diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py index 89893323a6787f0ef40183a9d1a2ae4321cd534a..2cff9231cffc91418d604e2caabb0c57292f647a 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()