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 Megablast has been superseded already by Blast+.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

_______________________________________________
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev