Question: How To Show More Blast Results Using Biopython?
1
gravatar for Niek De Klein
9.0 years ago by
Niek De Klein2.5k
Netherlands
Niek De Klein2.5k wrote:

Hi,

I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't find how to make that number higher. So my question is, how can you show more results from BLAST using biopython. I'm using NCBIWWW.qblast from BIO.BLAST.

from Bio.Blast import  NCBIWWW
File = "MIF"
fasta_string = open(File+".fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)

Thanks, Niek

python biopython blast • 3.7k views
ADD COMMENTlink modified 9.0 years ago by Peter5.8k • written 9.0 years ago by Niek De Klein2.5k

Which blast service are you using?

ADD REPLYlink written 9.0 years ago by Daniel Swan13k

NCBIWWW.qblast
File = "MIF" fasta_string = open(File+".fasta").read() result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)

ADD REPLYlink written 9.0 years ago by Niek De Klein2.5k

NCBIWWW.qblast

File = "MIF"
fasta_string = open(File+".fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
ADD REPLYlink written 9.0 years ago by Niek De Klein2.5k

NCBIWWW.qblast

File = "MIF"
fasta_string = open(File+".fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
ADD REPLYlink written 9.0 years ago by Niek De Klein2.5k

I editted it in my post.

ADD REPLYlink written 9.0 years ago by Niek De Klein2.5k
3
gravatar for Science_Robot
9.0 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

From here:

qblast(program, database, sequence, ncbi_gi=None, descriptions=None, alignments=None, exp

ect=None, matrix=None, filter=None, format_type=None, hitlist_size=None, entrez_query='(n one)')

Did you try setting descriptions, alignments, and/or hitlist_size?

ADD COMMENTlink written 9.0 years ago by Science_Robot1.1k

Yes thank you! I've been looking for a site like that.

ADD REPLYlink written 9.0 years ago by Niek De Klein2.5k
3
gravatar for Daniel Swan
9.0 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

According to this post here (a little outdated I admit), you will want to override the hitlist_size defaults.

ADD COMMENTlink written 9.0 years ago by Daniel Swan13k
0
gravatar for Peter
8.9 years ago by
Peter5.8k
Scotland, UK
Peter5.8k wrote:

Hello Niek,

Daniel pointed out an email to the Biopython mailing list which answers your question - basically try reading the built in documentation. This is also mentioned in the Biopython Tutorial, quote:

For more about the optional BLAST arguments, we refer you to the NCBI’s own documentation, or that built into Biopython:

from Bio.Blast import NCBIWWW

help(NCBIWWW.qblast)

Also audyyy pointed out some old (but apparently still relevant) documentation from Andrew Dalke's homepage.

You said I've been looking all over but can't find how to make that number higher. so you probably looked at some of these bits of documentation (right?). Could you suggest how it could be made clearer for newcomers? Feedback does help to improve the docs.

Thanks,

Peter

ADD COMMENTlink written 8.9 years ago by Peter5.8k
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