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Fixed stand-alone version of multiple-seq-alignment #218

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Fixed stand-alone version of multiple-seq-alignment #218

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7 changes: 5 additions & 2 deletions deblur/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -492,7 +492,7 @@ def op(x): return x in aligned_seq_ids
return output_fp, okseqs, [blast_output_filename]


def multiple_sequence_alignment(seqs_fp, threads=1):
def multiple_sequence_alignment(seqs_fp, threads=1, output_fp=None):
"""Perform multiple sequence alignment on FASTA file using MAFFT.

Parameters
Expand All @@ -517,7 +517,10 @@ def multiple_sequence_alignment(seqs_fp, threads=1):
if stat(seqs_fp).st_size == 0:
logger.warning('msa failed. file %s has no reads' % seqs_fp)
return None
msa_fp = seqs_fp + '.msa'
if output_fp is None:
msa_fp = seqs_fp + '.msa'
else:
msa_fp = output_fp
params = ['mafft', '--quiet', '--preservecase', '--parttree', '--auto',
'--thread', str(threads), seqs_fp]
sout, serr, res = _system_call(params, stdoutfilename=msa_fp)
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6 changes: 2 additions & 4 deletions scripts/deblur
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Original file line number Diff line number Diff line change
Expand Up @@ -325,10 +325,8 @@ def multiple_seq_alignment(seqs_fp, output_fp, threads_per_sample,
"""Multiple sequence alignment"""
start_log(level=log_level * 10, filename=log_file)
alignment = multiple_sequence_alignment(seqs_fp,
threads=threads_per_sample)

with open(output_fp, 'w') as f:
f.write(alignment.to_fasta())
threads=threads_per_sample,
output_fp=output_fp)


# DE NOVO CHIMERA REMOVAL COMMAND
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