#!/usr/bin/env python3
"""
optparse is deprecated in favor of argparse as of Python 2.7. However,
since 2.7 is not always present on many systems, at this writing,
it is safer to stick with optparse for now. It should be easy
to change later, since the syntax is very similar between argparse and optparse.
from optparse import OptionParser
"""
from optparse import OptionParser
import datetime
import getpass
import os
import re
import stat
import subprocess
import sys
import time
'''
bl_trim_galore.py - Set environment variables for BioLegato Helper Applications
Synopsis: bl_trim_galore.py --tsv tsvfile [options]
The --adapter, --illumina, --nextera and --small_rna options of trim_galore have been
distilled into a single option:
--adapter illumina|nexera|small_rna|sequence
where sequence is any adapter sequence. The first three choices
will call the --illumina, --nextera and --small_rna options.
If anything else is specified, the --adapter option will be included.
@modified: Feb. 29, 2020
@author: Brian Fristensky
@contact: Brian.Fristensky@umanitoba.ca
'''
#blib = os.environ.get("BIRCHPYLIB")
#sys.path.append(blib)
#from birchlib import Birchmod
PROGRAM = "bl_trim_galore.py : "
USAGE = "\n\tUSAGE: bl_trim_galore.py [options] filenames..."
DEBUG = True
if DEBUG :
print('bl_trim_galore: Debugging mode on')
#BM = Birchmod(PROGRAM, USAGE)
# - - - - - - - - - - - - - Utility classes - - - - - - - - - - - - - - - - -
def chmod_ar(filename):
"""
Make a file world-readable.
"""
if os.path.exists(filename):
st = os.stat(filename)
os.chmod(filename, st.st_mode | stat.S_IREAD \
| stat.S_IRGRP | stat.S_IROTH)
def chmod_arx(filename):
"""
Make a file or directory world-readable and world-executable/searchable.
"""
if os.path.exists(filename):
st = os.stat(filename)
os.chmod(filename, st.st_mode | stat.S_IEXEC | stat.S_IREAD \
| stat.S_IXGRP | stat.S_IRGRP | stat.S_IXOTH \
| stat.S_IROTH)
def LocalHostname():
"""
Return the name of the local machine. Tries a number of methods
to get a name other than 'localhost' or a null result.
"""
import socket
import platform
def CheckName(name) :
if name == None or name.startswith("localhost") or name == "" :
OKAY = False
else :
OKAY = True
return OKAY
name = os.getenv('HOSTNAME')
if not CheckName(name) :
name = platform.uname()[1]
if not CheckName(name) :
if socket.gethostname().find('.')>=0:
name=socket.gethostname()
else:
name=socket.gethostbyaddr(socket.gethostname())[0]
return name
def SendEmail(From,To,Subject,Text) :
"""
Very simple email method adapted from:
http://stackoverflow.com/questions/882712/sending-html-email-using-python
There are more elaborate examples on this site for sending
HTML messages and attachments.
"""
import smtplib
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
Host = 'localhost'
msg = MIMEMultipart('alternative')
msg['Subject'] = Subject
Html = """\
%s
""" %(Text)
part1 = MIMEText(Text, 'plain')
part2 = MIMEText(Html, 'html')
msg.attach(part1)
msg.attach(part2)
try:
server = smtplib.SMTP(Host)
server.sendmail(From, To, msg.as_string())
server.quit()
print("Successfully sent email")
except:
print("Error: unable to send email")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class Parameters:
"""
Wrapper class for command line parameters
"""
def __init__(self):
"""
Initializes arguments:
TSVFILE = ""
QUALITY = 20
FASTQC = False
FQCTHREADS = 0
ADAPTER = ""
ADAPTER2 = ""
STRINGENCY = 1
ERRORRATE = 0.1
GZIP = True
DONT_GZIP = False
LENGTH = 20
OUTDIR = ""
TRIM1 = False
EMAIL = ""
Then calls read_args() to fill in their values from command line
"""
self.TSVFILE = ""
self.QUALITY = 20
self.FASTQC = False
self.FQCTHREADS = 0
self.ADAPTER = ""
self.ADAPTER2 = ""
self.STRINGENCY = 1
self.ERRORRATE = 0.1
self.GZIP = False
