[Biopython] Tutorial Question 7.4 alignment.title
Ara Kooser
akooser at unm.edu
Fri Oct 8 03:06:00 UTC 2010
Hello all,
I am a new user to Biopython. I've been working my way through the
tutorial. I have a question about how the alignment.title works in the
example given in section 7.4 of the tutorial. I wrote the following
code:
from Bio.Blast import NCBIXML
E_VALUE_THRESH = 1e-30
result_handle = open("test.xml")
blast_records = NCBIXML.parse(result_handle)
blast_record = blast_records.next()
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_VALUE_THRESH:
print '****Alignment****'
print 'sequence:', alignment.title
print 'e value:', hsp.expect
print 'length:', alignment.length
print 'start:', hsp.query_start
print 'end:',hsp.query_end
To look at a .xml file that was produced by BLAST. I was wondering if
there was a way to break up the string for information produced by the:
print 'sequence:', alignment.title
Basically I would like the organisms name first, followed by the locus
number. I wasn't sure how to split up the print command.
I looked at the docs over at http://biopython.org/DIST/docs/api/ to
see if there was a tag specifically for the locus number and organism
name.
Thank you for your time and help.
Regards,
Ara
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