Hi ...
I'm trying to parse a blast tabular format file (outfmt 6) to access it's individual elements for further manipulation .
I need to retrieve the
qseqid, qstart, qend, qlen, qseq, sseqid, sstart, send, slen, sseq and pident for each hit
and here's the script :
blast_qresult=SearchIO.parse('Aegilops_Brachypodium.txt','blast-tab')
for i,blast_hit in enumerate(blast_qresult) :
for m,blast_hsp in enumerate(blast_hit):
for n in range(len(blast_hsp)):
print("Query ID: %s"%blast_hit.id)
print("Query start: %s"%blast_hsp[n].query_start)
print("Query end: %s"%blast_hsp[n].query_end)
print("Query seq: %s"%blast_hsp[n].query)
print("Hit ID: %s"%blast_hit[m].id)
print("Hit start: %s"%blast_hsp[n].hit_start)
print("Hit end: %s"%blast_hsp[n].hit_end)
print("Hit seq: %s"%blast_hsp[n].hit)
print("Identity: %s"%blast_hsp[n].ident_pct)
Till here it does produce some results , and halts at certain hit throwing this error :
builtins.ValueError: Hit 'BRADI2G54940.1' already present in this QueryResult.
And when I try to access the other individual values like :
print(blast_hsp[n].seq_len)
print(blast_hit[m].seq_len)
They give these errors respectively :
builtins.AttributeError: 'HSP' object has no attribute 'seq_len'
builtins.AttributeError: 'Hit' object has no attribute 'seq_len'
My questions are :
1. How can I access the ...