self.DONT_GZIP = False
self.LENGTH = 20
self.OUTDIR = ""
self.TRIM1 = False
self.EMAIL = ""
self.read_args()
if DEBUG :
print('------------ Parameters from command line ------')
print(' TSVFILE: ' + self.TSVFILE)
print(' QUALITY: ' + str(self.QUALITY))
print(' FASTQC: ' + str(self.FASTQC))
print(' FQCTHREADS: ' + str(self.FQCTHREADS))
print(' ADAPTER: ' + self.ADAPTER)
print(' ADAPTER2: ' + self.ADAPTER2)
print(' STRINGENCY: ' + str(self.STRINGENCY))
print(' ERRORRATE: ' + str(self.ERRORRATE))
print(' GZIP: ' + str(self.GZIP))
print(' DONT_GZIP: ' + str(self.DONT_GZIP))
print(' LENGTH: ' + str(self.LENGTH))
print(' OUTDIR: ' + self.OUTDIR)
print(' TRIM1: ' + str(self.TRIM1))
print(' EMAIL: ' + self.EMAIL)
print()
def read_args(self):
"""
Read command line arguments into a Parameter object
"""
parser = OptionParser()
parser.add_option("--tsvfile", dest="tsvfile", action="store", default="",
help="list of paired/unpaired read files")
parser.add_option("--quality", dest="quality", action="store", default=20,
help="trim N bases in addition to adapter removal")
parser.add_option("--fastqc", dest="fastqc", action="store_true", default=False,
help="run FASTQC on trimmed reads")
parser.add_option("--fqcthreads", dest="fqcthreads", action="store", default=0,
help="number of threads to use when running fastqc")
parser.add_option("--adapter", dest="adapter", action="store", default="",
help="adapter to be trimmed")
parser.add_option("--adapter2", dest="adapter2", action="store", default="",
help="optional adapter to trim from 2nd read in paired-end files")
parser.add_option("--stringency", dest="stringency", action="store", default=1,
help="nucleotides to trim from overlap with adapter")
parser.add_option("-e", dest="errorrate", action="store", default=0.1,
help="Max. allowed errors")
parser.add_option("--gzip", dest="gzip", action="store_true", default=False,
help="Compress output using gzip")
parser.add_option("--dont_gzip", dest="dont_gzip", action="store_true", default=False,
help="Do not compress output using gzip")
parser.add_option("--length", dest="length", action="store", default=20,
help="discard reads shorter than N")
parser.add_option("--trim1", dest="trim1", action="store_true", default=False,
help="trim 1 bp off every read at 3' end.")
parser.add_option("--email", dest="email", action="store", default="",
help="send email upon completion")
parser.add_option("--output_dir", dest="outdir", action="store", default="",
help="output directory")
(options, args) = parser.parse_args()
self.TSVFILE = options.tsvfile
self.QUALITY = options.quality
self.FASTQC = options.fastqc
self.FQCTHREADS = int(options.fqcthreads)
self.ADAPTER = options.adapter
self.ADAPTER2 = options.adapter2
self.STRINGENCY = options.stringency
self.ERRORRATE = options.errorrate
self.GZIP = options.gzip
self.DONT_GZIP = options.dont_gzip
self.LENGTH = options.length
self.OUTDIR = options.outdir
self.EMAIL = options.email
self.TRIM1 = options.trim1
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
class TSVFiles :
"""
Methods for reading lists of paired read TSV files, and for
writing lists to output.
"""
def __init__(self):
"""
Initializes arguments:
READPAIRS = []
"""
self.READPAIRS = []
def ReadTSVfile(self,FN) :
"""
TSV file containing names of paired-end and/or single end read files.
Paired-end files are on lines such as
leftreadfile.fq.gzrightreadfile.fq.gz
Single-end files have a each file on a separate line
reads1.fq.gz
reads2.fq.gz
reads3.fq.gz
"""
TAB = '\t'
F = open(FN,"r")
for line in F.readlines() :
line = line.strip()
if len(line) > 0 and not line.startswith('#') :
# get rid of double quotes that enclose fields when some programs write
# output, and then split by TABs.
tokens = line.replace('"','').split(TAB)
