[BioPython] Problems with NCBIXML.py

[Bruno Santos]

I am trying to build a simple script that given a multi FASTA sequence file
perform a web BLAST and replace the name of the sequence by the hit with the
lowest E-Value.

But now I’m getting an exception that I don’t now why it’s happening:

 

Traceback (most recent call last):

  File
"C:\Python25\Lib\site-packages\pythonwin\pywin\framework\scriptutils.py",
line 310, in RunScript

    exec codeObject in __main__.__dict__

  File "C:\Documents and Settings\POSTO_21\Os meus documentos\Meta
Genómica\BLAST.py", line 16, in <module>

    for blast_record in blast_records:

  File "C:\Python25\lib\site-packages\Bio\Blast\NCBIXML.py", line 592, in
parse

    expat_parser.Parse(text, False)

ExpatError: mismatched tag: line 2823, column 362

 

And where is my script:

 

from Bio import SeqIO

from Bio.Blast import NCBIWWW

import cStringIO

from Bio.Blast import NCBIXML

#for file in dir

file_handle =
open(r'C:/FASTASeq/Results/Well9/assembled_file_well9_Dt_DIST.fna') #Open
file to an handler

records = SeqIO.parse(file_handle, format="fasta") #Store the file in a Seq
Object

save_file = open(r'C:/FASTASeq/Results/Well9/D1_Blast.xml', "w")

for record in records:

    sequence = record.seq.data #Converts record to Plain Text

    result_handle = NCBIWWW.qblast("blastn", "nr", sequence) #Performs a
Blastn against the database nr

    blast_results = result_handle.read() #Catch the results

    save_file.write(blast_results) #Write all the information to an XML file

result_handle = open(r'C:/FASTASeq/Results/Well9/D1_Blast.xml')

blast_records = NCBIXML.parse(result_handle)

for blast_record in blast_records:

    alignment = blast_record.alignments

    nIdent =
(alignment[0].hsps[0].positives/float(alignment[0].hsps[0].align_length))*10
0.0

    if nIdent >= 97:

        record.name = alignment[0].hit_def

for record in records:

    print('>description_%s length_%d\n' % (record.name, len(record.seq)))

    print('%s\n' % record.seq)

                                

save_file.close()

file_handle.close()

 

Thank you,

Bruno Santos