In biopython emboss applications, is it possible that asequence and bsequence attributes of needle/watercommandline object be a variable instead of fasta file ? i.e I want to write the sequence either directly or through variable as shown below
bseq= "aaatttccggtt"
needle_cline = NeedleCommandline(asequence="acgtggcc", bsequence=bseq,
... gapopen=10, gapextend=0.5, outfile="needle.txt")
Is it possible to do it ?
1 answer
This isn't a Biopython specific thing, but an EMBOSS trick - you can use their pretend file format to give the sequence in place of a filename using asis:aaatttccggtt, see also http://emboss.sourceforge.net/docs/themes/SequenceFormats.html - e.g.
>>> from Bio.Emboss.Applications import NeedleCommandline
>>> aseq = "acgtggcc"
>>> bseq = "aaatttccggtt"
>>> needle_cline = NeedleCommandline(asequence="asis:"+aseq, bsequence="asis:"+bseq, gapopen=10, gapextend=0.5, outfile="needle.txt")
>>> stdout, stderr = needle_cline()
>>> print stdout + stderr
Needleman-Wunsch global alignment of two sequences
Also you might be able to specify you want to read the a-sequences from stdin rather than a file, and supply this when you actually run Needle, e.g. with needle_cline(stdin=aseq) (not tested).
Log in to answer this question.
-
Non-zero return code 127 from Needle
written by Park •
-
EMBOSS dosen't output file in biopython
written by Thesnak •
-
Is there a maximum length in EMBOSS needle?
written by xien0114 •
-
Biopython Emboss Needle gives no output file
written by weihan •
-
can not get the alignment result from needle alignment
written by Medhat
-
alignment using needleman wunsch in biopython
written by sumithrasank75
-
EMBOSS needle question
written by mossig89 •
-
EMBOSS needle question
written by mossig89 •
-
Emboss Needle From Biopython, No Output File
written by Maria •
-
The Biopython Needlecommandline Class Complains About Needle Returning Non-Zero
written by jergosh
