def load_HXB2(cropped=False, fragment=None, trim_primers=False):
'''Load HXB2 reference sequence'''
if fragment is None:
return SeqIO.read(get_HXB2_entire(cropped=cropped), 'fasta')
else:
return SeqIO.read(get_HXB2_fragmented(fragment,
trim_primers=trim_primers),
'fasta')
SeqIO.write(seq_cropped, get_HXB2_entire(cropped=True), 'fasta')
# 3. Extract fragments coordinates and sequences (this is sample specific)
frag_coos = {f: [co[0][0], co[1][1]] for f, co in pci.iteritems()}
frag_seqs = {f: seq[co[0]: co[1]] for f, co in frag_coos.iteritems()}
# Extract fragments without the inner primers
frag_coos_trimmed = {f: [co[0][1], co[1][0]] for f, co in pci.iteritems()}
frag_seqs_trimmed = {f: seq[co[0]: co[1]] for f, co in frag_coos_trimmed.iteritems()}
# Relabel sequences
for f in frag_seqs:
# Relabel fragments with primers
fs = frag_seqs[f]
fs.name = 'HXB2_reference_'+f
fs.id = fs.name
fs.description = re.sub('_', ' ', fs.id)
# Relabel fragments without primers
fs_trimmed = frag_seqs_trimmed[f]
fs_trimmed.name = 'HXB2_reference_'+f+'_trim_primers'
fs_trimmed.id = fs_trimmed.name
fs_trimmed.description = re.sub('_', ' ', fs_trimmed.id)
# Write to file both the fragmented (in separated files)
for f in frag_seqs:
SeqIO.write(frag_seqs[f], get_HXB2_fragmented(f), 'fasta')
SeqIO.write(frag_seqs_trimmed[f],
get_HXB2_fragmented(f, trim_primers=True), 'fasta')
print f
