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ENH: added --p-max-seq-len to extract-seq-segments and associated test code #209

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Nov 19, 2024
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ENH: added --p-max-seq-len to extract-seq-segments and associated test code #209

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dac2412
added maxseqlen and test code
mikerobeson Nov 4, 2024
4a4030a
added default length settings as per code review
mikerobeson Nov 19, 2024
2111b29
remove commented lines
mikerobeson Nov 19, 2024
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7 changes: 4 additions & 3 deletions rescript/extract_seq_segments.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,8 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
reference_segment_sequences: DNAFASTAFormat,
perc_identity: float = 0.7,
target_coverage: float = 0.9,
min_seq_len: int = None,
min_seq_len: int = 32,
max_seq_len: int = 50000,
threads: int = 1
) -> (DNAFASTAFormat, DNAFASTAFormat):
# Note: the `--db` is actually comprised of the short amplicon
Expand Down Expand Up @@ -43,11 +44,11 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
'--id', str(perc_identity),
'--target_cov', str(target_coverage),
'--strand', 'plus',
'--minseqlength', str(min_seq_len),
'--maxseqlength', str(max_seq_len),
'--threads', str(threads),
'--qmask', 'none',
'--qsegout', extr_f.name,
'--notmatched', no_match_f.name]
if min_seq_len:
cmd += ['--minseqlength', '%i' % min_seq_len]
run_command(cmd)
return (extr_seq_segs, no_matches)
11 changes: 7 additions & 4 deletions rescript/plugin_setup.py
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Expand Up @@ -1130,6 +1130,7 @@
inclusive_start=False,
inclusive_end=True),
'min_seq_len': Int % Range(1, None),
'max_seq_len': Int % Range(1, None),
},
outputs=[('extracted_sequence_segments', FeatureData[Sequence]),
('unmatched_sequences', FeatureData[Sequence])],
Expand All @@ -1151,10 +1152,12 @@
'\'reference-segment-sequences\' must have '
'in order to extract matching segments '
'from \'input-sequences\'.',
'min_seq_len': 'Minimum length of sequence allowed '
'for searching. Any sequence less than '
'this will be discarded. If not set, default '
'program settings will be used.'},
'min_seq_len': 'Minimum length of reference sequence segment '
'allowed for searching. Any sequence less than '
'this will be discarded.',
'max_seq_len': 'Maximum length of reference sequence segment '
'allowed for searching. Any sequence greater '
'than this will be discarded.'},
output_descriptions={
'extracted_sequence_segments': 'Extracted sequence segments '
'from \'input-sequences\' '
Expand Down
88 changes: 88 additions & 0 deletions rescript/tests/test_extract_seq_segments.py
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Expand Up @@ -134,3 +134,91 @@ def test_high_coverage_extract_seq_segments(self):
'GATAAAACTAAGGTTTATCAAACTAAGGATTTGGCTCAGGATTGCCCAT'),
'fulllen05': 'AAAATTTTGGGGCCCCAAAATTTTGGGGCCCC'}
self.assertEqual(obs_unmat_seqs, exp_unmat_seqs)

def test_extract_seq_segments_min_max(self):
ext_segs, unmat_seqs, = extract_seq_segments(
input_sequences=self.seqs,
reference_segment_sequences=self.segref,
perc_identity=0.9,
target_coverage=0.7,
min_seq_len=45,
max_seq_len=53)

obs_ext_segs = {seq.metadata['id']: str(seq)
for seq in ext_segs.view(DNAIterator)}
exp_ext_segs = {
'fulllen01': ('ATCTTTATGTTTAGAAAAACAAGGGTTTTAATTGAAA'
'AACTAGAAGAAAAAGG')}
self.assertEqual(obs_ext_segs, exp_ext_segs)

