def get_sequence(self, transcripts):
sequences = []
for transcript in transcripts:
# get DNA sequence
seq = self._seq_handle.fetch(transcript.chromosome, transcript.start, transcript.stop).upper()
# get DNA sequence of transcript
# reverse complement, if necessary
if transcript.strand=="-":
seq = seq[::-1]
seq = ''.join(np.array(list(seq))[transcript.mask].tolist())
seq = utils.make_complement(seq)
else:
seq = ''.join(np.array(list(seq))[transcript.mask].tolist())
# get RNA sequence
seq = ''.join(['U' if s=='T' else s for s in seq])
sequences.append(seq)
return sequences
def get_sequence(self, transcripts):
sequences = []
for transcript in transcripts:
# get DNA sequence
seq = self._seq_handle.fetch(transcript.chromosome,
transcript.start,
transcript.stop).upper()
# get DNA sequence of transcript
# reverse complement, if necessary
if transcript.strand == "-":
seq = seq[::-1]
seq = ''.join(np.array(list(seq))[transcript.mask].tolist())
seq = utils.make_complement(seq)
else:
seq = ''.join(np.array(list(seq))[transcript.mask].tolist())
# get RNA sequence
seq = ''.join(['U' if s == 'T' else s for s in seq])
sequences.append(seq)
return sequences
positions = transcript.start + np.where(transcript.mask)[0]
reads = [
seq[i:i + options.footprint_length]
for i in xrange(L - options.footprint_length + 1)
]
# write synthetic reads
fastq_handle.write(''.join(["@%s:%d:%s\n%s\n+\n%s\n"%(transcript.chromosome, \
position,transcript.strand,read,qual) \
for position,read in zip(positions,reads)]))
# get reverse strand reads
transcript.mask = transcript.mask[::-1]
transcript.strand = "-"
seq = seq[::-1]
seq = ''.join(utils.make_complement(seq))
positions = transcript.start + transcript.mask.size - np.where(
transcript.mask)[0]
reads = [
seq[i:i + options.footprint_length]
for i in xrange(L - options.footprint_length + 1)
]
# write synthetic reads
fastq_handle.write(''.join(["@%s:%d:%s\n%s\n+\n%s\n"%(transcript.chromosome, \
position,transcript.strand,read,qual) \
for position,read in zip(positions,reads)]))
seq_handle.close()
fastq_handle.close()
transcript.mask = transcript.mask[::-1]
transcript.strand = "+"
seq = ''.join(np.array(list(sequence))[transcript.mask].tolist())
L = len(seq)
positions = transcript.start + np.where(transcript.mask)[0]
reads = [seq[i:i+options.footprint_length]
for i in xrange(L-options.footprint_length+1)]
# write synthetic reads
fastq_handle.write(''.join(["@%s:%d:%s\n%s\n+\n%s\n"%(transcript.chromosome, \
position,transcript.strand,read,qual) \
for position,read in zip(positions,reads)]))
# get reverse strand reads
transcript.mask = transcript.mask[::-1]
transcript.strand = "-"
seq = seq[::-1]
seq = ''.join(utils.make_complement(seq))
positions = transcript.start + transcript.mask.size - np.where(transcript.mask)[0]
reads = [seq[i:i+options.footprint_length]
for i in xrange(L-options.footprint_length+1)]
# write synthetic reads
fastq_handle.write(''.join(["@%s:%d:%s\n%s\n+\n%s\n"%(transcript.chromosome, \
position,transcript.strand,read,qual) \
for position,read in zip(positions,reads)]))
seq_handle.close()
fastq_handle.close()
