Пример #1
0
    
    --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
Пример #2
0
    
"""
# 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
Пример #3
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# Find FASTQ files by prefix
if args['prefix']:
    indir, prefix = os.path.split(args['<prefix>'])
    print indir, prefix
    args['<infastq>'] = fastqFind.findFastq(prefix = prefix,
        dirList = [indir], pair = False)
    args['<infastq>'].sort()
# Check number of FASTQ files
if len(args['<infastq>']) < 2:
    sys.exit('\nCannot concatenate %s files\n' %(len(args['<infastq>'])))
# Check output file doesnt exist
if os.path.isfile(args['<outfastq>']):
    sys.exit('\nOutput file exists. No command submitted\n')
# Print input and out files
print '\nInput files:\n%s\n\nOutput file:\n%s\n' %(
    '\n'.join(args['<infastq>']), args['<outfastq>'])
# Get user response before concatenation
print "Enter 'concat' to concatenate: "
response = raw_input()
# Submit command
if response == 'concat':
    # Create and submit command
    command = 'zcat %s | gzip > %s' %(
        ' '.join(args['<infastq>']),
        args['<outfastq>']
    )
    moabID = moab.submitJob(command)
    print '\n%s\n' %(moabID)
else:
    print '\nNo command submitted\n'
Пример #4
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inDir, inPrefix = os.path.split(args['<inprefix>'])
outDir = os.path.join(args['<outdir>'], args['<samplename>'])
if not os.path.isdir(outDir):
    os.mkdir(outDir)
outPrefix = os.path.join(outDir, args['<samplename>'])
outLog = outPrefix + '.rsem.log'
# Create job dictionary

# Extract fastq files and generate output file names
read1, read2 = fastqFind.findFastq(prefix=inPrefix,
                                   dirList=[inDir],
                                   pair=True,
                                   gzip=True)
rsemCommand = fastqAlign.rsemBowtie2Align(index=args['<index>'],
                                          outPrefix=outPrefix,
                                          read1=read1,
                                          read2=read2,
                                          rsemPath=args['--rsem'],
                                          bowtie2Path=args['--bowtie2'],
                                          threads=args['--threads'],
                                          forProb=args['--forprob'],
                                          genomeBam=args['--genomebam'],
                                          estimateRspd=False,
                                          check=True)
print rsemCommand
jobID = moab.submitJob(rsemCommand,
                       processor=args['--threads'],
                       stdout=outLog,
                       stderr=outLog)
print args['<samplename>'], jobID
Пример #5
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"""
# Import required modules
import os
from ngs_python.fastq import fastqFind, fastqAlign
from general_python import docopt, toolbox, moab
# Extract and process arguments
args = docopt.docopt(__doc__,version = 'v1')
args['--threads'] = int(args['--threads'])
args['--forprob'] = float(args['--forprob'])
toolbox.check_var(args['--forprob'], 'num', mn = 0, mx = 1)
inDir, inPrefix = os.path.split(args['<inprefix>'])
outDir = os.path.join(args['<outdir>'], args['<samplename>'])
if not os.path.isdir(outDir):
    os.mkdir(outDir)
outPrefix = os.path.join(outDir, args['<samplename>'])
outLog = outPrefix + '.rsem.log'
# Create job dictionary

# Extract fastq files and generate output file names
read1, read2 = fastqFind.findFastq(prefix = inPrefix, dirList = [inDir],
    pair = True, gzip = True)
rsemCommand = fastqAlign.rsemBowtie2Align(index = args['<index>'],
    outPrefix = outPrefix, read1 = read1, read2 = read2,
    rsemPath = args['--rsem'], bowtie2Path = args['--bowtie2'],
    threads = args['--threads'], forProb = args['--forprob'],
    genomeBam = args['--genomebam'], estimateRspd = False, check = True)
print rsemCommand
jobID = moab.submitJob(rsemCommand, processor = args['--threads'],
    stdout = outLog, stderr = outLog)
print args['<samplename>'], jobID