# ---------------------------------------------------------------------------- # Copyright (c) 2017-2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- from qiime2.plugin import ( Plugin, Citations, MetadataColumn, Categorical, Float, Range, Int, List, Str, Bool, Threads, ) from q2_types.multiplexed_sequences import ( MultiplexedSingleEndBarcodeInSequence, MultiplexedPairedEndBarcodeInSequence, ) from q2_types.sample_data import SampleData from q2_types.per_sample_sequences import ( SequencesWithQuality, PairedEndSequencesWithQuality, ) import q2_cutadapt import q2_cutadapt._demux import q2_cutadapt._trim import q2_cutadapt._examples as ex plugin = Plugin( name='cutadapt', version=q2_cutadapt.__version__, website='https://github.com/qiime2/q2-cutadapt', package='q2_cutadapt', description='This QIIME 2 plugin uses cutadapt to work with ' 'adapters (e.g. barcodes, primers) in sequence data.', short_description='Plugin for removing adapter sequences, primers, and ' 'other unwanted sequence from sequence data.', citations=Citations.load('citations.bib', package='q2_cutadapt') ) plugin.methods.register_function( function=q2_cutadapt._trim.trim_single, inputs={ 'demultiplexed_sequences': SampleData[SequencesWithQuality], }, parameters={ 'cores': Threads, 'adapter': List[Str], 'front': List[Str], 'anywhere': List[Str], 'error_rate': Float % Range(0, 1, inclusive_start=True, inclusive_end=True), 'indels': Bool, 'times': Int % Range(1, None), 'overlap': Int % Range(1, None), 'match_read_wildcards': Bool, 'match_adapter_wildcards': Bool, 'minimum_length': Int % Range(1, None), 'discard_untrimmed': Bool, 'max_expected_errors': Float % Range(0, None), 'max_n': Float % Range(0, None), 'quality_cutoff_3end': Int % Range(0, None), 'quality_cutoff_5end': Int % Range(0, None), 'quality_base': Int % Range(0, None), }, outputs=[ ('trimmed_sequences', SampleData[SequencesWithQuality]), ], input_descriptions={ 'demultiplexed_sequences': 'The single-end sequences to be trimmed.', }, parameter_descriptions={ 'cores': 'Number of CPU cores to use.', 'adapter': 'Sequence of an adapter ligated to the 3\' end. The ' 'adapter and any subsequent bases are trimmed. If a `$` ' 'is appended, the adapter is only found if it is at the ' 'end of the read. If your sequence of interest is "framed" ' 'by a 5\' and a 3\' adapter, use this parameter to define ' 'a "linked" primer - see https://cutadapt.readthedocs.io ' 'for complete details.', 'front': 'Sequence of an adapter ligated to the 5\' end. The adapter ' 'and any preceding bases are trimmed. Partial matches at the ' '5\' end are allowed. If a `^` character is prepended, the ' 'adapter is only found if it is at the beginning of the ' 'read.', 'anywhere': 'Sequence of an adapter that may be ligated to the 5\' or ' '3\' end. Both types of matches as described under ' '`adapter` and `front` are allowed. If the first base of ' 'the read is part of the match, the behavior is as with ' '`front`, otherwise as with `adapter`. This option is ' 'mostly for rescuing failed library preparations - do ' 'not use if you know which end your adapter was ligated ' 'to.', 'error_rate': 'Maximum allowed error rate.', 'indels': 'Allow insertions or deletions of bases when matching ' 'adapters.', 'times': 'Remove multiple occurrences of an adapter if it is ' 'repeated, up to `times` times.', 'overlap': 'Require at least `overlap` bases of overlap between read ' 'and adapter for an adapter to be found.', 'match_read_wildcards': 'Interpret IUPAC wildcards (e.g., N) in ' 'reads.', 'match_adapter_wildcards': 'Interpret IUPAC wildcards (e.g., N) in ' 'adapters.', 'minimum_length': 'Discard reads shorter than specified value. Note, ' 'the cutadapt default of 0 has been overridden, ' 'because that value produces empty sequence ' 'records.', 'discard_untrimmed': 'Discard reads in which no adapter was found.', 'max_expected_errors': 'Discard reads that exceed maximum expected ' 'erroneous nucleotides.', 