[Biopython] help with NCBIXML.parse
ferreirafm at usp.br
ferreirafm at usp.br
Wed Mar 28 14:03:51 UTC 2012
Hi Peter,
Thanks for answer.
Citando Peter Cock <p.j.a.cock at googlemail.com>:
> You seem to be calling BLAST multiple times in a loop and
> trying to give it SeqRecord objects.
Yes, because I want just only one hit per sequence. If someone has a
overcome to this, it would be great. If a run it with a multiple fasta
file, I'll take several hits per sequence. Like this:
P02977 emm1.22.pep 100.00 2 0 0 15 16
90 91 9.4 9.2
P02977 emm1.22.pep 100.00 2 0 0 14 15
104 105 9.4 9.2
P02977 emm1-2.3.pep 62.50 8 3 0 8 15
196 203 0.033 17.5
P02977 emm1.23.pep 62.50 8 3 0 8 15
196 203 0.033 17.5
P02977 emm1-2.4.pep 100.00 2 0 0 15 16
99 100 5.0 9.2
P02977 emm1.24.pep 100.00 2 0 0 15 16
88 89 7.5 9.2
P02977 emm1.24.pep 100.00 2 0 0 14 15
102 103 7.5 9.2
P02977 emm1.25.pep 100.00 2 0 0 15 16
81 82 4.3 9.2
> It wants FASTA files,
> and you can call BLAST once with a single FASTA query
> file (containing multiple records) and a single database or
> FASTA subject file (also containing multiple records).
>
> As to the specific error, did you look at your blast_out.xml
> file and what it said on line 88?
>
line 88 is a second "header" of the xml file. It seems xmlparse can't
handle it.
</BlastOutput><?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN"
"http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
> Peter
>
More information about the Biopython
mailing list