if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-r', '--readDir', help='directory containing fastq files', required=True)
parser.add_argument('-a', '--alignmentParDir', help='parent directory where directory for alignments for this data set will be created', default="/srv/gsfs0/projects/salzman/Linda/alignments")
parser.add_argument('-t', '--taskDir', help='name of directory under alignmentParDir to output task file', default="taskIdFiles")
parser.add_argument('-d', '--dataSet', required=True,
help='name of directory under alignmentParDir that all alignment files will be written to')
parser.add_argument('-v', '--verbose', help='print extra debugging info', action='store_true')
parser.add_argument('-u', '--unalignedMode', help='pass this flag if we are aligning the unaligned reads from previous pipeline run', action='store_true')
args = parser.parse_args()
try:
### create output directories if they don't exist, and the alignment subdirectories
utils_os.createDirectory("/".join([args.alignmentParDir, args.taskDir]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "denovo"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "still_unaligned"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "genome"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "junction"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ribo"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "reg"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids", "denovo"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids", "genome"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids", "junction"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids", "ribo"]))
utils_os.createDirectory("/".join([args.alignmentParDir, args.dataSet, "orig", "ids", "reg"]))
action='store_true')
args = parser.parse_args()
if args.verbose:
print "parentDir:", args.parentDir
print "sampleId:", args.sampleId
print "outDirName:", args.outDirName
print "style:", args.fastqIdStyle
print "a1:", args.aScore1
print "a2:", args.aScore2
print "overhang:", args.overhang
print "id dir suffix:", args.junctionIdDirSuffix
print "unaligned:", args.unalignedMode
# make output dirs if they don't exist
utils_os.createDirectory("/".join([args.parentDir, args.outDirName]))
utils_os.createDirectory("/".join(
[args.parentDir, args.outDirName,
"reports"])) # these are the reports using the naive method
utils_os.createDirectory("/".join([
args.parentDir, args.outDirName, "glmReports"
])) # GLM will be run later and those reports will be stored here
utils_os.createDirectory("/".join([
args.parentDir, args.outDirName, "glmModels"
])) # GLM will be run later and those models will be stored here
utils_os.createDirectory("/".join([
args.parentDir, args.outDirName, "ids"
])) # txt files of read ids assigned to circular or linear category
# just doing read1s
if args.sampleId.endswith("1"):
required=True,
help="looking for PE > X base pairs apart. Linda's default window is 100K."
)
args = parser.parse_args()
if args.origDir[-1] != "/":
inpath = args.origDir + "/"
else:
inpath = args.origDir
if args.outputDir[-1] != "/":
outpath = args.outputDir + "/DistantPEFiles/"
else:
outpath = args.outputDir + "DistantPEFiles/"
utils_os.createDirectory(outpath)
UserBPdistance = int(args.UserBPdistance)
# change the input path to the path where your file exists
os.chdir(inpath)
genomefiles = sorted(glob.glob(inpath + "genome/sorted*" + args.stem +
"*.sam"))
regfiles = sorted(glob.glob(inpath + "reg/sorted*" + args.stem + "*.sam"))
print genomefiles
print regfiles
# print SamFiles
#opening paired files
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--fastaFile', required=True, help='path to fasta file with chromosome sequences')
parser.add_argument('-a', '--annotationFile', required=True, help='path to gff file with exon annotations')
parser.add_argument('-o', '--outDir', help='directory to output files, will be created if it does not exist', default='output')
parser.add_argument('-e', '--exonOutDir', help='directory to output exon pickle files, will be created within outDir if it does not exist', default='exons')
parser.add_argument('-g', '--geneOutDir', help='directory to output gene pickle files, will be created within outDir if it does not exist', default='genes')
parser.add_argument('-r', '--recOutDir', help='directory to output seq record pickle files, will be created within outDir if it does not exist', default='records')
