Ejemplos de assing_kind_to_seqs en Python

Ejemplo n.º 1

Archivo: test_pairing.py Proyecto: djinnome/seq_crumbs

    def test_all_orphan():
        'All reads end up in orphan'
        seqs = [SeqRecord(Seq('ACT'), id='seq1'),
                SeqRecord(Seq('ACT'), id='seq2')]
        seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
        assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'

        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, ordered=False,
                    out_format='fasta')
        assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
        assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()

Ejemplo n.º 2

Archivo: test_read_pairing.py Proyecto: bharatpatel/seq_crumbs

    def test_all_orphan():
        "All reads end up in orphan"
        seqs = [SeqRecord(Seq("ACT"), id="seq1"), SeqRecord(Seq("ACT"), id="seq2")]
        seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, out_format="fasta")
        assert orphan_out_fhand.getvalue() == ">seq1\nACT\n>seq2\nACT\n"

        seq_fhand = NamedTemporaryFile(suffix=".fasta")
        write_seqs(seqs, seq_fhand, file_format="fasta")
        seq_fhand.flush()
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs_unordered(seq_fhand.name, out_fhand, orphan_out_fhand, out_format="fasta")
        assert ">seq1\nACT\n" in orphan_out_fhand.getvalue()
        assert ">seq2\nACT\n" in orphan_out_fhand.getvalue()

Ejemplo n.º 3

Archivo: test_read_pairing.py Proyecto: milw/seq_crumbs

    def test_all_orphan():
        'All reads end up in orphan'
        seqs = [SeqRecord(Seq('ACT'), id='seq1'),
                SeqRecord(Seq('ACT'), id='seq2')]
        seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
        assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'

        #seq_fhand = NamedTemporaryFile(suffix='.fasta')
        #write_seqs(seqs, seq_fhand, file_format='fasta')
        #seq_fhand.flush()
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, ordered=False,
                    out_format='fasta')
        assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
        assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()

Ejemplo n.º 4

    def test_all_orphan():
        'All reads end up in orphan'
        seqs = [
            SeqRecord(Seq('ACT'), id='seq1'),
            SeqRecord(Seq('ACT'), id='seq2')
        ]
        seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
        assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'

        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs,
                    out_fhand,
                    orphan_out_fhand,
                    ordered=False,
                    out_format='fasta')
        assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
        assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()

Ejemplo n.º 5

Archivo: test_read_pairing.py Proyecto: terrycojones/seq_crumbs

    def test_all_orphan():
        'All reads end up in orphan'
        seqs = [
            SeqRecord(Seq('ACT'), id='seq1'),
            SeqRecord(Seq('ACT'), id='seq2')
        ]
        seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
        assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'

        seq_fhand = NamedTemporaryFile(suffix='.fasta')
        write_seqs(seqs, seq_fhand, file_format='fasta')
        seq_fhand.flush()
        out_fhand = StringIO()
        orphan_out_fhand = StringIO()
        match_pairs_unordered(seq_fhand.name,
                              out_fhand,
                              orphan_out_fhand,
                              out_format='fasta')
        assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
        assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()