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windowQualPrinseqLite_R1andR2.py
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windowQualPrinseqLite_R1andR2.py
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#!/usr/bin/python
import sys
import os
import argparse
import logging
import re
## A command-line script for cleaning read pairs of reads < XX bp and reads with > Y Ns
## Offers length-based and N-presence-based cleaning only, no quality checking
## input: filePath/forwardReads.fastq filePath/reverseReads.fastq --rm_ambig Y/N --outDir (optional: )
## output: trimmed reads and log files in output folder 'TrimByPython/forwardReads_prinseq/'
### requires >= prinseq-lite.pl 0.20.x and >= perl/5.22.x
def readable_dir(prospective_dir):
if not os.path.isdir(prospective_dir):
raise argparse.ArgumentTypeError("readable_dir:{0} is not a valid path".format(prospective_dir))
if os.access(prospective_dir, os.R_OK):
if( not prospective_dir.endswith("/") ):
prospective_dir = prospective_dir + "/"
return prospective_dir
else:
raise argparse.ArgumentTypeError("readable_dir:{0} is not a readable dir".format(prospective_dir))
## for checking that --min-length is between 35 and 145, inclusive
def bandwidth_type(x):
xx = int(x)
if( xx < 34 ):
raise argparse.ArgumentTypeError("Minimum min-length should be 35")
elif( xx > 144 ):
raise argparse.ArgumentTypeError("Maximum min-length should be 145")
return xx
logger = logging.getLogger("windowQualPrinseqLite_R1andR2.py")
logger.setLevel(logging.INFO)
parser = argparse.ArgumentParser(description="Wrapper for prinseq-lite", usage="python windowQualPrinseqLite_R1andR2.py inputPath/reads_R1_001.fastq inputPath/reads_R2_001.fastq --rm_ambig Y/N --min_len 100 --trim_qual [Y/N] --min_score 28 --qual_window 20 --clean_output [Y/N] --outDir outputPath")
## minimum read length
parser.add_argument('--min_len', '-min', type=bandwidth_type, default=100, help="Remove reads less than --min_len: Default=100, 39 < --min_len < 146")
## remove Ns
parser.add_argument('--rm_ambig', '-rm', required=True, choices=['Y','N'], help="Remove amp")
parser.add_argument('--ambig_allow', '-ns_max_n', type=int, default=1, choices=range(0,5), help="Ns tolerance: 0 to 5 per read, default = 1")
## Trim by PHRED Q-score
parser.add_argument('--trim_qual', default='N', choices=['Y','N'], help="trim by base pair quality (Y|N)?")
parser.add_argument('--min_score', default=28, type=int, choices=range(19,30), help="quality score on which to trim [20 to 30: default 28]")
parser.add_argument('--qual_window', default=20, type=int, choices=range(10, 46), help="sliding window size used to calculate quality score [10 to 45: default 20]")
## input files
parser.add_argument('forward', type=argparse.FileType('r'))
parser.add_argument('reverse', type=argparse.FileType('r'))
## output folder
parser.add_argument('--outDir', '-D', type=readable_dir, required=True, action='store')
## cleanup of output folder
parser.add_argument('--clean_output', '-clean', default='Y', choices=['Y','N'], help="Delete fail and singleton files: Y or N (use 'N' when additional processing downstream needed)")
## force overwrite of previous output folder
parser.add_argument('--force', default='N', choices=['Y','N'], help="Overwrite previous output from same filename: Y or N")
args = parser.parse_args()
## output folder
outFolder = args.outDir
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)
formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
#add formatter to ch
ch.setFormatter(formatter)
#add ch to logger
logger.addHandler(ch)
intMinLen = args.min_len
intTrimN = args.ambig_allow
intWindow = args.qual_window
forward = args.forward.name
reverse = args.reverse.name
logger.info("Parameters loaded.")
## two pipelines, one for fastq input, the other for fastq.gz
origWD = os.getcwd()
## Simple filename extractor function
def getIsolateStr(filePathString, format):
splitStr = re.split(pattern='/', string=filePathString)
fileNameIdx = len(splitStr) - 1
fileString = splitStr[fileNameIdx]
if(format == 1):
isolateString = re.split(pattern='\.', string=splitStr[fileNameIdx])
#print(isolateString)
if(re.search(pattern='_R1_001\.fastq', string=isolateString[0])):
fileString = re.sub(r'R1_001\.fastq', 'winPrinseq', isolateString[0])
else:
fileString = isolateString[0] + '_winPrinseq'
#print(fileString)
return fileString
## Simple output file renaming
outputFileString = getIsolateStr(forward, 1)
newOutputFolder = outFolder + outputFileString
## Validate input file names: FILTER 1
if(forward == reverse):
logger.warn("Forward reads and reverse reads files cannot have the same name and path!")
