Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Merged
merged 3 commits into from
Nov 19, 2024
Merged

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

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions rescript/extract_seq_segments.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
perc_identity: float = 0.7,
target_coverage: float = 0.9,
min_seq_len: int = None,
max_seq_len: int = None,
mikerobeson marked this conversation as resolved.
Show resolved Hide resolved
threads: int = 1
) -> (DNAFASTAFormat, DNAFASTAFormat):
# Note: the `--db` is actually comprised of the short amplicon
Expand Down Expand Up @@ -49,5 +50,7 @@ def extract_seq_segments(input_sequences: DNAFASTAFormat,
'--notmatched', no_match_f.name]
if min_seq_len:
cmd += ['--minseqlength', '%i' % min_seq_len]
if max_seq_len:
cmd += ['--maxseqlength', '%i' % max_seq_len]
mikerobeson marked this conversation as resolved.
Show resolved Hide resolved
run_command(cmd)
return (extr_seq_segs, no_matches)
11 changes: 8 additions & 3 deletions rescript/plugin_setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
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 +1152,14 @@
'\'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 '
'min_seq_len': 'Minimum length of reference sequence segment '
'allowed for searching. Any sequence less than '
'this will be discarded. If not set, default '
'program settings will be used.'},
'program settings will be used.',
'max_seq_len': 'Maximum length of reference sequence segment '
'allowed for searching. Any sequence greater '
'than this will be discarded. If not set, '
'default program settings will be used.'},
mikerobeson marked this conversation as resolved.
Show resolved Hide resolved
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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)
Loading