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Copy pathintersectAndComplement_colTabSNPs.py
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intersectAndComplement_colTabSNPs.py
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#!/usr/bin/python
import sys, os.path, argparse, re, logging, warnings, csv, subprocess
from collections import defaultdict
## Reads two seven-column .txt, .csv, or .tsv files to compute intersection of SNPs positions
## The seven columns should have the following headers:
## CHROM POS REF ALT QUAL INFO-DP CONSENS
## Function: A closure for .tsv or .csv extension checking
def tsv_check(expected_ext1, expected_ext2, expected_ext3, openner):
def extension(filename):
if not (filename.lower().endswith(expected_ext1) or filename.lower().endswith(expected_ext2)):
raise ValueError()
return openner(filename)
return extension
## Function: Intersection (default)
def Intersection(list1, list2):
return sorted(set(list1).intersection(list2))
## Function: Union
def Union(list1, list2):
return list(set().union(list1, list2))
## Function: Complement
def Compl(list1, intersec):
snpSet1 = set(list1)
snpSet2 = set(intersec)
return list(snpSet1 - snpSet2)
logger = logging.getLogger("intersectAndComplement_colTabSNPs.py")
logger.setLevel(logging.INFO)
parser = argparse.ArgumentParser(description='Find intersection of SNPs positions from two plain text, single-column files', usage="intersectAndComplement_colTabSNPs.py snpFile1.tsv snpFile2.tsv")
parser.add_argument("listFile1", type=tsv_check('.txt', '.tsv', '.csv', argparse.FileType('r')))
parser.add_argument("listFile2", type=tsv_check('.txt', '.tsv', '.csv', argparse.FileType('r')))
parser.add_argument('--union', '-u', default='N', choices=['Y','N'], help="Calculate union instead of intersection for SNP positions?")
parser.add_argument('--outputType', '-o', default='S', choices=['C', 'D', 'I', 'S'], help="'S' = output summary of intersection/union, 'C' = output single column, 'I' = output intersection in original tabular format, or 'D' output non-intersection snps in tabular format.")
args = parser.parse_args()
columns1 = defaultdict(list)
columns2 = defaultdict(list)
header1 = []
header2 = []
with open(args.listFile1.name, 'r') as table1:
csvTable1 = csv.DictReader(table1, delimiter="\t")
header1 = list(list(csvTable1)[0].keys())
table1.seek(0)
for row in csvTable1:
for (key, val) in row.items():
columns1[key].append(val)
with open(args.listFile2.name, 'r') as table2:
csvTable2 = csv.DictReader(table2, delimiter="\t")
header2 = list(list(csvTable2)[0].keys())
table2.seek(0)
for row in csvTable2:
for (key2, val2) in row.items():
columns2[key2].append(val2)
#print(header1)
snpsPos1 = [x for x in header1 if re.search(r'(\bPOS\b|\bPosition\b)', x)]
refID = [x for x in header1 if re.search(r'(\bCHROM\b|\bRef(\s|_)ID\b)', x)]
refBase = [x for x in header1 if re.search(r'(\bRef\b|\bREF\b)', x)]
altBase = [x for x in header1 if re.search(r'(\bAlt\b|\bALT\b)', x)]
stats = [x for x in header1 if re.search(r'(\bQual\b|\bQUAL\b)', x)]
depth = [x for x in header1 if re.search(r'(\bINFO\-DP\b|\bCoverage\b)', x)]
consensus = [x for x in header1 if re.search(r'(\bCONSENS\b|\bFraction\b)', x)]
try:
temp = snpsPos1[0]
except (IndexError):
print("SNPs position header, 'POS', not found in {}".format(args.listFile1.name))
sys.exit()
snpsPos2 = [x for x in header2 if re.search(r'(\bPOS\b|\bPosition\b)', x)]
try:
temp = snpsPos2[0]
except (IndexError):
print("SNPs position header, 'POS', not found in {}".format(args.listFile2.name))
sys.exit()
#print(columns1[snpsPos1[0]])
snpsFile1 = columns1[snpsPos1[0]]
snpsFile1.pop(0)
snpsFile1 = [int(y) for y in snpsFile1]
#print(columns2[snpsPos2[0]])
snpsFile2 = columns2[snpsPos2[0]]
snpsFile2.pop(0)
snpsFile2 = [int(z) for z in snpsFile2]
if(args.union == 'Y'):
allPositions = Union(snpsPos1[0], snpsPos2[0])
else:
allPositions = Intersection(snpsFile1, snpsFile2)
uniqueFile1 = Compl(snpsFile1, allPositions)
uniqueFile2 = Compl(snpsFile2, allPositions)
