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()
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()
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()
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()
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()