obs_unmat_seqs = {seq.metadata['id']: str(seq)
for seq in unmat_seqs.view(DNAIterator)}
exp_unmat_seqs = {
'fulllen02': (
'CGCGACATAAAGACTCCTTATTTTCTTTTTCTTTATTTTATTGAAATTTCATAAACC'
'TAAATTTAAAACTGAACTAAAGGATAAATATGATAAATGAGGCAAAATCTACTGAAG'
'TATTATACTACAAAAAATACTGATATACTACAAAGAATACTGAGATGGATTGTATCA'
'ATATCCGGACCTTATTGTATATACACAAATAATGGATATAGAAAAATAAAAAGAAAA'
'AGGTCCTTTATCTTGTTCTTGATTTGTTCTGCAGAGATTTAACTACTCTAACTTTTA'
'TTCATAATTTGAAGTTCCTATCGCATAAGAATCGGTGTCCCTTTGAAAGGAAAGAGA'
'GGAAGAAGCCTTTTCAATATTCTTTAATTTCAAAAATACATTATCAATCATGCAAAA'
'AAACTCAAACAAATAGAGAAAAGCCAGCTATCGGAGTCGAACCGATGACCATCGCAT'
'TACAAATGCGATGCTCTAAAAAAAAAAGAAAAGAATCGACCGTTCGAGTATTCCAAA'
'TTGCACGAGAAAAATGATTCGAAGAGAGACATATATAATAAATGTGGTATATATGCA'
'TCTATATTGAATTGTGGATACAGAAATGATAGAATAATTTCTGATTAAACCAAATAT'
'AGGTTTCCAATAGAGATGAAGGGGGGATAGATAAGAAAAAATAAGAGGAAACACTTT'
'TATATGAATCGGTATCTAATGACTTTAACAGTTCCAGTAGAATATAAATGAAAAGGG'
'GGGGAATGACGTAATAGTAATAATAAGATCTGAATTTCAAAACACAAAACAAAATAA'
'AGGGGATATGGCGAAATTGGTAGACGCTACGGACTTAATTGGATTGAGCCTTGGTAT'
'GGAAACTTACTAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAAAAAGGGGGCAA'
'TCCTGAGCCAAATCCTGTTTTTCGAAAACAAACAAAGGTTTGTAAAGACAGAAGCAG'
'AATACAAAAACAAAAGGATAGGTGCAGAGACTCAATGGAAGTTGTTCTAACAATAAC'
'AAATAGAGTTGACTGCGTTGCATTAGTCAAGTAAAGGAATATTTTTGTTAAAACTCC'
'AGATCTAGAAAGGATAAAAAAAACTCCAGACCAGAAAAGATAAAGGAAAGTATAACC'
'GTATACTCTATACATACGTATACGTACTGAAATACTATCTCAAATGATTAATGACAA'
'CCGACCCGAATCTGTATTTTATTATATTTCTATGGAAAATGAAATAAAATAAATTGT'
'TTTGAATCGATTCCAAGTTGCCGAAAGGATCGAATATTAATTGATCAAATCATTCAC'
'CCCGTAGTCTGATAGATAACTAATTAATCGGACGAGAGTAAAGATAGAGCCCCATTC'
'TACATGTCAATATTCTACATGTCAATATCGACAACAAAGAAATTTATAGTAAGAGGA'
'AAATCCGTCGACTTTAGAAATCGTGAGGGTTCAAGTCCCTCTATCCCCAAAAAAGGC'
'CTGCTCGGCTCCCTAATTATTTATCTTATTCTCTCTTTTCTTCTCTCTTTTCGTTAA'
'CGGTTCAAAATTCGTTATCTTTCTCATTCATTCGATTCTTTCACAAATGCATCTGGG'
'ATGCATTTTTTTCTTTTCACAAGTCTTGTGGTAGATATGATACACATACAAATGAAC'
'TTATTTGAGTAAAACAAGGATAAAACAAGGAATCCCTTTTGGAAATTGGAATGATTA'
'ACAATGATAAAACTTTCAAATACCTTTTGTTTTTTTTTAATTGACATAGACCCAAGT'
