Blast result processing

Blast result processing

#Multiple alignment result of Blast
#query/alignment/identity/positive/coverage are collected
#Only for the best result

from Bio.Blast import NCBIStandalone
import os, sys
path='/.../.../...'
for i in os.listdir(path):
	result_handle = open(str(i))
	blast_parser = NCBIStandalone.BlastParser()
	blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)
	#blast_record = blast_iterator.next()

	f = open(str(i)+'.out','w')

	for blast_record in blast_iterator:
		query = "".join(blast_record.query.replace('\n',' '))
		try:
			blast_record.descriptions[0]!=''
			for alignment in blast_record.alignments:
				for hsp in alignment.hsps:
					identity = round(100* float(hsp.identities[0])/float(hsp.identities[1]),1)
					positive = round(100* float(hsp.positives[0])/float(hsp.positives[1]),1)
					coverage = round(100* float(hsp.align_length)/float(blast_record.query_letters),1)
				#if identity > 95 and identity < 100:
					f.write(str(query)+'	'+str(alignment.title)+'	'+ str(identity)+'	'+str(positive)+'	'+str(coverage)+'\n')
					break
				break
		except IndexError:
			f.write(str(query)+'	None	0	0	0'+'\n')
	f.close()
	result_handle.close()

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