From fdc51c7448a1d4aecf5d3b8a4f465ce981463640 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 18 Dec 2019 11:22:07 +0100
Subject: [PATCH] Decode output of Blast to return a string with outfmt=1.
---
modules/bindings/pymod/blast.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 89893323a..2cff9231c 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -208,8 +208,8 @@ def BlastVersion(blast_location=None):
def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
blast_location=None, outfmt=0, filter_low_complexity=True):
"""
- Runs a protein vs. protein blast search. The results are returned as a
- list of :class:`BlastHit` instances.
+ Runs a protein vs. protein blast search. The results are returned
+ according to the value of the ``outfmt`` parameter.
:param query: the query sequence
:type query: :class:`seq.ConstSequenceHandle`
@@ -224,10 +224,13 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
:param gap_ext: Gap extension penalty. Only a subset of gap extension
penalties are supported for each of the substitution matrices. Consult the
blast docs for more information.
- :param outfmt: output format, where '0' corresponds to default output (parsed blast output and 1 to raw output)
+ :param outfmt: output format, where '0' corresponds to default output (parsed
+ blast output and 1 to raw string output).
:param filter_low_complexity: Mask off segments of the query sequence that
have low compositional complexity, as determined by the SEG program of
Wootton & Federhen (Computers and Chemistry, 1993)
+ :rtype: :class:`BlastHit` (with ``outfmt=0``) or :class:`str`
+ (with ``outfmt=1``)
"""
subst_mats=('BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70',)
if matrix not in subst_mats:
@@ -281,4 +284,4 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
if outfmt==0:
return ParseBlastOutput(stdout.decode())
else:
- return stdout
+ return stdout.decode()
--
GitLab