sys.exit(1)
#elif()
firstLineFwd = None
firstLineRev = None
lineCountFwd = 0
lineCountRev = 0
## Validate input file suffixes: FILTER 2
if(re.search(r'\.gz$', forward, flags=re.IGNORECASE) and re.search(r'\.gz$', reverse, flags=re.IGNORECASE)):
firstLineFwd = os.popen("zcat {} | head -1".format(forward)).read()
firstLineRev = os.popen("zcat {} | head -1".format(reverse)).read()
lineCountFwd = os.popen("zcat {} | wc -l".format(forward)).read()
lineCountRev = os.popen("zcat {} | wc -l".format(reverse)).read()
elif(re.search(r'\.fastq$', forward, flags=re.IGNORECASE) and re.search(r'\.fastq$', reverse, flags=re.IGNORECASE)):
firstLineFwd = os.popen("cat {} | head -1".format(forward)).read()
firstLineRev = os.popen("cat {} | head -1".format(reverse)).read()
lineCountFwd = os.popen("cat {} | wc -l".format(forward)).read()
lineCountRev = os.popen("cat {} | wc -l".format(reverse)).read()
else:
logger.warn("{} and {} must both be gzipped or both gunzipped.".format( getIsolateStr(forward, 0), getIsolateStr(reverse, 0)))
sys.exit(1)
if(lineCountFwd != lineCountRev):
logger.warn("Forward and reverse files do not have equal number of reads!")
sys.exit(1)
#print(lineCountFwd + " " + lineCountRev)
lineIDFwd = re.split(pattern=' ', string=firstLineFwd)
lineIDRev = re.split(pattern=' ', string=firstLineRev)
## print("{} should equal {}".format(lineIDFwd[0], lineIDRev[0]))
fwdR1 = lineIDFwd[1].strip()
revR2 = lineIDRev[1].strip()
##print("R1 has {} and R2 has {}".format(fwdR1, revR2))
## Validate input file run matching: FILTER 3
if(lineIDFwd[0] == lineIDRev[0]):
logger.info("Input file IDs validated.")
else:
logger.warn("{} and {} are not paired ends of same sequencing run.".format( getIsolateStr(forward, 0), getIsolateStr(reverse, 0)))
print("Exiting.")
sys.exit(1)
## Inspect input file read-pairing: FILTER 4
if(fwdR1.startswith("1") and revR2.startswith("2")):
logger.info("Input file forward and reverse indicators validated.")
else:
logger.warn("End-pairing not apparent in {} and {}.".format( getIsolateStr(forward, 0), getIsolateStr(reverse, 0)))
## Test if output folder exists
if(os.path.exists(newOutputFolder)):
if(args.force == 'Y'):
os.system("rm -v {}/*".format(newOutputFolder))
os.rmdir(newOutputFolder)
os.mkdir(newOutputFolder)
else:
print("Output folder {} already exists,\n for outDir = {} . . . ".format(outputFileString, outFolder))
print("Use --force Y or change path for --outDir\nExiting.")
sys.exit(1)
else:
os.mkdir(newOutputFolder)
logger.info("Output folder validated/created.")
##if(re.search(r'\.gz$', forward, flags=re.IGNORECASE)):
outputSuccess = newOutputFolder + "/" + outputFileString
outputFAIL = newOutputFolder + "/" + outputFileString + "FAIL"
runLog = newOutputFolder + "/prinseq.runtime.log"
intMinScore = int(args.min_score)
### Begin performing read clean
logger.info("starting prinseq-lite")
if(re.search(r'\.fastq$', forward, flags=re.IGNORECASE) and re.search(r'\.fastq$', reverse, flags=re.IGNORECASE)):
if((args.rm_ambig == 'Y') and (args.trim_qual == 'Y')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_ns_left 1 -trim_ns_right 1 -ns_max_n {} -trim_qual_right {} -trim_qual_type mean -trim_qual_window {} -trim_qual_step 5 2> {}".format(forward, reverse, outputSuccess, outputFAIL, intMinLen, intTrimN, intMinScore, intWindow, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads with > {} Ns removed/trimmed; reads 3-prime end Q < {} trimmed with trim_qual_window = {} bp; reads less than {} bp length removed' > {}".format(intTrimN, intMinScore, intWindow, intMinLen, outputLog))
elif((args.rm_ambig == 'N') and (args.trim_qual == 'Y')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_qual_right {} -trim_qual_type mean -trim_qual_window {} -trim_qual_step 5 2> {}".format(forward, reverse, outputSuccess, outputFAIL, intMinLen, intMinScore, intWindow, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads 3-prime end Q < {} trimmed with trim_qual_window = {} bp; reads less than {} bp length removed' > {}".format(intMinScore, intWindow, intMinLen, outputLog))
