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parahunter-dnds.py
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parahunter-dnds.py
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#!/usr/bin/env python3
from collections import defaultdict
import re
import os
import textwrap
import argparse
# import numpy as np
import sys
def firstNonspace(ls):
for i in ls:
if i != "":
break
return i
def gc(seq):
gc = 0
for bp in seq:
if bp == "C" or bp == "G":
gc += 1
return gc/len(seq)
def Dictparser(Dictionary):
lowest = float(1000)
for i in Dictionary:
if float(Dictionary[i]) < float(lowest):
lowest = Dictionary[i]
key = i
return [key, lowest]
def reverseComplement(seq):
out = []
for i in range(len(seq)-1, -1, -1):
nucleotide = seq[i]
if nucleotide == "C":
nucleotide = "G"
elif nucleotide == "G":
nucleotide = "C"
elif nucleotide == "T":
nucleotide = "A"
elif nucleotide == "A":
nucleotide = "T"
out.append(nucleotide)
outString = "".join(out)
return outString
def Complement(seq):
out = []
for i in range(0, len(seq)):
nucleotide = seq[i]
if nucleotide == "C":
nucleotide = "G"
elif nucleotide == "G":
nucleotide = "C"
elif nucleotide == "T":
nucleotide = "A"
elif nucleotide == "A":
nucleotide = "T"
out.append(nucleotide)
outString = "".join(out)
return outString
def ribosome(seq):
NTs = ['T', 'C', 'A', 'G']
stopCodons = ['TAA', 'TAG', 'TGA']
Codons = []
for i in range(4):
for j in range(4):
for k in range(4):
codon = NTs[i] + NTs[j] + NTs[k]
# if not codon in stopCodons:
Codons.append(codon)
CodonTable = {}
AAz = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
AAs = list(AAz)
k = 0
for base1 in NTs:
for base2 in NTs:
for base3 in NTs:
codon = base1 + base2 + base3
CodonTable[codon] = AAs[k]
k += 1
prot = []
for j in range(0, len(seq), 3):
codon = seq[j:j + 3]
try:
prot.append(CodonTable[codon])
except KeyError:
prot.append("X")
protein = ("".join(prot))
return protein
def SeqCoord(seq, start, end):
return seq[start:end]
def howMany(ls, exclude):
counter = 0
for i in ls:
if i != exclude:
counter += 1
return counter
def stabilityCounter(int):
if len(str(int)) == 1:
string = (str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 2:
string = (str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 3:
string = (str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 4:
string = (str(0) + str(int))
return (string)
if len(str(int)) > 4:
string = str(int)
return (string)
def sum(ls):
count = 0
for i in ls:
count += float(i)
return count
def ave(ls):
count = 0
for i in ls:
count += float(i)
return count/len(ls)
def derep(ls):
outLS = []
for i in ls:
if i not in outLS:
outLS.append(i)
return outLS
def cluster(data, maxgap):
'''Arrange data into groups where successive elements
differ by no more than *maxgap*
#->>> cluster([1, 6, 9, 100, 102, 105, 109, 134, 139], maxgap=10)
[[1, 6, 9], [100, 102, 105, 109], [134, 139]]
#->>> cluster([1, 6, 9, 99, 100, 102, 105, 134, 139, 141], maxgap=10)
[[1, 6, 9], [99, 100, 102, 105], [134, 139, 141]]
'''
# data = sorted(data)
data.sort(key=int)
groups = [[data[0]]]
for x in data[1:]:
if abs(x - groups[-1][-1]) <= maxgap:
groups[-1].append(x)
else:
groups.append([x])
return groups
def GCcalc(seq):
count = 0
for i in seq:
if i == "G" or i == "C":
count += 1
return count/len(seq)
def lastItem(ls):
x = ''
for i in ls:
if i != "":
x = i
return x
def RemoveDuplicates(ls):
empLS = []
counter = 0
for i in ls:
if i not in empLS:
empLS.append(i)
else:
pass
return empLS
def allButTheLast(iterable, delim):
