[Biopython-dev] [Bug 2654] Bio.Blast.NCBIStandalone does not support the output file argument
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Mar 19 17:08:16 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2654
biopython-bugzilla at maubp.freeserve.co.uk changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|NEW |RESOLVED
Resolution| |FIXED
------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk 2009-03-19 13:08 EST -------
Fixed in Bio/Blast/NCBIStandalone.py CVS revision 1.86
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython
Note that the three tools themselves all use -o (lower case) for the output
file, but refer to it slightly differently:
$ ./rpsblast --help | grep " -o "
-o Output File for Alignment [File Out] Optional
$ ./blastpgp --help | grep " -o "
-o Output File for Alignment [File Out] Optional
$ ./blastall --help | grep " -o "
-o BLAST report Output File [File Out] Optional
Our function for rpsblast already supported this argument under the name
"align_outfile" which I have therefore also used for blastpgp (this is good
name as blastpgp outputs more than one type of file).
For blastall "align_outfile" doesn't seem entirely appropriate, and although it
is inconsistent I have gone for "outfile" instead.
Example usage:
#imports and setting up input parameters omitted
out_handle, err_handle = NCBIStandalone.blastall(blastall_exe, "blastp",
blastdb_nr, query_file,
expectation=0.000001,
nprocessors=1, filter="F",
outfile=output_file,
alignments=5, descriptions=5)
assert "" == err_handle.read()
assert "" = out_handle.read() #Important so we wait for BLAST to finish!
err_handle.close()
out_handle.close()
assert os.path.isfile(output_file)
count = 0
for blast_record in NCBIXML.parse(open(output_file)) :
count += 1
print "Found %i BLAST results" % count
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