Question: AttributeError: 'Hit' object has no attribute 'sacc_ver'
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gravatar for bioinfoSeeker
22 months ago by
United Kingdom
bioinfoSeeker20 wrote:

Hi, I am trying to write a script to parse and summarize the ncbi web blast output (14 columns). I am using biopython searchIO on the tab delimited output file with the first seven lines commented by default.

I get the following error : AttributeError: 'Hit' object has no attribute 'sacc_ver'

In my previous post, I had described how I had to use the fields from searchIO documentation http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-pysrc.html to replace the corresponding fields from the blast report, in the script. A: Blast parse script: ValueError: Required query and/or hit ID field not found.

from Bio import SeqIO
from Bio import SearchIO

file = "out.txt"
custom_fields = 'qseqid sseqid qaccver sacc_ver nident length mismatch gapopen qstart qend sstart send evalue score'

blast_generator = SearchIO.parse(file, 'blast-tab', fields=custom_fields, comments=True)
for blast_qresult in blast_generator:
    print "This is blast_qresult ", blast_qresult
    for k,blast_hit in enumerate(blast_qresult):
        print "This is blast_qresult.hit ", blast_hit
        query = blast_hit.id
        print "This is blast_hit.id ", query
        subject = blast_hit.sacc_ver
        print "This is blast_hit subject accession ", subject

As per http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html, the sacc_ver attribute is present in the blast_hit object. So, I am not sure why it gives this error. Can you please help me to identify my error.

blast biopython searchio python • 813 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by bioinfoSeeker20

What version of Biopython do you have? If updating does not fix this you might want to report this at https://github.com/biopython/biopython/issues

ADD REPLYlink written 22 months ago by Peter5.8k
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