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Commit fdc51c74 authored by Xavier Robin's avatar Xavier Robin
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Decode output of Blast to return a string with outfmt=1.

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...@@ -208,8 +208,8 @@ def BlastVersion(blast_location=None): ...@@ -208,8 +208,8 @@ def BlastVersion(blast_location=None):
def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
blast_location=None, outfmt=0, filter_low_complexity=True): blast_location=None, outfmt=0, filter_low_complexity=True):
""" """
Runs a protein vs. protein blast search. The results are returned as a Runs a protein vs. protein blast search. The results are returned
list of :class:`BlastHit` instances. according to the value of the ``outfmt`` parameter.
:param query: the query sequence :param query: the query sequence
:type query: :class:`seq.ConstSequenceHandle` :type query: :class:`seq.ConstSequenceHandle`
...@@ -224,10 +224,13 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', ...@@ -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 :param gap_ext: Gap extension penalty. Only a subset of gap extension
penalties are supported for each of the substitution matrices. Consult the penalties are supported for each of the substitution matrices. Consult the
blast docs for more information. 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 :param filter_low_complexity: Mask off segments of the query sequence that
have low compositional complexity, as determined by the SEG program of have low compositional complexity, as determined by the SEG program of
Wootton & Federhen (Computers and Chemistry, 1993) 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',) subst_mats=('BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70',)
if matrix not in subst_mats: if matrix not in subst_mats:
...@@ -281,4 +284,4 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62', ...@@ -281,4 +284,4 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
if outfmt==0: if outfmt==0:
return ParseBlastOutput(stdout.decode()) return ParseBlastOutput(stdout.decode())
else: else:
return stdout return stdout.decode()
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