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trim_qc.py
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trim_qc.py
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import os
import os.path
from os.path import basename
from urllib import urlopen
from urlparse import urlparse
import subprocess
from subprocess import Popen, PIPE
import urllib
import shutil
import glob
# custom Lisa module
import clusterfunc
# 1. Get data from spreadsheet
def get_data(thefile):
count = 0
url_data = {}
with open(thefile, "rU") as inputfile:
headerline = next(inputfile).split(',')
# print headerline
position_name = headerline.index("ScientificName")
position_reads = headerline.index("Run")
position_ftp = headerline.index("download_path")
for line in inputfile:
line_data = line.split(',')
name = "_".join(line_data[position_name].split())
read_type = line_data[position_reads]
ftp = line_data[position_ftp]
name_read_tuple = (name, read_type)
print name_read_tuple
# check to see if Scientific Name and run exist
if name_read_tuple in url_data.keys():
# check to see if ftp exists
if ftp in url_data[name_read_tuple]:
print "url already exists:", ftp
else:
url_data[name_read_tuple].append(ftp)
else:
url_data[name_read_tuple] = [ftp]
return url_data
# run trimmomatic
def run_trimmomatic_TruSeq(missing, trimmed, remaining, trimdir, file1, file2, sra):
bash_filename=trimdir+sra+".trim.TruSeq.sh"
clusterfunc.check_dir(trimdir+"qsub_files/")
listoffile = os.listdir(trimdir+"qsub_files/")
# print listoffile
trim_file = trimdir+"qsub_files/""trim."+sra+".log"
# print trim_file
matching = [s for s in listoffile if "trim."+sra+".log" in s]
matching_string = "TrimmomaticPE: Completed successfully"
if os.path.isfile(trim_file):
with open(trim_file) as f:
content = f.readlines()
if len(matching)!=0:
trim_complete = [m for m in content if matching_string in m]
if len(trim_complete)!=0:
print "Already trimmed:",matching
trimmed.append(sra)
else:
missing.append(trimdir)
j="""
java -jar /mnt/home/ljcohen/bin/Trimmomatic-0.33/trimmomatic-0.33.jar PE \\
-baseout {}.trim.fq \\
{} {} \\
ILLUMINACLIP:/mnt/home/ljcohen/bin/Trimmomatic-0.33/adapters/combined.fa:2:40:15 \\
SLIDINGWINDOW:4:2 \\
LEADING:2 \\
TRAILING:2 \\
MINLEN:25 &> trim.{}.log
""".format(sra,file1,file2,sra)
orphan_string=make_orphans(trimdir,sra)
commands = [j,orphan_string]
process_name="trim"
module_name_list=""
filename=sra
clusterfunc.qsub_file(trimdir,process_name,module_name_list,filename,commands)
else:
remaining.append(trimdir)
j="""
java -jar /mnt/home/ljcohen/bin/Trimmomatic-0.33/trimmomatic-0.33.jar PE \\
-baseout {}.trim.fq \\
{} {} \\
ILLUMINACLIP:/mnt/home/ljcohen/bin/Trimmomatic-0.33/adapters/combined.fa:2:40:15 \\
SLIDINGWINDOW:4:2 \\
LEADING:2 \\
TRAILING:2 \\
MINLEN:25 &> trim.{}.log
""".format(sra,file1,file2,sra)
orphan_string=make_orphans(trimdir,sra)
commands = [j,orphan_string]
process_name="trim"
module_name_list=""
filename=sra
clusterfunc.qsub_file(trimdir,process_name,module_name_list,filename,commands)
return missing,trimmed,remaining
def make_orphans(trimdir,sra):
# if os.path.isfile(trimdir+"orphans.fq.gz"):
# if os.stat(trimdir+"orphans.fq.gz").st_size != 0:
# print "orphans file exists:",trimdir+"orphans.fq.gz"
# else:
# print "orphans file exists but is empty:",trimdir+"orphans.fq.gz"
# else:
file1 = trimdir+"qsub_files/"+sra+".trim_1U.fq"
file2 = trimdir+"qsub_files/"+sra+".trim_2U.fq"
orphanlist=file1 + " " + file2
orphan_string="gzip -9c "+orphanlist+" > "+trimdir+"orphans.fq.gz"
#print orphan_string
# s=subprocess.Popen(orphan_string,shell=True)
# s.wait()
return orphan_string
def move_files(trimdir,sra):
tmp_trimdir = trimdir + "qsub_files/"
file1 = tmp_trimdir+sra+".trim_1P.fq"
file2 = tmp_trimdir+sra+".trim_2P.fq"
print file1
print file2
if os.path.isfile(file1):
if os.path.isfile(file2):
mv_string1 = "cp "+file1+" "+trimdir
mv_string2 = "cp "+file2+" "+trimdir
# s=subprocess.Popen(mv_string1,shell=True)
# s.wait()
# t=subprocess.Popen(mv_string2,shell=True)
# t.wait()
# if os.path.isfile(trimdir+sra+".trim_1P.fq"):
# if os.path.isfile(trimdir+sra+".trim_2P.fq"):
# print "Files all here:",os.listdir(trimdir)
return mv_string1,mv_string2
def run_move_files(trimdir,sra):
orphan_string=make_orphans(trimdir,sra)
mv_string1,mv_string2 = move_files(trimdir,sra)
commands = [orphan_string,mv_string1,mv_string2]
process_name="move"
module_name_list=""
filename=sra
#clusterfunc.qsub_file(trimdir,process_name,module_name_list,filename,commands)
def check_files(trimdir,sra):
file1 = trimdir+sra+".trim_1P.fq"
file2 = trimdir+sra+".trim_2P.fq"
if os.path.isfile(file1):
if os.path.isfile(file2):
print "Files all here:",os.listdir(trimdir)
else:
print "Still waiting:",trimdir
def execute(url_data,datadir):
missing = []
trimmed = []
remaining = []
for item in url_data.keys():
organism=item[0].replace("'","")
org_seq_dir=datadir+organism+"/"
url_list=url=url_data[item]
for url in url_list:
sra=basename(urlparse(url).path)
newdir=org_seq_dir+sra+"/"
trimdir=newdir+"trim/"
interleavedir=newdir+"interleave/"
clusterfunc.check_dir(trimdir)
clusterfunc.check_dir(interleavedir)
file1=newdir+sra+"_1.fastq"
file2=newdir+sra+"_2.fastq"
#if os.path.isfile(file1) and os.path.isfile(file2):
# print file1
# print file2
missing,trimmed,remaining= run_trimmomatic_TruSeq(missing,trimmed,remaining,trimdir,file1,file2,sra)
#run_move_files(trimdir,sra)
# check_files(trimdir,sra)
# else:
# print "Files do not exist:",file1,file2
print "Missing trimmed:",len(missing)
print missing
print "Trimmed:",len(trimmed)
print "remaining:",len(remaining)
print remaining
datafile="SraRunInfo.csv"
datadir="/mnt/scratch/ljcohen/mmetsp/"
url_data=get_data(datafile)
print url_data
execute(url_data,datadir)