[Biopython-dev] [Biopython - Bug #3419] Bio.SearchIO.FastaIO

[redmine at redmine.open-bio.org]

Issue #3419 has been updated by Wibowo Arindrarto.


Hi Jason,

Thanks for the report :). Do you have an example file handy which I can try to include in our test suite? The FASTA parser was not tested using [t]fast[y|x], so there may be some lines / cases which the parser couldn't handle.
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Bug #3419: Bio.SearchIO.FastaIO
https://redmine.open-bio.org/issues/3419

Author: Jason Stajich
Status: New
Priority: Low
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: 


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


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