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str(object='') -> string

Return a nice string representation of the object.
If the argument is a string, the return value is the same object.

src/s/e/seq_crumbs-HEAD/crumbs/trim.py   seq_crumbs(Download)
 
from crumbs.utils.optional_modules import Seq
from crumbs.utils.tags import (TRIMMING_RECOMMENDATIONS, QUALITY, OTHER,
                               VECTOR, TRIMMING_KINDS, SEQS_PASSED,
                               ORPHAN_SEQS)
        else:
            packet = list(group_pairs(packet, n_seqs_in_pair=1))
        yield {SEQS_PASSED: packet, ORPHAN_SEQS: []}
 
 
            trimmed_seqs.append([self._do_trim(s) for s in paired_seqs])
        return {SEQS_PASSED: trimmed_seqs,
                ORPHAN_SEQS: trim_packet[ORPHAN_SEQS]}
 
    def _do_trim(self, seq):
    def __call__(self, trim_packet):
        'It trims the seqs'
        trimmed_seqs = []
        orphan_seqs = trim_packet[ORPHAN_SEQS]
        for paired_seqs in trim_packet[SEQS_PASSED]:

src/s/e/seq_crumbs-HEAD/crumbs/seqio.py   seq_crumbs(Download)
from crumbs.utils.file_formats import get_format, peek_chunk_from_file
 
from crumbs.utils.tags import (GUESS_FORMAT, SEQS_PASSED, SEQS_FILTERED_OUT,
                               SEQITEM, SEQRECORD, ORPHAN_SEQS,
    SANGER_FASTQ_FORMATS, ILLUMINA_FASTQ_FORMATS)
    _write_filter_trim_packets(passed_fhand, orphan_fhand, trim_packets,
                               file_format=file_format, workers=workers,
                               seqs_diverted=ORPHAN_SEQS)
 
 

src/s/e/seq_crumbs-HEAD/test/test_trim.py   seq_crumbs(Download)
    seq_to_trim_packets)
from crumbs.utils.bin_utils import BIN_DIR
from crumbs.utils.tags import (SEQRECORD, SEQITEM, TRIMMING_RECOMMENDATIONS,
                               VECTOR, ORPHAN_SEQS, SEQS_PASSED)
from crumbs.seq import get_str_seq, get_annotations, get_int_qualities, get_name
        seqs.append([SeqWrapper(SEQRECORD, SeqRecord(Seq('AC')), None)])
 
        trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
        trim_lowercased_seqs = TrimLowercasedLetters()
        trim = TrimOrMask()
        seq = SeqItem('s', ['>s\n', 'aaCTTTC\n'])
        seqs.append([SeqWrapper(SEQITEM, seq, 'fasta')])
        trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
        trim_packet = trim(trim_lowercased_seqs(trim_packet))
        res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
        seqs.append([SeqWrapper(SEQITEM, seq2, 'fasta'),
                     SeqWrapper(SEQITEM, seq3, 'fasta')])
        trim_packet = {SEQS_PASSED: seqs, ORPHAN_SEQS: []}
        trim_lowercased_seqs = TrimLowercasedLetters()
        trim = TrimOrMask()
        # pylint: disable=W0141
        trim_packet = trim(trim_lowercased_seqs(trim_packet))
        res = [get_str_seq(s) for l in trim_packet[SEQS_PASSED] for s in l]
        orphan_res = [get_str_seq(s) for s in trim_packet[ORPHAN_SEQS]]