parser.add_argument('-v', '--verbose', help='print info about data obtained', action='store_true')
args = parser.parse_args()
exonOutFullPath = '/'.join([args.outDir, args.exonOutDir])
geneOutFullPath = '/'.join([args.outDir, args.geneOutDir])
recOutFullPath = '/'.join([args.outDir, args.recOutDir])
# create output directories if necessary
utils_os.createDirectory(args.outDir)
utils_os.createDirectory(exonOutFullPath)
utils_os.createDirectory(geneOutFullPath)
utils_os.createDirectory(recOutFullPath)
# read in the sequences
f_handle = open(args.fastaFile, "rU")
f_dict = SeqIO.to_dict(SeqIO.parse(f_handle, "fasta"))
f_handle.close()
# only want exons for now. unfortunately can't limit by strand so have to do that after the fact
# we can speed things up a bit by limiting to just the chromosomes we have sequences for
limit_info = dict(
gff_id = f_dict.keys(),
gff_type = ["exon"])
default="swap")
parser.add_argument('-v',
'--verbose',
help='print extra debugging info',
action='store_true')
args = parser.parse_args()
try:
swappedDataSet = args.dataSet + "Swapped"
origSam = "/".join([args.alignmentParDir, args.dataSet, "orig"])
swappedSam = "/".join([args.alignmentParDir, swappedDataSet, "orig"])
if args.mode == "swap":
### create output directories if they don't exist, and the alignment subdirectories
### these are all that are created by writeTaskIdFiles.py for original run, all other directories are output as usual during the run in analysis mode
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet]))
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet, "orig"]))
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet, "orig", "denovo"]))
utils_os.createDirectory("/".join([
args.alignmentParDir, swappedDataSet, "orig", "still_unaligned"
]))
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet, "orig", "genome"]))
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet, "orig", "junction"]))
utils_os.createDirectory("/".join(
[args.alignmentParDir, swappedDataSet, "orig", "ribo"]))
utils_os.createDirectory("/".join(
parser.add_argument("-w", "--window", required=True, help = "size = w of window where if read occurs at X, then window starts at X-w and ends at X+w")
parser.add_argument("-n","--UserBPdistance", required = True, help = "looking for PE > X base pairs apart. Linda's default window is 100K.")
args=parser.parse_args()
if args.origDir[-1] != "/":
inpath = args.origDir + "/"
else:
inpath = args.origDir
if args.outputDir[-1] != "/":
outpath = args.outputDir + "/DistantPEFiles/"
else:
outpath = args.outputDir + "DistantPEFiles/"
utils_os.createDirectory(outpath)
UserBPdistance = int(args.UserBPdistance)
# change the input path to the path where your file exists
os.chdir(inpath)
genomefiles = sorted(glob.glob(inpath + "genome/sorted*" + args.stem + "*.sam"))
regfiles = sorted(glob.glob(inpath + "reg/sorted*" + args.stem + "*.sam"))
print genomefiles
print regfiles
handle.write("swapped_circOrLinear\tswapped_decoyOrAnom\tswapped_unmapped\tswapped_pval\ttotal_reads\n")
for j in junctions:
handle.write(str(junctions[j]) + "\n")
handle.close()
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-a', '--dirA', help='directory containing original pipeline reports (parent of reports, ids, etc)', required=True)
parser.add_argument('-b', '--dirB', help='directory containing swapped pipeline reports (parent of reports, ids, etc directories)', required=True)
parser.add_argument('-q', '--fastqIdStyle', help='type of read ids used', required=True, choices=['appended', 'complete'])
parser.add_argument('-v', '--verbose', help='print extra debugging info', action='store_true')
args = parser.parse_args()
utils_os.createDirectory("/".join([args.dirA, "combinedReports"]))
for f in os.listdir("/".join([args.dirA, "reports"])):
reportFileName = os.path.basename(f)
if args.verbose:
print reportFileName
if patt_filename.search(reportFileName):
idFileName = reportFileName.replace("report", "_output") # could be denovo or annotated report file, all handled the same
if args.verbose:
print reportFileName
print idFileName
junctions = {}
combineResults(reportFileName, idFileName)
print len(allJunctions)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-w', '--window', help='sliding window size to create junctions', default=100000, type=int)
parser.add_argument('-e', '--exonDir', help='directory containing exon pickle files', default='output/exons')
