Question: Wiki Erratum...
0
Richard Bruskiewich • 30 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 Megablast has been superseded already by Blast+.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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modified 8.0 years ago
by
Peter • 260
•
written
8.0 years ago by
Richard Bruskiewich • 30
