def get_fasta(self, chr_pos, strand):
"""finds the sequence of a genomic interval '1:387941-388099', '+' """
assert self._has_fasta()
samtools_cmm = ['samtools', 'faidx', self.fasta_file, chr_pos]
samtools_out = sp.check_output(samtools_cmm).decode()
seq = self.fasta2seq(samtools_out)
if strand == '-':
seq = fn.comp_rev(seq)
return seq.upper()
def get_fasta(self, chr_pos, strand):
"""finds the sequence of a genomic interval '1:387941-388099', '+' """
assert self._has_fasta()
samtools_cmm = ['samtools', 'faidx', self.fasta_file, chr_pos]
samtools_out = sp.check_output(samtools_cmm).decode()
seq = self.fasta2seq(samtools_out)
if strand == '-':
seq = fn.comp_rev(seq)
return seq.upper()
def test_trans_seq_strand(self):
if os.path.isdir('/Users/martin'):
seq_out = self.parser.get_trans_seqs(self.trans_exons_strand)
self.assertEquals(fn.comp_rev(self.seq_exp), seq_out['trans123'])
def test_get_fasta_strand(self):
self.assertEquals(fn.comp_rev(self.seq1), self.parser.get_fasta(self.pos1, '-'))
def test_comp_rev_low(self):
self.assertEquals('CAGTCAGT', fn.comp_rev('actgactg'))
def test_comp_rev(self):
self.assertEquals('CCAAGGTT', fn.comp_rev('AACCTTGG'))
def _rev_comp(self, genome_align):
for llave, seq in genome_align.items():
genome_align[llave] = fn.comp_rev(seq)
return genome_align
def _rev_comp(self, genome_align):
for llave, seq in genome_align.items():
genome_align[llave] = fn.comp_rev(seq)
return genome_align
def test_trans_seq_strand(self):
if os.path.isdir('/Users/martin'):
seq_out = self.parser.get_trans_seqs(self.trans_exons_strand)
self.assertEquals(fn.comp_rev(self.seq_exp), seq_out['trans123'])
def test_get_fasta_strand(self):
self.assertEquals(fn.comp_rev(self.seq1),
self.parser.get_fasta(self.pos1, '-'))
def test_comp_rev_low(self):
self.assertEquals('CAGTCAGT', fn.comp_rev('actgactg'))
def test_comp_rev(self):
self.assertEquals('CCAAGGTT', fn.comp_rev('AACCTTGG'))