Example #1
0
 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)
Example #2
0
 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)
Example #3
0
 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])
Example #4
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 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])
Example #5
0
 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])
Example #6
0
 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])