Hi, could someone help me ? I am trying to parse hmmer results from a file with the code in biopython, however when I run it, it shows no "hits"attribute in the line with 'hits = qresult.hits' :
import Bio from Bio import SearchIO from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord with open ("file",'rU') as handle: # read used for search output files with a single query for qresult in SearchIO.read(handle, 'hmmer3-text'): query_id = qresult.id # seqID from fasta hits = qresult.hits num_hits = len(hits) # how many items (hits) by using len() if num_hits > 0: # if there are more than 0 hits in this query then extract the info for i in range(0, num_hits): hmm_name = hits[i].id # hit name hmm_description = hits[i].description # hit decription current_evalue = hits[i].evalue # evalue of hit handle.close() # close file
