[Biopython-dev] [Biopython (old issues only) - Bug #3419] (Closed) Bio.SearchIO.FastaIO

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Fri Jul 22 20:07:23 UTC 2016

Issue #3419 has been updated by Travis Wrightsman.

Status changed from New to Closed
% Done changed from 0 to 100
URL set to https://github.com/biopython/biopython/issues/886

Migrated to GitHub, see URL.

Bug #3419: Bio.SearchIO.FastaIO

* Author: Jason Stajich
* Status: Closed
* Priority: Low
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: https://github.com/biopython/biopython/issues/886
The strand of the translated sequence (query or subject depending on the analysis) is lost for tfastxy and fastx/y reports.

from Bio import SearchIO
qresults = SearchIO.parse('test.FASTY.out','fasta-m10')
for qresult in qresults:
    for hit in qresult:
        for hsp in hit.hsps:
                print qresult.id, " ", hit.id, " ", \
                hsp.query_start, "..",hsp.query_end, " ", hsp.query_strand, " ", \
                hsp.hit_start, "..",hsp.hit_end, " ", hsp.hit_strand

bll0026-vs-94.tfasty (32.8 KB)

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