def test_write_sequences_to_fasta_file(self): """Tests writing to a FASTA file""" seqs = st.read_sequences_from_fasta_file('testdata/fasta_test.fa') with open('/tmp/fasta_tmp.fa', 'w') as outputfile: st.write_sequences_to_fasta_file(outputfile, seqs) seqs2 = st.read_sequences_from_fasta_file('/tmp/fasta_tmp.fa') self.assertEquals(seqs, seqs2)
def test_write_sequences_to_fasta_file(self): """Tests writing to a FASTA file""" seqs = st.read_sequences_from_fasta_file('testdata/fasta_test.fa') with open('/tmp/fasta_tmp.fa', 'w') as outputfile: st.write_sequences_to_fasta_file(outputfile, seqs) seqs2 = st.read_sequences_from_fasta_file('/tmp/fasta_tmp.fa') self.assertEquals(seqs, seqs2)
def test_write_sequences_to_fasta_file_empty_seqs(self): """Tests ensures that only non-empty sequences will be written to FASTA""" seqs = [['seq1', 'TATATA'], ['seq2', '']] with open('/tmp/fasta_tmp.fa', 'w') as outputfile: st.write_sequences_to_fasta_file(outputfile, seqs) seqs2 = st.read_sequences_from_fasta_file('/tmp/fasta_tmp.fa') self.assertEquals(1, len(seqs2)) self.assertEquals(seqs[0][0], seqs2[0][0]) self.assertEquals(seqs[0][1], seqs2[0][1])
def test_write_sequences_to_fasta_file_empty_seqs(self): """Tests ensures that only non-empty sequences will be written to FASTA""" seqs = [['seq1', 'TATATA'], ['seq2', '']] with open('/tmp/fasta_tmp.fa', 'w') as outputfile: st.write_sequences_to_fasta_file(outputfile, seqs) seqs2 = st.read_sequences_from_fasta_file('/tmp/fasta_tmp.fa') self.assertEquals(1, len(seqs2)) self.assertEquals(seqs[0][0], seqs2[0][0]) self.assertEquals(seqs[0][1], seqs2[0][1])
def test_read_sequences_from_fasta_file(self): """test reading sequences from a string in FASTA format""" with open("testdata/fasta_test.fa") as inputfile: fasta_string = inputfile.read() seqs = st.read_sequences_from_fasta_file('testdata/fasta_test.fa') self.assertEquals(7, len(seqs)) seq = ("CCGAGGAAGACAGACGCAATTTCACATCGAACTCGTGTACGGCATCCTCT" + "TTATTGCCGGCTTTGCTTTTCTCGTCTTCCGCGTCGATCCCCGGGTGGCA" + "GCGTTCGAAGGAGGTCTCGTCATTGGTTACTTATTGAGAATTTAGGGGAA" + "AATGTCAATCTACGAGTGGA") self.assertEquals('VNG6198H', seqs[6][0]) self.assertEquals(seq, seqs[6][1])
def test_read_sequences_from_fasta_file(self): """test reading sequences from a string in FASTA format""" with open("testdata/fasta_test.fa") as inputfile: fasta_string = inputfile.read() seqs = st.read_sequences_from_fasta_file('testdata/fasta_test.fa') self.assertEquals(7, len(seqs)) seq = ("CCGAGGAAGACAGACGCAATTTCACATCGAACTCGTGTACGGCATCCTCT" + "TTATTGCCGGCTTTGCTTTTCTCGTCTTCCGCGTCGATCCCCGGGTGGCA" + "GCGTTCGAAGGAGGTCTCGTCATTGGTTACTTATTGAGAATTTAGGGGAA" + "AATGTCAATCTACGAGTGGA") self.assertEquals('VNG6198H', seqs[6][0]) self.assertEquals(seq, seqs[6][1])