'max_n': 'Discard reads with more than COUNT N bases. ' 'If COUNT_or_FRACTION is a number between 0 and 1, ' 'it is interpreted as a fraction of the read length.', 'quality_cutoff_3end': 'Trim nucleotides with Phred score quality ' 'lower than threshold from 3 prime end.', 'quality_cutoff_5end': 'Trim nucleotides with Phred score quality ' 'lower than threshold from 5 prime end.', 'quality_base': 'How the Phred score is encoded (33 or 64).', }, output_descriptions={ 'trimmed_sequences': 'The resulting trimmed sequences.', }, name='Find and remove adapters in demultiplexed single-end sequences.', description='Search demultiplexed single-end sequences for adapters and ' 'remove them. The parameter descriptions in this method are ' 'adapted from the official cutadapt docs - please see those ' 'docs at https://cutadapt.readthedocs.io for complete ' 'details.', ) plugin.methods.register_function( function=q2_cutadapt._trim.trim_paired, inputs={ 'demultiplexed_sequences': SampleData[PairedEndSequencesWithQuality], }, parameters={ 'cores': Threads, 'adapter_f': List[Str], 'front_f': List[Str], 'anywhere_f': List[Str], 'adapter_r': List[Str], 'front_r': List[Str], 'anywhere_r': List[Str], 'error_rate': Float % Range(0, 1, inclusive_start=True, inclusive_end=True), 'indels': Bool, 'times': Int % Range(1, None), 'overlap': Int % Range(1, None), 'match_read_wildcards': Bool, 'match_adapter_wildcards': Bool, 'minimum_length': Int % Range(1, None), 'discard_untrimmed': Bool, 'max_expected_errors': Float % Range(0, None), 'max_n': Float % Range(0, None), 'quality_cutoff_3end': Int % Range(0, None), 'quality_cutoff_5end': Int % Range(0, None), 'quality_base': Int % Range(0, None), }, outputs=[ ('trimmed_sequences', SampleData[PairedEndSequencesWithQuality]), ], input_descriptions={ 'demultiplexed_sequences': 'The paired-end sequences to be trimmed.', }, parameter_descriptions={ 'cores': 'Number of CPU cores to use.', 'adapter_f': 'Sequence of an adapter ligated to the 3\' end. The ' 'adapter and any subsequent bases are trimmed. If a `$` ' 'is appended, the adapter is only found if it is at the ' 'end of the read. Search in forward read. If your ' 'sequence of interest is "framed" by a 5\' and a 3\' ' 'adapter, use this parameter to define a "linked" primer ' '- see https://cutadapt.readthedocs.io for complete ' 'details.', 'front_f': 'Sequence of an adapter ligated to the 5\' end. The ' 'adapter and any preceding bases are trimmed. Partial ' 'matches at the 5\' end are allowed. If a `^` character ' 'is prepended, the adapter is only found if it is at the ' 'beginning of the read. Search in forward read.', 'anywhere_f': 'Sequence of an adapter that may be ligated to the 5\' ' 'or 3\' end. Both types of matches as described under ' '`adapter` and `front` are allowed. If the first base ' 'of the read is part of the match, the behavior is as ' 'with `front`, otherwise as with `adapter`. This option ' 'is mostly for rescuing failed library preparations - ' 'do not use if you know which end your adapter was ' 'ligated to. Search in forward read.', 'adapter_r': 'Sequence of an adapter ligated to the 3\' end. The ' 'adapter and any subsequent bases are trimmed. If a `$` ' 'is appended, the adapter is only found if it is at the ' 'end of the read. Search in reverse read. If your ' 'sequence of interest is "framed" by a 5\' and a 3\' ' 'adapter, use this parameter to define a "linked" primer ' '- see https://cutadapt.readthedocs.io for complete ' 'details.', 'front_r': 'Sequence of an adapter ligated to the 5\' end. The ' 'adapter and any preceding bases are trimmed. Partial ' 'matches at the 5\' end are allowed. If a `^` character ' 'is prepended, the adapter is only found if it is at the ' 'beginning of the read. Search in reverse read.', 'anywhere_r': 'Sequence of an adapter that may be ligated to the 5\' ' 'or 3\' end. Both types of matches as described under ' '`adapter` and `front` are allowed. If