Question: how to get the strand from a blast xml file
gravatar for bio90029
12 months ago by
bio9002910 wrote:

Hi, I am working with a blast xml as the one below:

      <Hsp_midline>||||||||  | || || || || |||||||| ||||| ||| | || |||||||||||||| || || ||| |  | || ||| ||||  | || | ||  || | ||| | | ||| | |||    |||| |  ||| | | ||  || ||||||||  |||||||||||||||||||||||||||| || || | ||  ||| |||||||| ||  | ||     | || |||||||||||||||||</Hsp_midline>

I am using a script based on the one provide by biopython Cook's book (below) but this is what I get;

(None, None)

from Bio.Blast import NCBIXML
 blast_record =
for alignment in blast_record.alignments:
... for hsp in alignment.hsps:
        print hsp.strand

Can anyone help me to extract in which strand the subj.sequence is, please? I would like to do this so I can work with the sequence. What I would like to do is to get to the contigs and add the missing bases but if it is in the strand -1 I need to reversed_complement() the sequence. Thanks

biopython python • 494 views
ADD COMMENTlink modified 9 months ago by toralmanvar630 • written 12 months ago by bio9002910
gravatar for toralmanvar
9 months ago by
toralmanvar630 wrote:

you may try greping <hsp_qseq> and <hsp_hseq> lines showing alignment of query with that of subject (irrepective of the strand in which it belong) and can replace the missing base in contigs.

ADD COMMENTlink written 9 months ago by toralmanvar630

Thanks, Unluckily, I cannot used grep as I wanted it as part of a python programme I was working on. By now I had finished it. I worked out the strand by the start and end positions.

ADD REPLYlink written 9 months ago by bio9002910
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