x = ''
length = len(iterable.split(delim))
for i in range(0, length-1):
x += iterable.split(delim)[i]
x += delim
return x[0:len(x)-1]
def secondToLastItem(ls):
x = ''
for i in ls[0:len(ls)-1]:
x = i
return x
def pull(item, one, two):
ls = []
counter = 0
for i in item:
if counter == 0:
if i != one:
pass
else:
counter += 1
ls.append(i)
else:
if i != two:
ls.append(i)
else:
ls.append(i)
counter = 0
outstr = "".join(ls)
return outstr
def replace(stringOrlist, list, item):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
emptyList.append(item)
outString = "".join(emptyList)
return outString
def remove(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
outString = "".join(emptyList)
return outString
def removeLS(stringOrlist, list):
emptyList = []
for i in stringOrlist:
if i not in list:
emptyList.append(i)
else:
pass
return emptyList
def fasta(fasta_file):
count = 0
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
count += 1
if count % 1000000 == 0:
print(count)
if len(seq) > 0:
Dict[header] = seq
header = i[1:]
# header = header.split(" ")[0]
seq = ''
else:
header = i[1:]
# header = header.split(" ")[0]
seq = ''
else:
seq += i
Dict[header] = seq
# print(count)
return Dict
def fasta2(fasta_file):
count = 0
seq = ''
header = ''
Dict = defaultdict(lambda: defaultdict(lambda: 'EMPTY'))
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
count += 1
if count % 1000000 == 0:
print(count)
if len(seq) > 0:
Dict[header] = seq
header = i[1:]
header = header.split(" ")[0]
# header = header.split("|")[1]
seq = ''
else:
header = i[1:]
header = header.split(" ")[0]
# header = header.split("|")[1]
seq = ''
else:
seq += i
Dict[header] = seq
# print(count)
return Dict
def allButTheFirst(iterable, delim):
x = ''
length = len(iterable.split(delim))
for i in range(1, length):
x += iterable.split(delim)[i]
x += delim
return x[0:len(x)]
def filter(list, items):
outLS = []
for i in list:
if i not in items:
outLS.append(i)
return outLS
def filterRe(list, regex):
ls1 = []
ls2 = []
for i in list:
if re.findall(regex, i):
ls1.append(i)
else:
ls2.append(i)
return ls1, ls2
def delim(line):
ls = []
string = ''
for i in line:
if i != " ":
string += i
else:
ls.append(string)
string = ''
ls = filter(ls, [""])
return ls
parser = argparse.ArgumentParser(
prog="parahunter-dnds.py",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
************************************************************************
Developed by Arkadiy Garber; University of Montana, Biological Sciences
Please send comments and inquiries to rkdgarber@gmail.com
************************************************************************
'''))
parser.add_argument('-clu', type=str, help="clu.tsv output from mmseqs", default="NA")
parser.add_argument('-nuc', type=str, help="genes in nucleotide format", default="NA")
parser.add_argument('-aa', type=str, help="genes in amino acid format", default="NA")
parser.add_argument('-ctl', type=str, help="template control file for codeml", default="NA")
args = parser.parse_args()
#
# os.system("echo ${ctl} > ctl.txt")
# file = open("ctl.txt")
# for i in file:
# ctlLocation = i.rstrip()
nuc = open(args.nuc)
nuc = fasta2(nuc)
pep = open(args.aa)
pep = fasta2(pep)
cluDict = defaultdict(list)
clu = open(args.clu)
for i in clu:
ls = (i.rstrip().split("\t"))
cluDict[ls[0]].append(ls[1])
cwd = os.getcwd()
os.system('mkdir ' + cwd + "/dnds-analysis")
DIR = cwd + "/dnds-analysis"
count = 0
for i in cluDict.keys():
if len(cluDict[i]) > 1:
name = allButTheLast(i, "_") + "_" + lastItem(i.split("_"))
outpep = open(cwd + "/dnds-analysis/%s.faa" % name, "w")
outnuc = open(cwd + "/dnds-analysis/%s.faa.fna" % name, "w")
for j in cluDict[i]:
outpep.write(">" + j + "\n")
outnuc.write(">" + j + "\n")
outpep.write(pep[j] + "\n")
outnuc.write(nuc[j] + "\n")
outpep.close()
outnuc.close()
count += 1
# ALIGNING PROTEIN SEQUENCES AND CREATING A CODON ALIGNMENT
os.system("for i in %s/*faa; do"
" muscle -in $i -out $i.aligned.fa;"
" pal2nal.pl $i.aligned.fa $i.fna -output fasta > $i.codonalign.fa;"
" done" % DIR)
# BUILDING CONTROL FILES
count = 0
codealign = os.listdir(DIR)
for file in codealign:
if re.findall(r'codonalign', file):
clu = file.split(".faa")[0]
setup = open(args.ctl)
out = open("%s/%s.ctl" % (DIR, str(clu)), "w")
for i in setup:
if re.findall('seqfile', i):
out.write('' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + 'seqfile' + ' ' + '=' + ' dnds-analysis/' + file + ' ' + '*' + ' ' + 'sequence' + ' ' + 'data' + ' ' + 'filename\n')
elif re.findall(r'outfile', i):
out.write('' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + 'outfile' + ' ' + '=' + ' '
+ 'dnds-analysis/mlcTree_' + str(clu) + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' '
+ '' + ' ' + '' + ' ' + '' + ' ' + '*' + ' ' + 'main' + ' ' + 'result' + ' ' + 'file' + ' ' + 'name\n')
out.write('' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + 'treefile' + ' ' + '=' + ' '
+ 'tmp.trees' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' ' + '' + ' '
+ '' + ' ' + '' + ' ' + '' + ' ' + '*' + ' ' + 'main' + ' ' + 'result' + ' ' + 'file' + ' ' + 'name\n')
else:
out.write(i)
out.close()
# RUNNING CODEML FOR DN/DS CALCULATION
codealign = os.listdir(DIR)
for file in codealign:
if lastItem(file.split(".")) == "ctl":
os.system("codeml dnds-analysis/%s" % (file))
# PARSING CODEML OUTPUT
dsDict = defaultdict(lambda: defaultdict(lambda: defaultdict(lambda: 'EMPTY')))
dndsDict = defaultdict(lambda: defaultdict(lambda: defaultdict(lambda: 'EMPTY')))
codealign = os.listdir(DIR)
for i in codealign:
clu = i
if re.findall(r'mlcTree', i):
file = open("%s/%s" % (DIR, i), "r")
print(i)
for j in file:
print(j)
if re.findall(r'(\) \.\.\.)', j):
ls = (j.rstrip().split("..."))
orf1 = (ls[0].split("(")[1][0:len(ls[0].split("(")[1])-2])
orf2 = (ls[1].split("(")[1][0:len(ls[1].split("(")[1])-1])
if re.findall(r' dS', j):
try:
secondHalf = (j.split("dN = ")[1])
except IndexError:
secondHalf = (j.split("dN =")[1])
dn = secondHalf.split(" ")[0]
dndsDict[orf1][orf2] = dn
dndsDict[orf2][orf1] = dn
dS = (j.rstrip().split(" dS")[1])
dS = remove(dS, [" ", "="])
dsDict[clu][orf1][orf2] = dS
dsDict[clu][orf2][orf1] = dS
MLCdict = defaultdict(lambda: defaultdict(lambda: defaultdict(lambda: 'EMPTY')))
for i in dsDict.keys():
for j in dsDict[i]:
closestNeighbor = Dictparser(dsDict[i][j])[0]
lowestDS = Dictparser(dsDict[i][j])[1]
MLCdict[i][j]["closestNeighbor"] = closestNeighbor
MLCdict[i][j]["lowestDS"] = lowestDS
out = open("dS_summary.csv", "w")
out.write("cluster" + "," + "gene" + "," + "closestNeighbor" + "," + "lowestDS" + "," + "dN" + "\n")
for i in MLCdict.keys():
for j in MLCdict[i]:
out.write(i + "," + j + "," + MLCdict[i][j]["closestNeighbor"] + "," + MLCdict[i][j]["lowestDS"] + "," + dndsDict[j][MLCdict[i][j]["closestNeighbor"]] + "\n")
out.write("####################################################################\n")
out.close()
os.system("rm 2NG.t 2NG.dN 2NG.dS rst1 rst 2ML.t 2ML.dN 2ML.dS 4fold.nuc rub")