if(args.outputType == 'C'): ### output single column of positions, intersection or union
for item in allPositions:
print(item)
elif(args.outputType == 'D'): ### output five-column .tsv of non-intersection
try:
columns1[refID[0]].pop(0)
columns1[refBase[0]].pop(0)
columns1[altBase[0]].pop(0)
columns1[stats[0]].pop(0)
columns1[depth[0]].pop(0)
columns1[consensus[0]].pop(0)
columns2[refID[0]].pop(0)
columns2[refBase[0]].pop(0)
columns2[altBase[0]].pop(0)
columns2[stats[0]].pop(0)
columns2[depth[0]].pop(0)
columns2[consensus[0]].pop(0)
except (IndexError):
print("Improperly-formatted headers in {}".format(args.listFile1.name))
sys.exit()
print("Unique to {}".format(args.listFile1.name))
print(refID[0] + "\t" + snpsPos1[0] + "\t" + refBase[0] + "\t" + altBase[0] + "\t" + stats[0] + "\t" + depth[0] + "\t" + consensus[0])
for item in uniqueFile1:
idx = 0
while(idx < len(columns1[snpsPos1[0]])):
if( item == int(columns1[snpsPos1[0]][idx]) and ( float(columns1[consensus[0]][idx]) > 0.25)):
print(columns1[refID[0]][idx] + "\t" + columns1[snpsPos1[0]][idx] + "\t" + columns1[refBase[0]][idx] + "\t" + columns1[altBase[0]][idx] + "\t" + columns1[stats[0]][idx] + "\t" + columns1[depth[0]][idx]+ "\t" + columns1[consensus[0]][idx])
idx = idx + 1
print("Unique to {}".format(args.listFile2.name))
print(refID[0] + "\t" + snpsPos1[0] + "\t" + refBase[0] + "\t" + altBase[0] + "\t" + stats[0] + "\t" + depth[0] + "\t" + consensus[0])
for item in uniqueFile2:
idx = 0
while(idx < len(columns2[snpsPos2[0]]) ):
if( item == int(columns2[snpsPos2[0]][idx] ) and ( float(columns2[consensus[0]][idx]) > 0.25)):
print(columns2[refID[0]][idx] + "\t" + columns2[snpsPos2[0]][idx] + "\t" + columns2[refBase[0]][idx] + "\t" + columns2[altBase[0]][idx] + "\t" + columns2[stats[0]][idx] + "\t" + columns2[depth[0]][idx] + "\t" + columns2[consensus[0]][idx])
idx = idx + 1
elif(args.outputType == 'I'): ### output five-column .tsv format
try:
columns1[refID[0]].pop(0)
columns1[refBase[0]].pop(0)
columns1[altBase[0]].pop(0)
columns1[stats[0]].pop(0)
columns1[depth[0]].pop(0)
columns1[consensus[0]].pop(0)
columns2[refID[0]].pop(0)
columns2[refBase[0]].pop(0)
columns2[altBase[0]].pop(0)
columns2[stats[0]].pop(0)
columns2[depth[0]].pop(0)
columns2[consensus[0]].pop(0)
except (IndexError):
print("Improperly-formatted headers in {}".format(args.listFile1.name))
sys.exit()
print("Shared SNPs in {}".format(args.listFile1.name))
print(refID[0] + "\t" + snpsPos1[0] + "\t" + refBase[0] + "\t" + altBase[0] + "\t" + stats[0] + "\t" + depth[0] + "\t" + consensus[0])
for item in allPositions:
idx = 0
while(idx < len(columns1[snpsPos1[0]])):
if( (item == int(columns1[snpsPos1[0]][idx]) and (float(columns1[consensus[0]][idx]) > 0.25) )):
print(columns1[refID[0]][idx] + "\t" + columns1[snpsPos1[0]][idx] + "\t" + columns1[refBase[0]][idx] + "\t" + columns1[altBase[0]][idx] + "\t" + columns1[stats[0]][idx] + "\t" + columns1[depth[0]][idx] + "\t" + columns1[consensus[0]][idx])
idx = idx + 1
print("Shared SNPs in {}".format(args.listFile2.name))
print(refID[0] + "\t" + snpsPos1[0] + "\t" + refBase[0] + "\t" + altBase[0] + "\t" + stats[0] + "\t" + depth[0] + "\t" + consensus[0])
for item in allPositions:
idx = 0
while(idx < len(columns2[snpsPos1[0]])):
if( (item == int(columns2[snpsPos1[0]][idx]) and (float(columns2[consensus[0]][idx]) > 0.25) )):
print(columns2[refID[0]][idx] + "\t" + columns2[snpsPos1[0]][idx] + "\t" + columns2[refBase[0]][idx] + "\t" + columns2[altBase[0]][idx] + "\t" + columns2[stats[0]][idx] + "\t" + columns2[depth[0]][idx] + "\t" + columns2[consensus[0]][idx])
idx = idx + 1
elif((args.outputType == 'S') and (args.union == 'N')): ### output verbose description of intersection
print("{} has {} unique snps and {} has {} unique snps.".format(args.listFile1.name, str(len(list(uniqueFile1))), args.listFile2.name, str(len(list(uniqueFile2)))) )
if(args.union == 'Y'):
print("Their union contains {} snps.".format(str(len(allPositions))))
else:
print("Their intersection contains {} snps.".format(str(len(allPositions))))