Python group_pairs_by_name Examples

Example #1

File: test_pairing.py Project: fw1121/ngs_crumbs

    def test_pair_grouper(self):
        seqs = _build_some_paired_seqs()
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T', 'G']
        assert len(paired_seqs) == 2

        seqs = seqs[0], seqs[2], seqs[1], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['C']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['G']
        assert len(paired_seqs) == 4

        seqs = _build_some_paired_seqs()
        seqs = seqs[:-1]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']

        seqs = _build_some_paired_seqs()
        seqs = seqs[:-1]
        try:
            paired_seqs = list(group_pairs_by_name(seqs,
                                                   all_pairs_same_n_seqs=True))
            self.fail('InterleaveError expected')
        except InterleaveError:
            pass

Example #2

File: test_pairing.py Project: fw1121/ngs_crumbs

    def test_no_name(self):
        seqs = _build_some_paired_seqs()
        seq = SeqWrapper(SEQITEM, SeqItem('s', ['>s\n', 'N\n']), 'fasta')

        seqs = seqs[0], seqs[1], seqs[2], seq, seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['G']

        seqs = _build_some_paired_seqs()
        seqs = seqs[0], seq, seqs[1], seqs[2], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['C']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['T', 'G']

        seqs = _build_some_paired_seqs()
        seqs = seq, seqs[0], seqs[1], seqs[2], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['T', 'G']

Example #3

    def test_no_name(self):
        seqs = _build_some_paired_seqs()
        seq = SeqWrapper(SEQITEM, SeqItem('s', ['>s\n', 'N\n']), 'fasta')

        seqs = seqs[0], seqs[1], seqs[2], seq, seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['G']

        seqs = _build_some_paired_seqs()
        seqs = seqs[0], seq, seqs[1], seqs[2], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['C']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['T', 'G']

        seqs = _build_some_paired_seqs()
        seqs = seq, seqs[0], seqs[1], seqs[2], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['N']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['T', 'G']

Example #4

    def test_pair_grouper(self):
        seqs = _build_some_paired_seqs()
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T', 'G']
        assert len(paired_seqs) == 2

        seqs = seqs[0], seqs[2], seqs[1], seqs[3]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']
        assert [get_str_seq(s) for s in paired_seqs[2]] == ['C']
        assert [get_str_seq(s) for s in paired_seqs[3]] == ['G']
        assert len(paired_seqs) == 4

        seqs = _build_some_paired_seqs()
        seqs = seqs[:-1]
        paired_seqs = list(group_pairs_by_name(seqs))
        assert [get_str_seq(s) for s in paired_seqs[0]] == ['A', 'C']
        assert [get_str_seq(s) for s in paired_seqs[1]] == ['T']

        seqs = _build_some_paired_seqs()
        seqs = seqs[:-1]
        try:
            paired_seqs = list(
                group_pairs_by_name(seqs, all_pairs_same_n_seqs=True))
            self.fail('InterleaveError expected')
        except InterleaveError:
            pass

Example #5

File: bulk_filters.py Project: fw1121/ngs_crumbs

def _read_pairs(in_fhands, paired_reads):
    seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
    if paired_reads:
        pairs = group_pairs_by_name(seqs)
    else:
        pairs = group_pairs(seqs, n_seqs_in_pair=1)
    return pairs

Example #6

def _read_pairs(in_fhands, paired_reads):
    seqs = read_seqs(in_fhands, prefered_seq_classes=[SEQITEM])
    if paired_reads:
        pairs = group_pairs_by_name(seqs)
    else:
        pairs = group_pairs(seqs, n_seqs_in_pair=1)
    return pairs

Example #7

File: trim.py Project: fw1121/ngs_crumbs

def seq_to_trim_packets(seq_packets, group_paired_reads=False):
    'It yields packets suitable for the filters'

    for packet in seq_packets:
        if group_paired_reads:
            packet = list(group_pairs_by_name(packet))
        else:
            packet = list(group_pairs(packet, n_seqs_in_pair=1))
        yield {SEQS_PASSED: packet, ORPHAN_SEQS: []}

Example #8

def seq_to_trim_packets(seq_packets, group_paired_reads=False):
    'It yields packets suitable for the filters'

    for packet in seq_packets:
        if group_paired_reads:
            packet = list(group_pairs_by_name(packet))
        else:
            packet = list(group_pairs(packet, n_seqs_in_pair=1))
        yield {SEQS_PASSED: packet, ORPHAN_SEQS: []}

Example #9

File: test_pairing.py Project: fw1121/ngs_crumbs

 def test_empty_iter():
     paired_seqs = list(group_pairs_by_name([]))
     assert not paired_seqs

Example #10

 def test_empty_iter():
     paired_seqs = list(group_pairs_by_name([]))
     assert not paired_seqs