def sortBed(inBed, outBed, path = 'bedtools', delete = True):
''' Function to sort bed files, first by cheomsome and then by start
position. Function takes four arguments
1) inBed - Input bed file.
2) outBed - Output bed file.
3) path - path to bedtools exectuable.
4) delete - Whether to delete input bed file
'''
# Check arguments
toolbox.checkArg(delete, 'bool')
# Create sort command:
sortCommand = '%s sort -i %s > %s' %(path, inBed, outBed)
# Append deletion command
if delete == True:
sortCommand += ' && rm %s' %(inBed)
# Return command
return(sortCommand)
def bed2bedGraph(inBed, outBG, chrFile, path = 'bedtools', delete = False):
''' Function to create bedgraph from sorted bed file. Function takes
five arguments:
1) inBed - Input bed file.
2) outBG - Output bedgraph file.
3) chrFile - A tab delimited text file of chromosome name and sizes.
3) path - Path to bedtools executable.
4) delete - Boolean, whether to delete input BED file
'''
# Check arguments
toolbox.checkArg(delete, 'bool')
# Create bedgraph command
bgCommand = '%s genomecov -bg -i %s -g %s > %s' %(path, inBed, chrFile,
outBG)
# Append deletion command
if delete == True:
bgCommand += ' && rm %s' %(inBed)
# Return command
return(bgCommand)
--quality=<quality> Trimming quality [default: 20]
--adapter=<adapter> Adapter sequence [default: AGATCGGAAGAGC]
--path=<path> Path to cutadapt [default: cutadapt]
--help Output this message
"""
# Import required modules
import os
from ngs_python.fastq import fastqFind, fastqTrim
from general_python import docopt, toolbox, moab
# Extract and process arguments
args = docopt.docopt(__doc__,version = 'v1')
args['--quality'] = int(args['--quality'])
inDir, inPrefix = os.path.split(args['<inprefix>'])
toolbox.checkArg(args['--path'], 'exc')
# Extract fastq files and generate output file names
read1In, read2In = fastqFind.findFastq(prefix = inPrefix, dirList = [inDir],
pair = True, gzip = True)
read1Out = args['<outprefix>'] + '.R1.fastq.gz'
read2Out = args['<outprefix>'] + '.R2.fastq.gz'
trimLog = args['<outprefix>'] + '.log'
# Generate and submit trim command
trimCommand = fastqTrim.cutadaptTrimPaired(read1In = read1In,
read2In = read2In, read1Out = read1Out, read2Out = read2Out,
quality = args['--quality'], adapter = 'AGATCGGAAGAGC', length = 25,
path = args['--path']
)
jobID = moab.submitJob(trimCommand, stdout = trimLog, stderr = trimLog)
print jobID
--quality=<quality> Trimming quality [default: 20]
--adapter=<adapter> Adapter sequence [default: AGATCGGAAGAGC]
--path=<path> Path to cutadapt [default: cutadapt]
--help Output this message
"""
# Import required modules
import os
from ngs_python.fastq import fastqFind, fastqTrim
from general_python import docopt, toolbox, moab
# Extract and process arguments
args = docopt.docopt(__doc__, version='v1')
args['--quality'] = int(args['--quality'])
inDir, inPrefix = os.path.split(args['<inprefix>'])
toolbox.checkArg(args['--path'], 'exc')
# Extract fastq files and generate output file names
read1In, read2In = fastqFind.findFastq(prefix=inPrefix,
dirList=[inDir],
pair=True,
gzip=True)
read1Out = args['<outprefix>'] + '.R1.fastq.gz'
read2Out = args['<outprefix>'] + '.R2.fastq.gz'
trimLog = args['<outprefix>'] + '.log'
# Generate and submit trim command
trimCommand = fastqTrim.cutadaptTrimPaired(read1In=read1In,
read2In=read2In,
read1Out=read1Out,
read2Out=read2Out,
quality=args['--quality'],
