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vcf2phylip.py
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vcf2phylip.py
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#! /usr/bin/env python
# python version 3
# by Joana, script to convert vcf to phylip
# Some functions are recycled from the RAD python script written by Sam Wittwer
import sys, getpass, re, argparse, gzip
# Define the neccessary functions:
# Function to extract header info: extractHeaderInfo
# takes a vcf(.gz) file from line 1, goes through header, returns:
# 0[string] header
# 1[list[string]] individual IDs
# 2[int] number of individuals in vcf file
# 3[int] length of header
def extractHeaderInfo(input):
linecounter = 0
header = ""
for line in input:
linecounter += 1
if re.match("^\#\#", line):
header+=line
else:
header+=line
n_individuals = len(str(line.strip('\n')).split('\t'))-9
id_individuals = str(line.strip('\n')).split('\t')[9:]
break
return header, id_individuals, n_individuals, linecounter
# Function to make all sample names of equal length (could be simplified)
# FillUp: accepts list, fills up list with optional character (default is " ") until they are of equal length
def fillUp(list, fill = " "): # Checks length of entries in a list, fills up with specified fill string.
returnlist = []
for entry in list:
if len(entry) < len(max(list, key=len)):
returnlist.append(entry+(len(max(list, key=len))-len(entry))*fill)
else:
returnlist.append(entry)
return returnlist
# Function to write the the lines in phylip format
def writePhylipSequences(samplenames, sequences, outputdestination, writeref):
if writeref:
beginning = 0
nsamples = str(len(samplenames))
else:
beginning = 1
nsamples = str(len(samplenames)-1)
nbases = str(len(sequences[0]))
outputdestination.write(nsamples +"\t"+nbases+"\n")
outstring = ""
for i in range(beginning, len(samplenames)):
outstring += samplenames[i]+"".join(sequences[i])
outstring +="\n"
outputdestination.write(outstring.strip("\n"))
# Parse the arguments provided
parser = argparse.ArgumentParser(description='Convert vcf file to phylip file format')
parser.add_argument('-i', '--input', dest='i', help="input file in vcf(.gz) format [required]", required=True)
parser.add_argument('-o', '--output', dest='o', help="output file [required]", required=True)
parser.add_argument('-r', '--ref', action='store_true', help="if -r is specified, the reference sequence will be included in the phylip file)", default=False)
parser.add_argument('-f', '--fill', action='store_true', help="if -f is specified, all sites not in the vcf file will be printed as missing (N)", default=False)
parser.add_argument('-e', '--exclIndels', action='store_true', help="if -e is specified, indels are not printed (else replaced by N)", default=False)
parser.add_argument('-m', '--mtDNA', action='store_true', help="if -m is specified, haploid genotype calls are expected in the vcf", default=False)
args = parser.parse_args()
# Set the default values:
if args.i.endswith('.gz'):
input = gzip.open(args.i,'rt')
else:
input = open(args.i,'r')
output = open(args.o,'w')
writeref = args.ref
fill = args.fill
noIndels = args.exclIndels
haploid = args.mtDNA
prev=100000000000000000000000000000000000
# How to convert vcf-style genotypes to single letters
AmbiguityMatrix = [["A","M","R","W","N"],["M","C","S","Y","N"],["R","S","G","K","N"],["W","Y","K","T","N"],["N","N","N","N","N","N"]]
CoordinatesDictionary = { "A":0 , "C":1, "G":2, "T":3, ".":4 }
GetGenotype = lambda individual, altlist: AmbiguityMatrix[CoordinatesDictionary[altlist[int(individual[0])]]][CoordinatesDictionary[altlist[int(individual[1])]]]
# If -f and -e are specified
if noIndels and fill:
print("-f and -e are incompatible! Please decide if you want all sites or not")
sys.exit(2)
# Get the header info
headerinfo = extractHeaderInfo(input) #skips header, retains IDs in headerinfo
# Get the sample labels
IDs = [] #IDs holds all sample names without equal spacing
IDs.append("reference ")
resultsequences = [] #resultsequences holds all complete sequences to be written
resultsequences.append([]) #resultsequences[0] holds reference
for entry in headerinfo[1]:
IDs.append(entry.replace("-",".")+" ")
resultsequences.append([])
samplenames = fillUp(IDs)
linecounter = 0
print("\ngenerating phylip file with ",len(samplenames)-1," individuals")
# Go through the lines to get the genotypes
for line in input:
site = line.strip('\n').split('\t')
indel = False
pos = int(site[1])
# If missing positions should be filled up with Ns (-f specified, e.g. sites of low quality that were filtered out)
if pos > (prev + 1) and fill:
addLine=pos-(prev+1)
individualcounter = 1
for individual in site[9:]:
resultsequences[individualcounter]+= "N" * addLine
individualcounter += 1
linecounter += addLine
resultsequences[0] += "N" * addLine # reference
# site contains a deletion, replace by missing data
if len(site[3])>1:
indel=True
else:
alleles = site[4].split(",") # if there are more than 1 alternative alleles, they are separated by commas
for alt in alleles:
if len(alt)>1 or '*' in alt: # in case of an insertion
indel=True
break
alternativeslist = []
alternativeslist.append(site[3])
if site[4] != ".":
for entry in site[4].split(","):
alternativeslist.append(entry)
individualcounter = 1
# If the site is not an indel, i.e. if it is a SNP or monomorphic site
if not indel:
for individual in site[9:]:
indGeno = individual.split(":")
if haploid:
if '.' in indGeno[0]:
resultsequences[individualcounter]+="N"
else:
resultsequences[individualcounter] += alternativeslist[int(indGeno[0])]
else:
if '.' in indGeno[0]:
resultsequences[individualcounter]+="N"
else:
resultsequences[individualcounter] += GetGenotype(re.split('/|\|',indGeno[0]), alternativeslist)
individualcounter += 1
linecounter += 1
resultsequences[0] += site[3]
# If the site is an indel and noIndels is not specified, print as missing data (else not printed)
elif not noIndels:
for individual in site[9:]:
resultsequences[individualcounter]+= "N"
individualcounter += 1
linecounter += 1
resultsequences[0] += site[3][:1] # reference
prev=int(site[1])
input.close()
writePhylipSequences(samplenames, resultsequences, output, writeref)
output.write("\n")
output.close()