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ToposCreateTokens.py
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ToposCreateTokens.py
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from __future__ import print_function
import sys
import json
import argparse
# Usage: python ToposCreateTokens.py runNN-YYYYMMDD-miseq MIDS-miseq.txt SAMPLE-files
# Create pool: topos newPool
# Upload tokens: uploadFileAsToken [POOLNAME] [FILENAME] #
# or: uploadFilesInDirAsTokens [POOLNAME] [DIRNAME]
# Token pool is here: https://topos.grid.sara.nl/4.1/pools/POOLNAME/
def getSamples(myfile):
'''
Description: read sample names and return a list of all the file names
In: SAMPLE-file
Out: list
'''
samples = list()
try:
fh = open(myfile)
except:
sys.exit("cannot open file: " + myfile)
for line in fh:
line = line.strip()
samples.append(line)
fh.close()
return(samples)
def writeJson(f, js):
'''
Description: write json code to a file
In: f (filename str), js (json dict)
Out: -
'''
try:
fhOut = open(f, "w")
except:
sys.exit("cannot create file: " + f)
print(json.dumps(js), file=fhOut)
fhOut.close()
print("Wrote", f, "to disk")
def guessCellAndOrganism(myfile):
'''
Description: the file name usually contains the celltype and organism, guess which one it is
In: filename (str)
Out: cell (str), organism (str), celltype (str)
'''
cell = "UNKNOWN"
organism = "UNKNOWN"
if "human" in myfile:
organism = "human"
elif "mouse" in myfile:
organism = "mouse"
if "IGH" in myfile or "BCRh" in myfile or "IgM" in myfile or "IgG" in myfile or "IgD" in myfile:
cell = "IGH"
elif "TCRb" in myfile:
cell = "TRB"
elif "TCRa" in myfile:
cell = "TRA"
elif "IGL" in myfile or "BCRl" in myfile:
cell = "IGL"
elif "IGK" in myfile or "BCRk" in myfile:
cell = "IGK"
elif "HLA" in myfile:
cell = "HLA"
celltype = cell + "_" + organism.upper()
return(cell, organism, celltype)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Create ToPoS tokens (json)')
parser.add_argument('-r', '--run', default='runNN-YYYYMMDD-miseq', type=str, help='Sequence run directory (default: %(default)s)')
parser.add_argument('-m', '--mids', default='MIDS-miseq-umi.txt', type=str, help='MID scheme file name, e.g. MIDS-miseq-umi MIDS-miseq.txt MIDS-miseq-race-v2.txt (default: %(default)s)')
parser.add_argument('-o', '--outdir', default='results-tbcell', type=str, help='Output directory (default: %(default)s)')
parser.add_argument('-p', '--protocol', default='paired', type=str, help='single or paired (default: %(default)s)')
parser.add_argument('-b', '--barcodes', default="yes", type=str, help='Were additional internal MIDs used? yes/no (default: %(default)s)')
parser.add_argument('-u', '--umis', default="yes", type=str, help='Were UMIs used? yes/roche/race/no (default: %(default)s)')
parser.add_argument('-mm', '--mismatches', default=0, type=str, help='Number of mismatches in CDR3 extraction (default: %(default)s)')
parser.add_argument('-s', '--seqlength', default=0, type=str, help='Filter on sequence length (default: %(default)s)')
parser.add_argument('-c', '--cregion', default="no", type=str, help='Mask C-region (default: %(default)s)')
parser.add_argument("sample_files", type=str, nargs='+', help='Path(s) to SAMPLE file(s)')
args = parser.parse_args()
if args.run == "runNN-YYYYMMDD-miseq":
parser.print_help()
exit()
for myfile in args.sample_files:
outfile = "tokens/" + myfile.split("/")[-1] + ".json"
(cell, organism, celltype) = guessCellAndOrganism(myfile)
js = {
"run": args.run,
"cell": cell,
"organism": organism,
"celltype": celltype,
"mids": args.mids,
"outdir": args.outdir,
"protocol": args.protocol,
"barcodes": args.barcodes,
"umis": args.umis,
"mismatches": args.mismatches,
"seqlength": args.seqlength,
"cregion": args.cregion
}
js["samples"] = getSamples(myfile)
writeJson(outfile, js)