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')
import os
import re
import Bio.SeqIO as SeqIO
from hivwholeseq.reference import load_HXB2
from hivwholeseq.data.primers import primers_coordinates_HXB2_inner as pci
from hivwholeseq.data.primers import primers_coordinates_HXB2_outer as pco
from hivwholeseq.sequencing.filenames import get_HXB2_fragmented, get_HXB2_entire
# Script
if __name__ == '__main__':
# Make output folder if necessary
dirname = os.path.dirname(get_HXB2_entire())
if not os.path.isdir(dirname):
os.mkdir(dirname)
# Get the annotated sequence
seq = load_HXB2()
# 1. Copy the entire reference verbatim
SeqIO.write(seq, get_HXB2_entire(), 'fasta')
# 2. Make a cropped sequence from F1o to F6o (outer primers), to reduce LTR
# degeneracy problems during premapping
start = pco['F1'][0][0]
end = pco['F6'][1][1]
seq_cropped = seq[start: end]
seq_cropped.id = seq_cropped.name = seq.name+'_cropped_F1o_F6o'