parser.add_argument('-s', '--singleFile', help='path to single exon file that should be parsed for junctions')
parser.add_argument('-r', '--recordDir', help='directory containing seq record pickle files', default='output/records')
parser.add_argument('-f', '--fastaDir', help='directory to output junction fasta files, will be created if does not exist', default='output/fasta')
parser.add_argument('-v', '--verbose', help='print extra debugging info', action='store_true')
args = parser.parse_args()
# create fastaDir if it doesn't exist
utils_os.createDirectory(args.fastaDir)
# only run for a single file
if args.singleFile:
if args.verbose:
print "running for single file", args.singleFile
exonObj = os.path.basename(args.singleFile)
fileId = utils_os.getFileId(patt_exonfilename, 1, args.singleFile) # usually something like chr# which is in the name of each created file
createJunctions(fileId, exonObj)
else:
if args.verbose:
print "running for directory", args.exonDir
# or loop through files in exonDir to create junction file for each
for exonObj in os.listdir(args.exonDir):
if patt_exonfile.search(exonObj): # only parse if this is an exon pickled file
fileId = utils_os.getFileId(patt_exonfilename, 1, exonObj) # usually something like chr# which is in the name of each created file
parser.add_argument('-v', '--verbose', help='print extra debugging info', action='store_true')
args = parser.parse_args()
if args.verbose:
print "parentDir:", args.parentDir
print "sampleId:", args.sampleId
print "outDirName:", args.outDirName
print "style:", args.fastqIdStyle
print "a1:", args.aScore1
print "a2:", args.aScore2
print "overhang:", args.overhang
print "id dir suffix:", args.junctionIdDirSuffix
print "unaligned:", args.unalignedMode
# make output dirs if they don't exist
utils_os.createDirectory("/".join([args.parentDir, args.outDirName]))
utils_os.createDirectory("/".join([args.parentDir, args.outDirName, "reports"])) # these are the reports using the naive method
utils_os.createDirectory("/".join([args.parentDir, args.outDirName, "glmReports"])) # GLM will be run later and those reports will be stored here
utils_os.createDirectory("/".join([args.parentDir, args.outDirName, "glmModels"])) # GLM will be run later and those models will be stored here
utils_os.createDirectory("/".join([args.parentDir, args.outDirName, "ids"])) # txt files of read ids assigned to circular or linear category
# just doing read1s
if args.sampleId.endswith("1"):
try:
# populate the ignoreIds, regIds, nonRegIds for this file and also print out regIds and nonRegIds to juncNonGR file
ignoreIds = {} # ribo and genome aligned
regIds = {} # regular junction overlapped and not ribo or genome aligned (aligned to reg-only index)
nonRegIds = {} # junction overlapped and not ribo or genome aligned or regular-junction aligned
# we treat denovo reads as the equivalent of the junction reads in unalignedMode
if args.unalignedMode:
parser.add_argument('-w', '--window', help='sliding window size to create junctions', default=1000000, type=int)
parser.add_argument('-e', '--exonDir', help='directory containing exon pickle files', default='output/exons')
parser.add_argument('-s', '--singleFile', help='path to single exon file that should be parsed for junctions')
parser.add_argument('-r', '--recordDir', help='directory containing seq record pickle files',
default='output/records')
parser.add_argument('-f', '--fastaDir',
help='directory to output junction fasta files, will be created if does not exist',
default='output/fasta')
parser.add_argument('-n1', '--name1', help='name of field in gtf to use for gene names', default='gene_name')
parser.add_argument('-n2', '--name2', help='name of field in gtf to use for gene names if n1 does not exist',
default='gene_id')
parser.add_argument('-v', '--verbose', help='print extra debugging info', action='store_true')
args = parser.parse_args()
# create fastaDir if it doesn't exist
utils_os.createDirectory(args.fastaDir)
# only run for a single file
if args.singleFile:
if args.verbose:
print "running for single file", args.singleFile
exonObj = os.path.basename(args.singleFile)
fileId = utils_os.getFileId(patt_exonfilename, 1,
args.singleFile) # usually something like chr# which is in the name of each created file
createJunctions(fileId, exonObj)
else:
if args.verbose:
print "running for directory", args.exonDir
