr10.maf" to "chrI.maf" so it would match the file I have.)
My result was:
Traceback (most recent call last):
File "program.py", line 3, in <module>
for multiple_alignment in AlignIO.parse("chrI.maf","maf"):
File "/Library/Python/2.7/site-packages/Bio/AlignIO/__init__.py", line 368, in parse
raise ValueError("Unknown format '%s'" % format)
ValueError: Unknown format 'maf'
Can anyone help?
That wiki page was misleading, the MAF code isn't in the main Biopython distribution yet,just on GitHub. Would you be interested in helping test it - especially the MAF specific indexing ideas?
I would definitely like to help test this code. How can I do it?
Ask on the Biopython mailing list for more details, but you'll need to install Biopython from Andrew's branch - currently https://github.com/polyatail/biopython/tree/alignio-maf I think.
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