adapter='AGATCGGAAGAGC',
def mpileup(
inBam, outFile, reference = '', minMapQ = 20, minBaseQ = 20,
countOrphans = False, countDup = False, disableBAQ = True,
maxDepth = 10000, minFilter = None, path = 'samtools'
):
# Check numeric arguments
toolbox.checkArg(minMapQ, 'int', mn = 2)
toolbox.checkArg(minBaseQ, 'int', mn = 0)
toolbox.checkArg(countOrphans, 'bool')
toolbox.checkArg(countDup, 'bool')
toolbox.checkArg(disableBAQ, 'bool')
toolbox.checkArg(maxDepth, 'int', gt = 0)
toolbox.checkArg(minFilter, 'int', mn = 0)
# Create initial command
command = [path, 'mpileup', '-q', str(minMapQ), '-Q', str(minBaseQ), '-d',
str(maxDepth)]
# Add otptions
if countOrphans:
command.append('-A')
if disableBAQ:
command.append('-B')
if reference:
command.extend(['-f', reference])
if not countDup:
command.extend(['--ff', '1024'])
# Process filter
if minFilter:
command.append(inBam)
awk = 'awk \'BEGIN{FS = "\\t"};{if ($4 >= %s) print $0}\'' %(minFilter)
finalCommand = '%s | %s > %s' %(' '.join(command), awk, outFile)
else:
command.extend(['-o', outFile, inBam])
finalCommand = ' '.join(command)
# Retutn command
return(finalCommand)
# Import required modules
import os
import sys
from ngs_python.fastq import fastqFind, fastqTrim, fastqQC, fastqAlign
from ngs_python.bam import picard
from ngs_python.bed import bedtools
from general_python import docopt, moab, toolbox
# Print sommand and extract argument
print '%s\n' % (' '.join(sys.argv))
args = docopt.docopt(__doc__, version='v1')
# Extract sample prefix and name
args['prefix'], args['name'] = args['<sampledata>'].split(',')
# Extract path data and check they are executable:
paths = toolbox.fileDict(args['<paths>'], sep='\t')
for program in paths:
toolbox.checkArg(paths[program], 'exc')
# Conver numric arguments
args['--minMapQ'] = int(args['--minMapQ'])
args['--threads'] = int(args['--threads'])
args['--interval'] = int(args['--interval'])
# Extract fastq files and check
args['read1'], args['read2'] = fastqFind.findFastq(
prefix=args['prefix'], dirList=args['<indir>'].split(','), pair=True)
if len(args['read1']) != len(args['read2']):
raise IOError('Unequal number of FASTQ files identified')
if len(args['read1']) < 1:
raise IOError('Insufficient number of FASTQ files identified')
# Check output directories
if not os.path.isdir(args['<outdir>']):
raise IOError('Output directory not found')
# Create directory names
# Import required modules
import os
import re
import numpy as np
from ngs_python.structure import interactionMatrix, analyseInteraction
from general_python import docopt, toolbox
# Extract arguments
args = docopt.docopt(__doc__,version = 'v1')
# Check numerical arguments
args['<mincount>'] = int(args['<mincount>'])
args['--threads'] = int(args['--threads'])
if args['nobed']:
args['<binsize>'] = int(args['<binsize>'])
# Check input files and output directory
if args['bed']:
toolbox.checkArg(args['<bedfile>'], 'file')
else:
toolbox.checkArg(args['<chrfile>'], 'file')
for f in args['<inputfiles>']:
toolbox.checkArg(f, 'file')
toolbox.checkArg(args['<outdir>'], 'dir')
# Modify label argument
if args['--label']:
toolbox.checkArg(args['--label'], 'str')
args['--label'] = '_' + args['--label']
# Extract and print sample names
sampleNames = [re.search('([^/]*)\.fragLigations\.gz$',f).group(1) for f in args['<inputfiles>']]
logData = 'Samples:\n %s\n' %(
'\n '.join(sampleNames)
)
# Extract and print parameters to create bins