Exemple #1
0
print "PLEASE NOTE! The output folder, containing your data, will be named - " + analysis_dir
os.makedirs(analysis_dir)
analysis_directory = analysis_dir + "/"

# setup directory containing fastq's and get them
indir = sys.argv[2]
for sample in os.listdir(indir):
    if sample.endswith(".1.fq.gz"):
        sample_name = re.sub(r"(.*).1.fq.gz", r"\1", sample)
        sample_name_uc = sample_name + "_unclipped"
    else:
        continue

# Preparation of bamfile + unclipped bamfile
pipeliners.system_call(
    'Cut Adapters',
    cutadapt(sample_name + ".1.fq.gz",
             analysis_directory + sample_name + "_ar.1.fq.gz"))
pipeliners.system_call(
    'Cut Adapters',
    cutadapt(sample_name + ".2.fq.gz",
             analysis_directory + sample_name + "_ar.2.fq.gz"))
exit()

pipeliners.system_call(
    'SMALT alignment',
    smalt(analysis_directory, sample_name + "_ar.1.fq.gz",
          sample_name + "_ar.2.fq.gz", sample_name + ".sam"))
pipeliners.system_call(
    'Convert samfile to bamfile',
    sam_to_bam(analysis_directory, sample_name + ".sam", sample_name + ".bam"))
Exemple #2
0
#
#
# script that runs a function with a set of infiles in serial
#
#
# Kim Brugger (29 Apr 2015), contact: [email protected]

import sys
#import pprint
#pp = pprint.PrettyPrinter(indent=4)
sys.path.append("/data/VMshare/github/pipeliners/modules")
import pipeliners

if (len(sys.argv) == 1):
    print "USAGE: serial.py [program to run] [file(s) to run on]"
    exit()

program = sys.argv[1]

pipeliners.set_verbose_level('INFO')

for arg in range(2, len(sys.argv)):
    infile = str(sys.argv[arg])
    cmd = str(program) + " " + infile
    print cmd
    pipeliners.system_call('serial_call', cmd)
Exemple #3
0
analysis_dir = sys.argv[1] + "_" + time_stamp
print "PLEASE NOTE! The output folder, containing your data, will be named - " + analysis_dir
os.makedirs(analysis_dir)
analysis_directory = analysis_dir + "/"

# setup directory containing fastq's and get them
indir = sys.argv[2]
for sample in os.listdir(indir):
	if sample.endswith(".1.fq.gz"):
		sample_name = re.sub(r"(.*).1.fq.gz", r"\1", sample)
		sample_name_uc = sample_name + "_unclipped"
	else:
		continue

# Preparation of bamfile + unclipped bamfile  
pipeliners.system_call('Cut Adapters', cutadapt(sample_name + ".1.fq.gz", analysis_directory + sample_name + "_ar.1.fq.gz"))
pipeliners.system_call('Cut Adapters', cutadapt(sample_name + ".2.fq.gz", analysis_directory + sample_name + "_ar.2.fq.gz"))
exit()

pipeliners.system_call('SMALT alignment', smalt(analysis_directory, sample_name + "_ar.1.fq.gz", sample_name + "_ar.2.fq.gz", sample_name + ".sam"))
pipeliners.system_call('Convert samfile to bamfile', sam_to_bam(analysis_directory, sample_name + ".sam", sample_name + ".bam"))

pipeliners.system_call('Unclipping bamfile', unclip_bamfile(analysis_directory, sample_name + ".bam"))

# Bamfile processing pipeline 
pipeliners.system_call('Sort the bamfile', sort_bamfile(analysis_directory, sample_name+ ".bam", sample_name + "_sorted"))
#pipeliners.system_call('Deduplicate bamfile', deduplicate_bamfile(sample_name + "_sorted.bam", sample_name + "_rmdups.bam", sample_name + "_rmdup.csv"))
pipeliners.system_call('Index bamfile', index_bamfile(analysis_directory, sample_name + "_sorted.bam"))
pipeliners.system_call('Fix HIV alignment', HIV_alignment_fix(analysis_directory, sample_name + "_sorted.bam", sample_name + "_fixed.bam"))
pipeliners.system_call('Index bamfile', index_bamfile(analysis_directory, sample_name + "_fixed.bam"))
Exemple #4
0
#
# 
# script that runs a function with a set of infiles in serial
# 
# 
# Kim Brugger (29 Apr 2015), contact: [email protected]

import sys
#import pprint
#pp = pprint.PrettyPrinter(indent=4)
sys.path.append("/data/VMshare/github/pipeliners/modules")
import pipeliners

if (len(sys.argv) == 1):
    print "USAGE: serial.py [program to run] [file(s) to run on]"
    exit()

program = sys.argv[1]

pipeliners.set_verbose_level('INFO');

for arg in range(2, len(sys.argv)):
    infile = str(sys.argv[ arg ])
    cmd = str(program) + " " + infile
    print cmd
    pipeliners.system_call('serial_call', cmd)