# ignore blank fields. Add either single or pair of filenames
# to list. Only process names from first two fields on a line
# and ignore other fields.
if len(tokens) > 0 :
r1 = tokens[0].strip()
if len(r1) > 0 :
fnames = [r1]
else :
fnames = []
if len(tokens) > 1 :
r2 = tokens[1].strip()
if len(r2) > 0 :
fnames.append(r2)
if len(fnames) > 0 :
self.READPAIRS.append(fnames)
if DEBUG :
print(str(self.READPAIRS))
F.close()
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
def RunTrimGalore(P,PR,LOGFILE) :
# Construct the command string - - - - - - - - - - - - - -
COMMAND=["trim_galore","--quality", str(P.QUALITY)]
if P.FASTQC :
COMMAND.append('--fastqc_args')
if P.FQCTHREADS > 0 :
COMMAND.append('"--threads ' + str(P.FQCTHREADS) + '"')
if P.ADAPTER == 'illumina' :
COMMAND.append('--illumina')
elif P.ADAPTER == 'nextera' :
COMMAND.append('--nextera')
elif P.ADAPTER == 'small_rna' :
COMMAND.append('--small_rna')
elif P.ADAPTER != "" :
COMMAND.extend(['--adapter',P.ADAPTER])
if P.ADAPTER2 != "" :
COMMAND.extend(['--adapter2',P.ADAPTER2])
COMMAND.extend(['--stringency',str(P.STRINGENCY)])
COMMAND.extend(['-e',str(P.ERRORRATE)])
if P.GZIP :
COMMAND.append('--gzip')
# --dont_gzip overrides --gzip
if P.DONT_GZIP :
COMMAND.append('--dont_gzip')
COMMAND.extend(['--length',str(P.LENGTH)])
if P.OUTDIR != "" :
COMMAND.extend(['--output_dir',P.OUTDIR])
if len(PR) == 2 :
COMMAND.append('--paired')
if P.TRIM1 :
COMMAND.append('--trim1')
COMMAND.extend([PR[0],PR[1]])
else :
COMMAND.extend([PR[0]])
# Run the command - - - - - - - - - - - - - - - - -
LOGFILE.write('======== trim_galore ==========' + '\n')
LOGFILE.write(str(COMMAND) + '\n')
StartTime = datetime.datetime.now()
LOGFILE.write('Start time: ' + str(StartTime) + '\n')
LOGFILE.write('\n')
LOGFILE.flush()
#LOGFILE.write('COMMAND: ' + str(COMMAND) + '\n')
p = subprocess.Popen(COMMAND,stdout=LOGFILE)
p.wait()
FinishTime = datetime.datetime.now()
LOGFILE.write('\n')
LOGFILE.write('Finish time: ' + str(FinishTime) + '\n')
ElapsedTime = FinishTime - StartTime
LOGFILE.write('Elapsed time: ' + str(ElapsedTime) + '\n')
#======================== MAIN PROCEDURE ==========================
def main():
"""
Called when not in documentation mode.
"""
# Read parameters from command line
P = Parameters()
TF = TSVFiles()
if not P.TSVFILE == "" :
TF.ReadTSVfile(P.TSVFILE)
OKAY = True
else :
OKAY = False
# Create output directory, if it doesn't already exist.
if OKAY and P.OUTDIR != "" :
if not os.path.isdir(P.OUTDIR) :
os.mkdir(P.OUTDIR)
LOGFN = os.path.join(P.OUTDIR,'bl_trim_galore.log')
LOGFILE = open(LOGFN,'w')
LOGFILE.write('\n')
# Run trim_galore
if OKAY :
for PR in TF.READPAIRS :
RunTrimGalore(P,PR,LOGFILE)
LOGFILE.close()
# Notify user when job is done, if email address was
# supplied using --email
if P.EMAIL != "" :
Sender = getpass.getuser() + '@' + LocalHostname()
Subject = 'bl_trim_galore.py completed'
Message = 'bl_trim_galore.py: Completed
'
LOGFILE = open(os.path.join('bl_trim_galore.log'),'r')
for line in LOGFILE.readlines() :
Message = Message + line + '
'
LOGFILE.close()
SendEmail(Sender,[P.EMAIL],Subject,Message)
if __name__ == "__main__":
main()
#else:
#used to generate documentation
# import doctest
# doctest.testmod()
#if (BM.documentor() or "-test" in sys.argv):
# pass
#else:
# main()