[BioPython] BLAST results and more title information

[Leighton Pritchard]

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Hi Aaron,

With your BLAST record as b_results, what you're looking for is probably
in the b_record.alignments list.  Each alignment in b_record.alignments
has the full version of the title that is truncated in the summary lines
you describe.  For example (untested code):

|>> b_results = NCBIWWW.qblast('blastp', 'nr', f_record, format_type="text")
|>> len(b_results.alignments)  # Number of alignments made
|>> descriptions = [alignment.title for alignment in
b_results.alignments] # Get a list of all descriptions
|>> for alignment in b_results.alignments:  # Print descriptions, one
per line
...	print alignment.title

might be what you need.

L.

Aaron Zschau wrote:
| I'm trying to figure out how to get the full description line from my
| blast search results
|
|
| I run the following command, where f_record contains a protein string:
|
| b_results = NCBIWWW.qblast('blastp', 'nr', f_record, format_type="text")
|
| and get a blast file containing the following lines (full file also
| attached)
|
|
| emb|CAA70306.1| hypoxia-inducible factor one alpha [Mus musculus]
| 1311   0.0
| gb|AAC52730.1| hypoxia-inducible factor 1 alpha
| 1305   0.0
| ref|NP_077335.1| hypoxia inducible factor 1, alpha subunit [Ratt...
| 1305   0.0
| emb|CAA70701.1| hypoxia-inducible factor 1 [Rattus norvegicus] >...
| 1305   0.0
| sp|Q61221|HIFA_MOUSE Hypoxia-inducible factor 1 alpha (HIF-1 alp...
| 1302   0.0
| ref|NP_034561.1| hypoxia inducible factor 1, alpha subunit [Mus ...
| 1300   0.0
| gb|AAH26139.1| Hypoxia inducible factor 1, alpha subunit [Mus mu...
| 1296   0.0
| emb|CAA70305.1| hypoxia-inducible factor one alpha [Mus musculus]
| 1291   0.0
|
|
| Is there an easy way to get more information out of the title
| information instead of being cut off (e.g. getting the full line instead
| of "hypoxia inducible factor 1, alpha subunit [Mus ... " since some
| results have longer title lines and sometimes push the species info out
| of view.
|
| thanks,
|
| Aaron Zschau
|
|
|
|
|
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|
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- --
Dr Leighton Pritchard AMRSC
D104, PPI, Scottish Crop Research Institute
Invergowrie, Dundee, DD2 5DA, Scotland, UK
E: lpritc at scri.sari.ac.uk
W: http://bioinf.scri.sari.ac.uk/lp/index.shtml
T: +44 (0)1382 532761 ext.2405		F: +44 (0)1382 568578
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