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 which is commented by default. I get the error ValueError: Required query and/or hit ID field not found.
I tried to remove the further summarizing openpyxl part of the script and simply run the barebones with searchIO. But the error persists.
file = "out.txt"
blast_generator = SearchIO.parse(file, 'blast-tab', comments=True)
for blast_qresult in blast_generator:
print blast_qresult
for k,blast_hit in enumerate(blast_qresult):
print k
print blast_hit
query = blast_qresult.id
print query
I then tried to repeat the script by adding the column headers exactly and verbatim as present in the blast report.
custom_fields = 'query id, subject ids, query acc.ver, subject acc.ver, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score'
blast_generator = SearchIO.parse(file, 'blast-tab', fields=custom_fields, comments=True)
I still get the same error.
Can you please advice me where I'm going wrong?
1 answer
I looked at SearchIO documentation http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-pysrc.html, and used to the table in there to replace the corresponding fields from the blast report, in the script.
custom_fields = 'qseqid, sseqid, qaccver, sacc_ver, nident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, score'
This still gave the same error. I then remove the commas, and kept the space to see if that helps.
custom_fields = 'qseqid sseqid qaccver sacc_ver nident length mismatch gapopen qstart qend sstart send evalue score'
This resolved the error when printing QueryResult. But I now instead get error "AttributeError: 'Hit' object has no attribute 'sacc_ver' " when I parse this QueryResult and Hit, as the headers now don't match. I will add that error as a separate post.
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In continuation to my post, i'm adding a snippet of my blast report file that I'm trying to parse.