the first base ' 'of the read is part of the match, the behavior is as ' 'with `front`, otherwise as with `adapter`. This ' 'option is mostly for rescuing failed library ' 'preparations - do not use if you know which end your ' 'adapter was ligated to. Search in reverse read.', 'error_rate': 'Maximum allowed error rate.', 'indels': 'Allow insertions or deletions of bases when matching ' 'adapters.', 'times': 'Remove multiple occurrences of an adapter if it is ' 'repeated, up to `times` times.', 'overlap': 'Require at least `overlap` bases of overlap between read ' 'and adapter for an adapter to be found.', 'match_read_wildcards': 'Interpret IUPAC wildcards (e.g., N) in ' 'reads.', 'match_adapter_wildcards': 'Interpret IUPAC wildcards (e.g., N) in ' 'adapters.', 'minimum_length': 'Discard reads shorter than specified value. Note, ' 'the cutadapt default of 0 has been overridden, ' 'because that value produces empty sequence ' 'records.', 'discard_untrimmed': 'Discard reads in which no adapter was found.', 'max_expected_errors': 'Discard reads that exceed maximum expected ' 'erroneous nucleotides.', 'max_n': 'Discard reads with more than COUNT N bases. ' 'If COUNT_or_FRACTION is a number between 0 and 1, ' 'it is interpreted as a fraction of the read length.', 'quality_cutoff_3end': 'Trim nucleotides with Phred score quality ' 'lower than threshold from 3 prime end.', 'quality_cutoff_5end': 'Trim nucleotides with Phred score quality ' 'lower than threshold from 5 prime end.', 'quality_base': 'How the Phred score is encoded (33 or 64).', }, output_descriptions={ 'trimmed_sequences': 'The resulting trimmed sequences.', }, name='Find and remove adapters in demultiplexed paired-end sequences.', description='Search demultiplexed paired-end sequences for adapters and ' 'remove them. The parameter descriptions in this method are ' 'adapted from the official cutadapt docs - please see those ' 'docs at https://cutadapt.readthedocs.io for complete ' 'details.', ) plugin.methods.register_function( function=q2_cutadapt._demux.demux_single, inputs={ 'seqs': MultiplexedSingleEndBarcodeInSequence, }, parameters={ 'barcodes': MetadataColumn[Categorical], 'error_rate': Float % Range(0, 1, inclusive_start=True, inclusive_end=True), 'anchor_barcode': Bool, 'batch_size': Int % Range(0, None), 'minimum_length': Int % Range(1, None), 'cut': Int, 'cores': Threads, }, outputs=[ ('per_sample_sequences', SampleData[SequencesWithQuality]), ('untrimmed_sequences', MultiplexedSingleEndBarcodeInSequence), ], input_descriptions={ 'seqs': 'The single-end sequences to be demultiplexed.', }, parameter_descriptions={ 'cores': 'Number of CPU cores to use.', 'barcodes': 'The sample metadata column listing the per-sample ' 'barcodes.', 'error_rate': 'The level of error tolerance, specified as the maximum ' 'allowable error rate. The default value specified by ' 'cutadapt is 0.1 (=10%), which is greater than ' '`demux emp-*`, which is 0.0 (=0%).', 'anchor_barcode': 'Anchor the barcode. The barcode is then ' 'expected to occur in full length at the beginning ' '(5\' end) of the sequence. Can speed up ' 'demultiplexing if used.', 'batch_size': 'The number of samples cutadapt demultiplexes ' 'concurrently. Demultiplexing in smaller batches will ' 'yield the same result with marginal speed loss, and ' 'may solve "too many files" errors related to sample ' 'quantity. Set to "0" to process all samples at once.', 'minimum_length': 'Discard reads shorter than specified value. Note, ' 'the cutadapt default of 0 has been overridden, ' 'because that value produces empty sequence ' 'records.', 'cut': 'Remove the specified number of bases from the sequences. ' 'Bases are removed before demultiplexing. If a positive value ' 'is provided, bases are removed from the beginning of the ' 'sequences. If a negative value is provided, bases are removed ' 'from the end of the sequences.', }, output_descriptions={ 'per_sample_sequences': 'The resulting