[BioPython] Qblast problem

[Omenkeukwu, Gregory]

Here is the FASTA file (m_cold.fasta) and below it is the code I am running

>gi|8332116|gb|BE037100.1|BE037100 MP14H09 MP Mesembryanthemum crystallinum cDNA 5' similar to cold acclimation protein, mRNA sequence
CACTAGTACTCGAGCGTNCTGCACCAATTCGGCACGAGCAAGTGACTACGTTNTGTGAACAGAAAATGGG
GAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATC
AATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATTACGGGTTTGGCA
CTCATTTCCTCAAATGGCTCGCCTGCCTTGCGGCTATTTACTTGTTGATATTGGATCGAACAAACTGGAG
AACCAACATGCTCACGTCACTTTTAGTCCCTTACATATTCCTCAGTCTTCCATCCGGGCCATTTCATCTG
TTCAGAGGCGAGGTCGGGAAATGGATTGCCATCATTGCAGTCGTGTTAAGGCTGTTCTTCAACCGGCATT
TCCCAGTTTGGCTGGAAATGCCTGGATCGTTGATACTCCTCCTGGTGGTGGCACCAGACTTCTTTACACA
CAAAGTGAAGGAGAGCTGGATCGGAATTGCAATTATGATAGCGATAGGGTGTCACCTGATGCAAGAACAT
ATCAGAGCCACTGGTGGCTTTTGGAATTCCTTCACACAGAGCCACGGAACTTTTAACACAATTGGGCTTA
TCCTTCTACTGGCTTACCCTGTCTGTTTATGGTCATCTTCATGATGTAGTAGCTTAGTCTTGATCCTAAT
CCTCAAATNTACTTTTCCAGCTCTTTCGACGCTCTTGCTAAAGCCCATTCAATTCGCCCCATATTTCGCA
CACATTCATTTCACCACCCAATACGTGCTCTCCTTCTCCCTCTCTCCCTCTCCTCCCTCTTTTCTTCCTC
TCACTTCTCTTCTCTTCTCTTCTTCAATACTCCCCTGGAGCGCCCTCTTCACCTCCCTACTCTCTACTCC
TCTCTCTCACTCTCTCTTCCTCTCTTATCTCTCTCCTCCTCTCCTTCTCATCCCTCCTCCTTCTCTTCCT
TTTCTTCTTTCTATCCACGCGCCATCCTCCCTCTTCCCTCTTCCCTTCTCTCTCCTCTCTTTCTCTCTCC
TCTCTTCCTCATCTCACCACCTCCTCCTCTCTTTCTTCCGTCCTCCTTCCCTTCCTTCTTC






from Bio import Fasta

file_for_blast = open('m_cold.fasta', 'r')
f_iterator = Fasta.Iterator(file_for_blast)

f_record = f_iterator.next()

from Bio.Blast import NCBIWWW
result_handle = NCBIWWW.qblast('blastn', 'nr', f_record)










-----Original Message-----
From: Peter [mailto:biopython at maubp.freeserve.co.uk]
Sent: Thursday, January 19, 2006 4:13 AM
To: Omenkeukwu, Gregory; BioPython at biopython.org
Subject: Re: [BioPython] Qblast problem


Omenkeukwu, Gregory wrote:
> I am new to Biopython and I am experiencing a little problem. I am
> running the Blast over the internet example and I keep getting stuck
> when I invoke the qblast function in NCBIWWW.py. Has anyone ever
> dealt with the problem below? Every time I run this code I get
> Invalid literal error for int(). I will appreciate any response
> thanks.

Do you have an example XML blast output file that we could use to 
recreate the problem?

Ideally could log a bug for us, and then attach the XML file to the bug?

Peter





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