# or loop through files in exonDir to create junction file for each
for exonObj in os.listdir(args.exonDir):
if patt_exonfile.search(exonObj): # only parse if this is an exon pickled file
'--dirB',
help=
'directory containing swapped pipeline reports (parent of glmReports, ids, etc directories)',
required=True)
parser.add_argument('-q',
'--fastqIdStyle',
help='type of read ids used',
required=True,
choices=['appended', 'complete'])
parser.add_argument('-v',
'--verbose',
help='print extra debugging info',
action='store_true')
args = parser.parse_args()
utils_os.createDirectory("/".join([args.dirA, "combinedReports"]))
for f in os.listdir("/".join([args.dirA, "glmReports"])):
reportFileName = os.path.basename(f)
if args.verbose:
print reportFileName
if patt_GLMfilename.search(reportFileName):
idFileName = reportFileName.replace(
"circJuncProbs",
"output").replace("linearJuncProbs",
"output") # could be linear or circular file
if args.verbose:
print reportFileName
print idFileName
choices=['all', 'within', 'between'],
default='all')
parser.add_argument('-p',
'--postpend',
help='text to add to end of output file names',
required=True)
parser.add_argument('-v',
'--verbose',
help='print info about data obtained',
action='store_true')
args = parser.parse_args()
if args.fastaDir and args.singleFile:
sys.exit("Only 1 of -d and -s can be specified")
# create output directory if it does not exist
utils_os.createDirectory(args.outDir)
# fasta junction ids look like chr10|TTC40:134751179|MYC1:134722640|reg|-
# where we are interested in TTC40, MYC1, and reg
id_patt = re.compile(".+?\|(.+?):.+?\|(.+?):.+?\|(.+?)\|.*")
if args.fastaDir:
# loop through files directory
for f in os.listdir(args.fastaDir):
if f.endswith(".fa"): # only parse if this is a fasta file
writeLimitedFasta('/'.join([args.fastaDir, f]))
elif args.singleFile:
writeLimitedFasta(args.singleFile)
'--recOutDir',
help=
'directory to output seq record pickle files, will be created within outDir if it does not exist',
default='records')
parser.add_argument('-v',
'--verbose',
help='print info about data obtained',
action='store_true')
args = parser.parse_args()
exonOutFullPath = '/'.join([args.outDir, args.exonOutDir])
geneOutFullPath = '/'.join([args.outDir, args.geneOutDir])
recOutFullPath = '/'.join([args.outDir, args.recOutDir])
# create output directories if necessary
utils_os.createDirectory(args.outDir)
utils_os.createDirectory(exonOutFullPath)
utils_os.createDirectory(geneOutFullPath)
utils_os.createDirectory(recOutFullPath)
# read in the sequences
f_handle = open(args.fastaFile, "rU")
f_dict = SeqIO.to_dict(SeqIO.parse(f_handle, "fasta"))
f_handle.close()
# only want exons for now. unfortunately can't limit by strand so have to do that after the fact
# we can speed things up a bit by limiting to just the chromosomes we have sequences for
limit_info = dict(gff_id=f_dict.keys(), gff_type=["exon"])
if args.verbose:
print "data we are searching for in gff: " + str(limit_info)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-d', '--fastaDir', help='directory containing fasta files to limit. Either -d or -s required.')
parser.add_argument('-s', '--singleFile', help='fasta file to limit. Either -d or -s required.')
parser.add_argument('-o', '--outDir', help='directory to output files. Will be created if it does not exist.', required=True)
parser.add_argument('-t', '--juncType', help='type of junction to limit to', choices=['reg', 'rev', 'dup'], required=True)
parser.add_argument('-b', '--bounds', help='type of junction to limit to', choices=['all', 'within', 'between'], default='all')
parser.add_argument('-p', '--postpend', help='text to add to end of output file names', required=True)
parser.add_argument('-v', '--verbose', help='print info about data obtained', action='store_true')
args = parser.parse_args()
if args.fastaDir and args.singleFile:
sys.exit("Only 1 of -d and -s can be specified")
# create output directory if it does not exist
utils_os.createDirectory(args.outDir)
# fasta junction ids look like chr10|TTC40:134751179|MYC1:134722640|reg|-
# where we are interested in TTC40, MYC1, and reg
id_patt = re.compile(".+?\|(.+?):.+?\|(.+?):.+?\|(.+?)\|.*")
if args.fastaDir:
# loop through files directory
for f in os.listdir(args.fastaDir):
if f.endswith(".fa"): # only parse if this is a fasta file
writeLimitedFasta('/'.join([args.fastaDir,f]))
elif args.singleFile:
writeLimitedFasta(args.singleFile)
