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loci2partitions.py
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loci2partitions.py
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#!/usr/bin/env python3
import argparse
import sys
<<<<<<< HEAD
def main():
=======
def main():
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
arguments = Get_Arguments()
check_if_exists(arguments.loci)
locus_num = 0
<<<<<<< HEAD
site_pos = 1
length_part = set()
=======
ind_count = 0
site_pos = 1
length_part = set()
length_list = list()
ind_count_list = list()
loc_list = list()
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
nexus = str(arguments.out) + ".nex"
partitions = str(arguments.out) + ".partitions"
with open(arguments.loci, "r") as fin:
with open(nexus, "w") as nex:
nex.write("#nexus\n")
nex.write("begin sets;\n")
with open(partitions, "w") as part:
# Call generator function on input .loci file
# Output is a NEXUS and RAxML-style partition input file.
<<<<<<< HEAD
for lcount, slen, total_len in locusGenerator(fin, locus_num):
upper_bound = write_nexpartition(nex, lcount, slen, site_pos)
write_partitions(part, lcount, slen, site_pos, upper_bound)
site_pos += slen
print(sum(total_len))
nex.write("end;\n")
=======
for locus, lcount, slen, ind_count in locusGenerator(fin, locus_num, length_part, ind_count):
loc_list.append(locus)
upper_bound = write_nexpartition(nex, lcount, slen, site_pos)
write_partitions(part, lcount, slen, site_pos, upper_bound)
length_list.append(slen)
site_pos += slen
nex.write("end;\n")
# Get all keys in list of dictionaries.
all_keys = set().union(*(d.keys() for d in loc_list))
#print(all_keys)
concatenate_alignments(all_keys, loc_list, length_list)
#print(length_list)
return 0
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
# Uses argparse library to parse command-line arguments; argparse must be imported
def Get_Arguments():
parser = argparse.ArgumentParser(description="Script to make NEXUS and "
" RAxML-style partitions files "
"from pyRAD/ipyrad .loci file ")
required_args = parser.add_argument_group("required arguments")
required_args.add_argument("-l", "--loci", type=str,
required=True,
help=".loci input filename")
parser.add_argument("-o", "--out", type=str,
required=False,
nargs="?",
default="out",
help="Prefix for output files")
args = parser.parse_args()
return args
def check_if_exists(filename):
try:
file = open(filename, "r")
except IOError:
print("\nError: The file " + filename + " does not exist.\n")
sys.exit(1)
def locusGenerator(file, locus_count, length_part, ind_count):
locus = dict()
<<<<<<< HEAD
length_set = set()
length_list = list()
total_length = 0
=======
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
for line in file:
line = line.strip()
lines = line.split()
if line.startswith("//"):
temp_locus = locus.copy()
locus.clear()
locus_count += 1
<<<<<<< HEAD
if len(length_set) > 1:
print("Unequal lengths: " + str(length_set))
length_set.clear()
length_list.append(seq_len)
yield locus_count, seq_len, length_list
else:
length_set.clear()
length_list.append(seq_len)
yield locus_count, seq_len, length_list
=======
if len(length_part) > 1:
print("Warning: Unequal sequence lengths at locus " + \
str(locus_count) + "\n")
length_part.clear()
yield temp_locus, locus_count, seq_len, ind_count
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
elif line and \
(line[0].isalpha() or \
line[0].isdigit() or \
line[0].startswith(">")):
locus[lines[0]] = lines[1]
ind_count += 1
seq_len = len(lines[1])
<<<<<<< HEAD
length_set.add(seq_len)
=======
length_part.add(seq_len)
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
def write_nexpartition(fout, loc_count, seqlen, site_pos):
upper_site_bound = (site_pos + seqlen - 1)
fout.write("\tcharset part" + str(loc_count) + " = " + str(site_pos) + "-" + \
str(upper_site_bound) + ";\n")
return upper_site_bound
def write_partitions(fout, loc_count, seqlen, site_pos, upper_site_bound):
fout.write("DNA, part" + str(loc_count) + " = " + str(site_pos) + "-" + \
str(upper_site_bound) + ";\n")
def concatenate_alignments(all_keys, list_of_dicts, slen):
<<<<<<< HEAD
if __name__ == "__main__":
=======
sorted_keys = sorted(all_keys)
#print(len(all_keys))
for k in sorted_keys:
merged = "".join(d.get(k, "N" * len( for d in list_of_dicts)
print(k + "\t" + str(merged))
for d in range(len(list_of_dicts)):
concat = dict()
for k in sorted_keys:
#print(slen[d])
missing = "N"
missing_len = missing * slen[d]
seqs = list_of_dicts[d].get(k, missing_len)
concat[k] = seqs
#$print(k + "\t")
"".join(concat[k])
#for k in concat.keys():
#print(concat[k])
#print(k, concat[k])
#print(joined)
#for k in sorted_keys:
#joined = "".join(str(concat[x]) for x in sorted(list_of_dicts[d]))
#print(joined)
#print(test)
#d.get(k, default)
#for i in sorted_keys:
#for d in list_of_dicts:
#if
##########################################################################################################################################
##############################################################MAIN########################################################################
if __name__ == "__main__":
>>>>>>> 0b5b1ca206309a823ef3ea043d06c2ae6977d166
rtrn_code = main()
print("Program finished with exit status " + str(rtrn_code) + "\n")
sys.exit(rtrn_code)