demultiplexed sequences.', 'untrimmed_sequences': 'The sequences that were unmatched to ' 'barcodes.', }, name='Demultiplex single-end sequence data with barcodes in-sequence.', description='Demultiplex sequence data (i.e., map barcode reads to ' 'sample ids). Barcodes are expected to be located within the ' 'sequence data (versus the header, or a separate barcode ' 'file).', examples={'demux_single': ex.cutadapt_demux_single }, ) plugin.methods.register_function( function=q2_cutadapt._demux.demux_paired, inputs={ 'seqs': MultiplexedPairedEndBarcodeInSequence, }, parameters={ 'forward_barcodes': MetadataColumn[Categorical], 'reverse_barcodes': MetadataColumn[Categorical], 'forward_cut': Int, 'reverse_cut': Int, 'error_rate': Float % Range(0, 1, inclusive_start=True, inclusive_end=True), 'anchor_forward_barcode': Bool, 'anchor_reverse_barcode': Bool, 'batch_size': Int % Range(0, None), 'minimum_length': Int % Range(1, None), 'mixed_orientation': Bool, 'cores': Threads, }, outputs=[ ('per_sample_sequences', SampleData[PairedEndSequencesWithQuality]), ('untrimmed_sequences', MultiplexedPairedEndBarcodeInSequence), ], input_descriptions={ 'seqs': 'The paired-end sequences to be demultiplexed.', }, parameter_descriptions={ 'cores': 'Number of CPU cores to use.', 'forward_barcodes': 'The sample metadata column listing the ' 'per-sample barcodes for the forward reads.', 'reverse_barcodes': 'The sample metadata column listing the ' 'per-sample barcodes for the reverse reads.', 'forward_cut': 'Remove the specified number of bases from the forward ' 'sequences. Bases are removed before demultiplexing. ' 'If a positive value is provided, bases are removed ' 'from the beginning of the sequences. If a negative ' 'value is provided, bases are removed from the end of ' 'the sequences. If --p-mixed-orientation is set, then ' 'both --p-forward-cut and --p-reverse-cut must be ' 'set to the same value.', 'reverse_cut': 'Remove the specified number of bases from the reverse ' 'sequences. Bases are removed before demultiplexing. ' 'If a positive value is provided, bases are removed ' 'from the beginning of the sequences. If a negative ' 'value is provided, bases are removed from the end of ' 'the sequences. If --p-mixed-orientation is set, then ' 'both --p-forward-cut and --p-reverse-cut must be ' 'set to the same value.', 'anchor_forward_barcode': 'Anchor the forward barcode. The ' 'barcode is then expected to occur in full ' 'length at the beginning (5\' end) of the ' 'forward sequence. Can speed up ' 'demultiplexing if used.', 'anchor_reverse_barcode': 'Anchor the reverse barcode. The ' 'barcode is then expected to occur in full ' 'length at the beginning (5\' end) of the ' 'reverse sequence. Can speed up ' 'demultiplexing if used.', 'error_rate': 'The level of error tolerance, specified as the maximum ' 'allowable error rate.', 'batch_size': 'The number of samples cutadapt demultiplexes ' 'concurrently. Demultiplexing in smaller batches will ' 'yield the same result with marginal speed loss, and ' 'may solve "too many files" errors related to sample ' 'quantity. Set to "0" to process all samples at once.', 'minimum_length': 'Discard reads shorter than specified value. Note, ' 'the cutadapt default of 0 has been overridden, ' 'because that value produces empty sequence ' 'records.', 'mixed_orientation': 'Handle demultiplexing of mixed orientation ' 'reads (i.e. when forward and reverse reads ' 'coexist in the same file).', }, output_descriptions={ 'per_sample_sequences': 'The resulting demultiplexed sequences.', 'untrimmed_sequences': 'The sequences that were unmatched to ' 'barcodes.', }, name='Demultiplex paired-end sequence data with barcodes in-sequence.', description='Demultiplex sequence data (i.e., map barcode reads to ' 'sample ids). Barcodes are expected to be located within the ' 'sequence data (versus the header, or a separate barcode ' 'file).', examples={'paired': ex.cutadapt_demux_paired, }, )