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Ncbixml.Parse doesn't process all the results

Greetings, I am trying to parse by Blast results using "NCBIXML.parse", however when i run it it only analysis few results and not the whole file. If anybody knows the solution to it I would really appreciate it.

from Bio.Blast import NCBIXML
E_VALUE_THRESH = 1
with open("Coilia_nasus_results.xml","r") as result:
    records= NCBIXML.parse(result)
    item=next(records)
    for alignment in item.alignments:
        for hsp in alignment.hsps:
            if hsp.expect < E_VALUE_THRESH:
                print('****Alignment****')
                print('sequence:', item.query)
                print('length:', alignment.length)
                print("e value:", hsp.expect)
                print('score:', hsp.score)
                print('gaps:', hsp.gaps)
                print(hsp.sbjct)
blast biopython python
• 839 views • link
written by Sasha • Sasha

1 answer

Was able to resolve this issue on my own!

from Bio.Blast import NCBIXML
E_VALUE_THRESH = 1
with open("Coilia_nasus_results.xml","r") as result:
    blast_records = NCBIXML.parse(result)
    for blast_record in blast_records:
        for alignment in blast_record.alignments:
            for hsp in alignment.hsps:
                if hsp.expect < E_VALUE_THRESH:
                    print('****Alignment****')
                    print('sequence:', blast_record.query)
                    print('length:', alignment.length)
                    print("e value:", hsp.expect)
                    print('score:', hsp.score)
                    print('gaps:', hsp.gaps)
                    print(hsp.sbjct)
• 0 views • link
written by Sasha • Sasha

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