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ENH: adds --p-n-threads option to trim-alignment #174

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merged 4 commits into from
Jun 5, 2024
Merged

ENH: adds --p-n-threads option to trim-alignment #174

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2ad213d
initial commit to add thread option to trim-alignment
mikerobeson Feb 6, 2024
3b534d9
added text to note that threads will only work when using primer pair…
mikerobeson Feb 8, 2024
d7e99cd
Merge branch 'master' into trim-align-threads
mikerobeson Feb 21, 2024
d594b66
Merge branch 'master' into trim-align-threads
Apr 10, 2024
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11 changes: 7 additions & 4 deletions rescript/plugin_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1056,23 +1056,26 @@
'primer_fwd': Str,
'primer_rev': Str,
'position_start': Int % Range(1, None),
'position_end': Int % Range(1, None)
'position_end': Int % Range(1, None),
'n_threads': Int % Range(1, None),
},
outputs=[('trimmed_sequences', FeatureData[AlignedSequence]), ],
input_descriptions={'aligned_sequences': 'Aligned DNA sequences.', },
parameter_descriptions={
'primer_fwd': 'Forward primer used to find the start position '
'for alignment trimming.',
'for alignment trimming. Provide as 5\'-3\'.',
'primer_rev': 'Reverse primer used to find the end position '
'for alignment trimming.',
'for alignment trimming. Provide as 5\'-3\'.',
'position_start': 'Position within the alignment where the trimming '
'will begin. If not provided, alignment will not'
'be trimmed at the beginning. If forward primer is'
'specified this parameter will be ignored.',
'position_end': 'Position within the alignment where the trimming '
'will end. If not provided, alignment will not be '
'trimmed at the end. If reverse primer is specified '
'this parameter will be ignored.'
'this parameter will be ignored.',
'n_threads': 'The number of threads. (Use `auto` to automatically use '
'all available cores)'
},
output_descriptions={
'trimmed_sequences': 'Trimmed sequence alignment.', },
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15 changes: 10 additions & 5 deletions rescript/trim_alignment.py
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Expand Up @@ -190,11 +190,13 @@ def _trim_alignment(expand_alignment_action,
primer_fwd=None,
primer_rev=None,
position_start=None,
position_end=None) -> AlignedDNAFASTAFormat:
position_end=None,
n_threads=1) -> AlignedDNAFASTAFormat:
"""
Trim alignment based on primer alignment or explicitly specified
positions. When at least one primer sequence is given, primer-based
trimming will be performed, otherwise position-based trimming is done.
trimming will be performed via the `addfragments` option of mafft,
otherwise position-based trimming is done.
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the n_threads param would not be effective as far as I can tell when position-based trimming is done, so this should be mentioned in the param description

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RE param description: Oooh, good catch! Will fix!

RE multi threading: Yes this does scale well. The table below is based on ~5k sequences randomly subsampled from SILVA's 50k position FASTA alignment file, on my M1 Max laptop. Mirroring @colinbrislawn's results.

threads time
8 6m 40.278s
4 9m 20.686s
2 14m 36.920s
1 25m 13.873s

Example command:

qiime rescript trim-alignment \
    --i-aligned-sequences silva-138-1-nr99-aln-dna-ss01.qza \
    --p-primer-fwd GTGYCAGCMGCCGCGGTAA \
    --p-primer-rev CCGYCAATTYMTTTRAGTTT \
    --p-n-threads  8 \
    --o-trimmed-sequences silva-138-1-nr99-aln-dna-ss01-v4v5-trimmed.qza \
    --verbose


Arguments:
expand_alignment_action: qiime action for multiple seq. alignment
Expand Down Expand Up @@ -222,7 +224,8 @@ def _trim_alignment(expand_alignment_action,
alignment_with_primers, = expand_alignment_action(
alignment=aligned_sequences,
sequences=primers,
addfragments=True)
addfragments=True,
n_threads=n_threads)

# find trim positions based on primer positions within alignment
trim_positions = _locate_primer_positions(alignment_with_primers)
Expand All @@ -244,7 +247,8 @@ def trim_alignment(ctx,
primer_fwd=None,
primer_rev=None,
position_start=None,
position_end=None):
position_end=None,
n_threads=1):
"""
Trim an existing alignment based on provided primers or specific,
pre-defined positions. Primers take precedence over the positions,
Expand All @@ -263,6 +267,7 @@ def trim_alignment(ctx,
primer_fwd,
primer_rev,
position_start,
position_end)
position_end,
n_threads=n_threads)

return qiime2.Artifact.import_data('FeatureData[AlignedSequence]', result)