Richard:
This beauty was mine. Thanks for pointing this out. It is now fixed.
Thanks,
anton
On Dec 9, 2010, at 10:04 PM, Richard Bruskiewich wrote:
Galaxy Colleagues,
I don't know who is maintaining the Galaxy wiki page at http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup but I noticed that the Python script under the Megablast instructions has an error: the "defline" operation after the "line.startswith" should be moved *after* the if length > 0 statement, otherwise, the defline is reset incorrectly before the previous sequence is written out. This results in a frameshift in the FASTA header line identifiers (i.e. the current sequence gets the next sequence identifier).
I've commented out the erroneous defline below and added the right one: import sys
length = 0 defline = '' seq = []
for line in sys.stdin : line = line.rstrip( '\r\n' )
if line.startswith( '>' ): # defline = line.split( "|" )[1] # defline should NOT be here if length > 0: print ">%s_%s" % ( defline, length ) print "\n".join( seq ) length = 0 seq = [] defline = line.split( "|" )[1] # defline should be here else: seq.append( line ) length += len( line )print ">%s_%s" % ( defline, length ) print "\n".join( seq ) While on the topic of this page, perhaps the software versions need to be revisited. Megablast has been superseded already by Blast+. Perhaps new releases of Galaxy should update this?
BTW, when is the new Galaxy release (cloud man AMI too...) coming out? I heard rumors that it was due this week.
Cheers Richard Bruskiewich
-- Richard Bruskiewich, PhD Senior Scientist, Computational and Systems Biology Applications Team for Computational Genomics T.T. Chang Genetic Resources Center International Rice Research Institute
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