def create_outfiles(options):
''' creates all parent directories given in the output prefix and returns the resulting file paths for the summary, plot and rdata file '''
wutils.make_parent_dirs(options.outPrefix)
# summary file, plot file, data file
return (options.outPrefix + '.txt', options.outPrefix + '.pdf',
options.outPrefix + '.Rdata')
def get_and_create_outfiles(cmdl_options):
'''
creates all parent folders for writing the output
'''
wutils.make_parent_dirs(cmdl_options.outPrefix)
if (cmdl_options.outCirc is not None):
wutils.make_parent_dirs(cmdl_options.outCirc)
def copy_file(source_path, target_path):
''' copies file of 'source_path' to 'target_path' (folder and filename) '''
# check if file to copy really exists
if (os.path.exists(source_path) and os.path.isfile(source_path)):
# create directory of the target location
wutils.make_parent_dirs(target_path)
# copy file
shutil.copy(source_path, target_path)
def create_outfiles(options):
''' creates parent directories and full filenames for the given file name prefix'''
# create parent directories
wutils.make_parent_dirs(options.outPrefix)
# full output paths
bedgraph_file = options.outPrefix+'.bedgraph'
tdf_file = options.outPrefix+'.bedgraph.tdf'
return bedgraph_file, tdf_file
def create_outfiles(options):
''' creates all parent folders for the output files if they do not exist'''
wutils.make_parent_dirs(options.out1)
wutils.make_parent_dirs(options.sam)
if(options.out2 is not None):
wutils.make_parent_dirs(options.out2)
def main():
''' main method for calling removeLinearReads from commandline '''
print('Program call:')
print(' '.join(sys.argv))
_,o = get_command_line_options()
wutils.make_parent_dirs(o.circOut)
t_start = wutils.get_current_time()
print(t_start[1]+'Start Removal of Linearly Mappable Reads')
algo.remove_linearly_mappable_reads(o.circRNAPrediction, o.mapping, o.circOut, o.minReads, o.paired)
t_end = wutils.get_current_time()
print(t_end[1]+'Finished. Check out the results in '+o.circOut)
wutils.print_resources(t_end[0]-t_start[0], child_processes=False)
if(o.returnFilePath is not None):
returnVars = [('filteredCircs', o.circOut)]
wutils.write_watchdog_return_file(o.returnFilePath, returnVars)
def get_and_create_outfiles(cmdl_options):
''' creates all parent folders for writing the output '''
wutils.make_parent_dirs(cmdl_options.countTable)
# parent directories for optional plots
if (cmdl_options.countPlot is not None):
wutils.make_parent_dirs(cmdl_options.countPlot)
if (cmdl_options.groupPlot is not None):
wutils.make_parent_dirs(cmdl_options.groupPlot)
def get_and_create_outfiles(parser, cmdl_options):
''' check output options and create output files '''
outfiles = ['', '', '']
# 3 separate paths for output file
if (cmdl_options.outPrefix is None):
for pos, (oname, option) in enumerate([
('outReads1', cmdl_options.outReads1),
('outReads2', cmdl_options.outReads2),
('outSingletons', cmdl_options.outSingletons)
]):
# check if option is used
if (option is None):
parser.error('Missing argument: outPrefix or ' + oname +
' option is required!')
outfiles[pos] = option
# 1 shared prefix for the output
else:
for pos, (oname, option) in enumerate([
('outReads1', cmdl_options.outReads1),
('outReads2', cmdl_options.outReads2),
('outSingletons', cmdl_options.outSingletons)
]):
if (option is not None):
parser.error('Argument clash: use only outPrefix or ' + oname +
'!')
outfiles[0] = cmdl_options.outPrefix + '1.fastq'
outfiles[1] = cmdl_options.outPrefix + '2.fastq'
outfiles[2] = cmdl_options.outPrefix + 'singleton.fastq'
# make parent folders for every outfile
for ofile in outfiles:
wutils.make_parent_dirs(ofile)
return outfiles
def create_output_dirs(options):
''' create all directories for writing the combined circRNA predictions'''
wutils.make_parent_dirs(options.outUnion)
wutils.make_parent_dirs(options.outIntersection)
wutils.make_parent_dirs(options.outIntersectedUnion)
def create_outfiles(options):
''' create all parent directories of the sam file with the aligned reads '''
wutils.make_parent_dirs(options.outSam)
def create_outfiles(options):
''' creates all parent directories of the resulting bed file that do not exist '''
wutils.make_parent_dirs(options.outBed)
def create_outfiles(options):
''' create all parent directories of the sai file with the output of bwa aln '''
wutils.make_parent_dirs(options.outSai)
def create_outfiles(options):
''' create all parent directories of the resulting bigwig file '''
wutils.make_parent_dirs(options.outBw)
def create_outfiles(options):
''' create all parent directories of the sam/bam file with the remaining reads '''
wutils.make_parent_dirs(options.outSamBam)
def create_output_dirs(cmdl_options):
''' create parent directories of concatenated output file '''
wutils.make_parent_dirs(cmdl_options.outFile)
def get_and_create_outfiles(cmdl_options):
'''
creates all parent folders for writing the output
'''
wutils.make_parent_dirs(join(cmdl_options.outdir, ''))