#!/usr/bin/python3
from fasta import FastaList
import argparse
import subprocess as sub
PARSER = argparse.ArgumentParser(description='Test of primerdelete')
PARSER.add_argument('-f', type=str, help='input fasta file', required=True)
PARSER.add_argument('-p',
type=str,
help='input primer fasta'
' file',
required=True)
PARSER.add_argument('-o', type=str, help='output file', required=True)
PARSER.add_argument('-m', type=str, help='muscle path', required=True)
ARGS = PARSER.parse_args()
fa = FastaList(ARGS.f)
fa.wr_fasta_file(ARGS.o, ARGS.p)
outfi = ARGS.o.split('.')[0] + '.afa'
muscle = sub.Popen(ARGS.m + ' -in ' + ARGS.o + ' -out ' + outfi + ' -quiet')
muscle.wait()
if os.path.isdir(ARGS.od):
shutil.rmtree(ARGS.od)
os.mkdir(ARGS.od)
refs = FastaList(ARGS.r)
for seqfile in os.listdir(ARGS.id):
if 'log' in seqfile:
continue
print('Cleaning: {}'.format(seqfile))
input_name = ARGS.id + seqfile
output_name = ARGS.od + seqfile
fa_in = FastaList(input_name)
# Remove primers if primers exit in seq. rmprimers return an empty list
# if no primers are found
if fa_in.rmprimers(ARGS.p):
fa_in.wr_fasta_file(output_name, ARGS.p)
fa_in = FastaList(output_name)
for item in refs.seq_list:
if seqfile.split('.')[0] in item.split('\n')[0]:
with open(output_name, 'a') as fi:
fi.write(item)
fi.close()
muscle_out = output_name.split('.')[0] + '.afa'
muscle = sub.Popen(ARGS.m + ' -in ' + output_name + ' -out ' + muscle_out +
' -gapopen -1000 -quiet')
muscle.wait()
reference_seq = ''
cropped_alignment = FastaList(muscle_out).crop_ends()
for item in cropped_alignment:
if [m.start() for m in re.finditer('ref', item)]:
reference_seq = item
#!/usr/bin/python3
# Removes columns containing degenerate nucleotides from alignment and writes
# a new alignment as output file.
import argparse
from fasta import FastaList
PARSER = argparse.ArgumentParser(description='Removes columns with degenerate '
'nucleotides from alignment '
'and writes a new alignment as '
'output file')
PARSER.add_argument('-i', type=str, help='fastq input filename', required=True)
PARSER.add_argument('-o',
type=str,
help='fastq output filename',
default='out.fa')
ARGS = PARSER.parse_args()
newseq_list = FastaList(ARGS.i)
newseq_list.rm_non_agct_columns()
newseq_list.wr_fasta_file(ARGS.o)