elif((args.rm_ambig == 'Y') and (args.trim_qual == 'N')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_ns_left 1 -trim_ns_right 1 -ns_max_n {} 2> {}".format(forward, reverse, outputSuccess, outputFAIL,intMinLen, intTrimN, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads with > {} Ns removed/trimmed; reads less than {} bp length removed' > {}".format(intTrimN, intMinLen, outputLog))
else:
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} 2> {}".format(forward, reverse, outputSuccess, outputFAIL, intMinLen, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads less than {} bp length removed' > {}".format(intMinLen, outputLog))
elif(re.search('\.fastq.gz', forward, flags=re.IGNORECASE) and re.search('\.fastq.gz', reverse, flags=re.IGNORECASE)):
gunzipForward = re.sub(r'\.gz$', '', forward)
gunzipReverse = re.sub(r'\.gz$', '', reverse)
### Unzip R1
logger.info("gunzip {}".format(forward))
os.system("gunzip -c {} > {}".format(forward, gunzipForward))
logger.info("forward (R1) gunzip complete")
outputSuccess = newOutputFolder + "/" + outputFileString
outputFAIL = newOutputFolder + "/" + outputFileString + "FAIL"
### Unzip R2
logger.info("gunzip {}".format(reverse))
os.system("gunzip -c {} > {}".format(reverse, gunzipReverse))
logger.info("reverse (R2) gunzip complete")
logger.info("forward (R1) and reverse (R2) files trimming start")
### Begin performing read clean
if((args.rm_ambig == 'Y') and (args.trim_qual == 'Y')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_ns_left 1 -trim_ns_right 1 -ns_max_n {} -trim_qual_right {} -trim_qual_type mean -trim_qual_window {} -trim_qual_step 5 2> {}"
.format(gunzipForward, gunzipReverse, outputSuccess, outputFAIL,intMinLen, intTrimN, intMinScore, intWindow, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads with > {} Ns removed/trimmed; reads 3-prime end Q < {} trimmed with trim_qual_window = {} bp; reads less than {} bp length removed' > {}".format(intTrimN, intMinScore, intWindow, intMinLen, outputLog))
elif((args.rm_ambig == 'N') and (args.trim_qual == 'Y')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_qual_right {} -trim_qual_type mean -trim_qual_window {} -trim_qual_step 5 2> {}"
.format(gunzipForward, gunzipReverse, outputSuccess, outputFAIL,intMinLen, intMinScore, intWindow, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads 3-prime end Q < {} trimmed with trim_qual_window = {} bp; reads less than {} bp length removed' > {}".format(intMinScore, intWindow, intMinLen, outputLog))
elif((args.rm_ambig == 'Y') and (args.trim_qual == 'N')):
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} -trim_ns_left 1 -trim_ns_right 1 -ns_max_n {} 2> {}"
.format(gunzipForward, gunzipReverse, outputSuccess, outputFAIL, intMinLen, intTrimN, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads with > {} Ns removed/trimmed; reads less than {} bp length removed' > {}".format(intTrimN, intMinLen, outputLog))
else:
os.system("prinseq-lite -fastq {} -fastq2 {} -out_good {} -out_bad {} -min_len {} 2> {}".format(gunzipForward, gunzipReverse, outputSuccess, outputFAIL, intMinLen, runLog))
outputLog = newOutputFolder + "/parameters.log"
os.system("echo 'prinseq-lite: reads less than {} bp length removed' > {}".format(intMinLen, outputLog))
os.system("rm -v {}".format(gunzipForward))
os.system("rm -v {}".format(gunzipReverse))
else:
logger.warn("Filetype - R1 {} R2 {} must both end in .fastq".format(forward, reverse))
logger.warn("Filetype - R1 {} and R2 {} must both end in .fastq.gz".format(forward, reverse))
logger.exception("Input files must be FASTQ ending in either .fastq or .fastq.gz")
if(args.clean_output == 'Y'):
os.system("rm -v {}'_1_singletons.fastq'".format(outputSuccess))
os.system("rm -v {}'_2_singletons.fastq'".format(outputSuccess))
os.system("rm -v {}'FAIL_1.fastq'".format(outputSuccess))
os.system("rm -v {}'FAIL_2.fastq'".format(outputSuccess))
os.system("gzip -c {}'_1.fastq' > {}'_R1_001.cleaned.fastq.gz'".format(outputSuccess, outputSuccess))
os.system("gzip -c {}'_2.fastq' > {}'_R2_001.cleaned.fastq.gz'".format(outputSuccess, outputSuccess))
os.system("rm -v {}'_1.fastq'".format(outputSuccess))
os.system("rm -v {}'_2.fastq'".format(outputSuccess))
logger.info("prinseq-lite trimming complete")