# Read configuration files
config = util.readConfigurationFiles()
header = config.getboolean("server", "PBS_header")
ppn = config.get("cellrangercount", "ppn")
mem = config.get("cellrangercount", "mem")
vmem = config.get("cellrangercount", "vmem")
genome = config.get("project", "genome")
cellrangerTranscriptome = config.get(genome, "cellrangerTranscriptome")
localcores = config.get("cellrangercount", "localcores")
localmem = config.get("cellrangercount", "localmem")
# Read samples file.
samplesDataFrame = util.readSamplesFile()
# Create scripts directory, if it does not exist yet, and cd to it.
if not os.path.exists(scriptsDirectory):
os.mkdir(scriptsDirectory)
os.chdir(scriptsDirectory)
# Cycle through all the samples and write the cellrangercount scripts.
for index, row in samplesDataFrame.iterrows():
sample = row["sample"]
# Create script file.
scriptName = "cellrangercount_" + sample + ".sh"
script = open(scriptName, 'w')
if header:
util.writeHeader(script, config, "cellrangercount")
script.write("cellranger count " + "\\\n")
outputDirectory = os.path.abspath(args.outputDirectory)
# Read configuration files
config = util.readConfigurationFiles()
header = config.getboolean("server", "PBS_header")
trim = config.getboolean("project", "trim")
stranded = config.getboolean("project", "stranded")
genome = config.get("project", "genome")
genomeFile = config.get(genome, "genomeFile")
gtfFile = config.get(genome, "gtfFile")
processors = config.get("stringtie", "processors")
# Read samples file.
samplesFile = util.readSamplesFile()
# Create scripts directory, if it does not exist yet, and cd to it.
if not os.path.exists(scriptsDirectory):
os.mkdir(scriptsDirectory)
os.chdir(scriptsDirectory)
# Create output directory, if it does not exist yet.
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
########################
# stringtie.sh scripts #
########################
for index, row in samplesFile.iterrows():
sample = row["sample"]
header = config.getboolean("server", "PBS_header")
stranded = config.getboolean("project", "stranded")
if genome is "Configuration file value":
if config.has_option("project", "genome"):
genome = config.get("project", "genome")
else:
sys.exit("No reference genome was specified at the command line or in the configuration file.")
genomeFile = config.get(genome, "genomeFile")
gtfFile = config.get(genome, "gtfFile")
bowtieIndex = config.get(genome, "bowtie1Index")
processors = config.get("bowtie1", 'processors')
k = config.get("bowtie1", "k")
v = config.get("bowtie1", "v")
# Read samples file.
samplesFile = util.readSamplesFile(inputDirectory)
# Create scripts directory, if it does not exist yet, and cd to it.
if not os.path.exists(scriptsDirectory):
os.mkdir(scriptsDirectory)
os.chdir(scriptsDirectory)
# Create output directories, if they do not exist yet..
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
# Cycle through all the samples and write the bowtie scripts.
for index, row in samplesFile.iterrows():
sample = row["sample"]
# Create output directories
if not os.path.exists(outputDirectory + "/" + sample):
