def make_READnome(self, fq_id, run_ID, buff=500, out_path=None):
if out_path != None:
fout_name = os.path.split(fq_id)[-1]
fout = os.path.join(out_path, fout_name)
else:
fout = os.path.split(fq_id)[-1]
asm = "{}.asm.out".format(fout)
fa = "{}.asm.fa".format(fout)
G = GenerateRADnome()
G.make_READnome(asm, fa, buff, run_ID, out_path)
return 1
def make_RADnome(self, fq1, fq2, run_ID, N_padding, insert_size,
proportion, overlap, out_path=None):
def seq_len(fq):
with open(fq,'rU') as fin:
fin.readline()
return len(fin.readline().strip())
if out_path != None:
fout1 = os.path.split(fq1)[-1]
fout2 = os.path.split(fq2)[-1]
fout1 = os.path.join(out_path, fout1)
fout2 = os.path.join(out_path, fout2)
run_ID = os.path.join(out_path, run_ID)
else:
fout1 = os.path.split(fq1)[-1]
fout2 = os.path.split(fq2)[-1]
rad1 = "{}.asm.fa".format(fout1)
rad2 = "{}.asm.fa".format(fout2)
r1_contig_len = seq_len(fq1)
r2_contig_len = seq_len(fq2)
contig_2_contig_dict = "{}.R1_to_R2_contig_associations.pkl".format(run_ID)
run_name = run_ID
# N_padding = 500
# insert_size = 50
# proportion = 0.8
# overlap = 10
self.create_faidx(rad1)
self.create_faidx(rad2)
G = GenerateRADnome()
G.contigs_2_RADnome(rad1, rad2, r1_contig_len,
r2_contig_len, contig_2_contig_dict,
run_name, N_padding, insert_size,
proportion, overlap)
return 1
