[Biopython] Blast Two Sequences

[Lenna Peterson]

Hi Islam,

If you need to avoid writing the sequence to disk for whatever reason, you
could create an in-memory file using StringIO:
https://docs.python.org/2/library/stringio.html

Lenna

On Thu, Mar 9, 2017 at 6:15 PM, Islam Amin <eng.islamamin at gmail.com> wrote:

> Many thanks Peter, I thought that It may be possible to pass raw sequences
> instead of passing fasta file.
>
> On Fri, Mar 10, 2017 at 9:43 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>> The NCBI BLAST+ arguments query and subject should be filenames, not
>> raw sequences.
>>
>> The example you linked to on BioStars had an example by Ryan showing
>> how to first create two temp files which he called "seq1.fasta" and
>> "seq2.fasta" using Biopython's SeqIO.
>>
>> Peter
>>
>>
>> On Thu, Mar 9, 2017 at 7:42 AM, Islam Amin <eng.islamamin at gmail.com>
>> wrote:
>> > Dear All,
>> > I got a script from the following link : https://www.biostars.org/p/426
>> 87/
>> > about how to blast two sequences in biopython, I wonder if is it
>> possible to
>> > pass the sequences direct to as following:
>> > NcbiblastpCommandline(query="FQTWEEFSRAAEKLYLADPMKVRV",subje
>> ct="FQTWEEFSRAEKLYLADPMK",
>> > outfmt=5)()[0]
>> > unfortunately, I got the error when I'm trying to pass the sequence
>> direct
>> > instead of read fasta file, is there any way to pass sequences direct.
>> >
>> >  the script is:
>> >
>> > from Bio.Blast.Applications import NcbiblastpCommandline
>> > from StringIO import StringIO
>> > from Bio.Blast import NCBIXML
>> > from Bio.Seq import Seq
>> > from Bio.SeqRecord import SeqRecord
>> > from Bio import SeqIO
>> >
>> > # Create two sequence files
>> > seq1 =
>> > SeqRecord(Seq("FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVC
>> LVYRTDQAQDVKKIEKF"),
>> >                    id="seq1")
>> > seq2 =
>> > SeqRecord(Seq("FQTWEEFSRAEKLYLADPMKVRVVLRYRHVDGNLCIKVTDDLICL
>> VYRTDQAQDVKKIEKF"),
>> >                    id="seq2")
>> > SeqIO.write(seq1, "seq1.fasta", "fasta")
>> > SeqIO.write(seq2, "seq2.fasta", "fasta")
>> >
>> > # Run BLAST and parse the output as XML
>> > output = NcbiblastpCommandline(query="seq1.fasta",
>> subject="seq2.fasta",
>> > outfmt=5)()[0]
>> > blast_result_record = NCBIXML.read(StringIO(output))
>> >
>> > # Print some information on the result
>> > for alignment in blast_result_record.alignments:
>> >     for hsp in alignment.hsps:
>> >         print '****Alignment****'
>> >         print 'sequence:', alignment.title
>> >         print 'length:', alignment.length
>> >         print 'e value:', hsp.expect
>> >         print hsp.query
>> >         print hsp.match
>> >         print hsp.sbjct
>> >
>> >
>> > _______________________________________________
>> > Biopython mailing list  -  Biopython at mailman.open-bio.org
>> > http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>
>
> --
> Best Regards,
> Islam Amin.
>
> www.egyptscience.net
> Scientific Research Group in EGYPT
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170309/2baca1a0/attachment.html>