'CATTTAGTGAGATGAGGAAGACGACGCGTTGGAAATGGTCGGGATAGCTCA'),
'fulllen03': (
'ACCATTTCCCATGCATCATCCTGGTGTAGTATTTGTGTCTATGTCAATTAAAGGGA'
'CTAAAAAGTAGTAAAAAATTTAACTAGTAAGCGTAAGGATAATGATATGGACTGTG'
'AATGATTCAATAATAGAGATTATTTGCCCATATATGTTTATTTGTAGAGGTATTGT'
'ATCTATCGAAATTGGGATAAGATCCAAGGATTTTAGTTCGGATACATTTGTGTTGT'
'GAAAGAGTGGAGTGAATGAGAAAGATAGTGAATTTTGTTTGAACTGAATCGCTGAT'
'GAAAAAAAAAGGAAGATAAATATTTAGGAAGTAAAATTACCTTTTTATTGGGGATA'
'GAGGGACTTGAACCCTCACGATTTCTAAAGTCGACGGATTTTCCTCTTACTATAAA'
'TTTCATTGTTGTCGGTATTGACATGTAGAATGGGACTCTCTCTTTATTCTCGTCCG'
'ATTAATCAGTTTTTCAAAAGATCTATCAAACTCTGGAATGAATGATTTAATAATTG'
'AATTGAATATTCAATTCTTCTTTCAACTTCCATTGGACTGGATTCACAATAACTCT'
'AATTCTGAATTTTTCATATTTTAATTATCCATATAATATAATGGATTCGAGTCATG'
'ATTAATCGTTTGATTTGATATGTCAGTATGTATACGTATTTATTAGGTATATAGGA'
'ACATCTTTTCTGTAATTTTGATAGACGGATTCCAACTACCAACGAAACGTAGTCAA'
'CTTCATTCGTTAGAACAGCTTCCATTGAGTCTCTGCACCTATCCGAATTCTAGTTT'
'GATAAAACTAAGGTTTATCAAACTAAGGATTTGGCTCAGGATTGCCCAT'),
'fulllen04': (
'ACCATTTCCCATGCATCATCCTGGTGTAGTGTTTGTGTCTATGTCAATTAAAGGGA'
'CTAAAAAGTAGTAAAAAATTTAACTAGTAAGCGTAAGGATAATGATATGGACTGTG'
'AATGATTCAATAATAGAGATTATTTTCCCATATATGCTTATTTGTAGAGGTATTGT'
'ATCTATCGAAATTGGGATAAGATCCAAGGATTTTAGTTCGGATACATTTGTGTTGT'
'GAAAGAGTGGAGTGAATGAGAAAGATAGTGAATTTTGTTTGAACTGAATCGCTGAT'
'GAAAAAAAAAGGAGGATAAATATTTAGGAAGTAAAATTACCTTTTTATTGGGGATA'
'GAGGGACTTGAACCCTCACGATTTCTAAAGTCGACGGATTTTCCTCTTACTATAAA'
'TTTCATTGTTGTCGGTATTGACATGTAGAATGGGACTCTCTCTTTATTCTCGTCCG'
'ATTAATCAGTTTTTCAAAAGATCTATCAAACTCTGGAATGAATGATTTAATAATTG'
'AATTGAATATTCAATTCTTCTTTCAACTTCCATTGGACTGGATTCACAATAACTCT'
'AATTCTGAATTTTTCATATTATAATTATCCATATAATATAATGGATTCGAGTCATG'
'ATTAATCGTTTGATTTGATATGTCAGTATGTATACGTATGTATTAGGTATATAGGA'
'ACATCTTTTCTGTAATTTTGATAGACGGATTCCAACTACCAACGAAACGTAGTCAA'
'CTTCATTCGTTAGAACAGCTTCCATTGAGTCTCTGCACCTATCCTTATTCTAGTTT'
'GATAAAACTAAGGTTTATCAAACTAAGGATTTGGCTCAGGATTGCCCAT'),
'fulllen05': (
'AAAATTTTGGGGCCCCAAAATTTTGGGGCCCC')}
self.assertEqual(obs_unmat_seqs, exp_unmat_seqs)
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