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"""
script to run RUST as a cli tool
Usage:
RUST <command> [<args>...]
Options:
-h --help Show this screen.
--version Show version.
"""
import RUST
# import sys
# import time
# import traceback
import argparse
def parser():
parser = argparse.ArgumentParser(description="RUST - Ribo-seq Unit Step Transform")
parser.usage = "RUST <command> [<args>]"
subparsers = parser.add_subparsers(help="mode of analysis")
amino = subparsers.add_parser("amino", help="Run RUST on each amino acid")
amino.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
amino.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
amino.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
amino.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
amino.add_argument(
"-P", "--Path", help='path to outputfile, default is "amino"', default="amino"
)
amino.set_defaults(mode="amino")
codon = subparsers.add_parser("codon", help="Run RUST on each codon")
codon.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
codon.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
codon.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
codon.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
codon.add_argument(
"-P", "--Path", help='path to outputfile, default is "codon"', default="codon"
)
codon.set_defaults(mode="codon")
nucleotide = subparsers.add_parser("nucleotide", help="Run RUST on each nucleotide")
nucleotide.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
nucleotide.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
nucleotide.add_argument(
"-o", "--offset", help="nucleotide offset to A-site", type=int
)
nucleotide.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
nucleotide.add_argument(
"-P",
"--Path",
help='path to outputfile, default is "nucleotide"',
default="nucleotide",
)
nucleotide.set_defaults(mode="nucleotide")
dipeptide = subparsers.add_parser("dipeptide", help="Run RUST on each dipeptide")
dipeptide.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
dipeptide.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
dipeptide.add_argument(
"-o", "--offset", help="nucleotide offset to A-site", type=int
)
dipeptide.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
dipeptide.add_argument(
"-P",
"--Path",
help='path to outputfile, default is "dipeptide"',
default="dipeptide",
)
dipeptide.set_defaults(mode="dipeptide")
tripeptide = subparsers.add_parser("tripeptide", help="Run RUST on each tripeptide")
tripeptide.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
tripeptide.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
tripeptide.add_argument(
"-o", "--offset", help="nucleotide offset to A-site", type=int
)
tripeptide.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
tripeptide.add_argument(
"-P",
"--Path",
help='path to outputfile, default is "tripeptide"',
default="tripeptide",
)
tripeptide.set_defaults(mode="tripeptide")
predict = subparsers.add_parser(
"predict",
help="Correlation between observed and predicted profiles from CDS start + 120 to CDS stop - 60",
)
predict.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
predict.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
predict.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
predict.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
predict.add_argument(
"-P",
"--Path",
help='path to outputfile, default is "amino"',
default="predict_profiles",
)
predict.add_argument("-r", "--rustfile", help="path to rust file produced by codon")
predict.add_argument(
"-p",
"--profiles",
action="store_true",
help="writes all profiles in csv files, may produce >10,000 files",
default=False,
)
predict.set_defaults(mode="predict")
synergy = subparsers.add_parser(
"synergy",
help="Identifies tripeptides that are candidates for synergistic interactions",
)
synergy.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
synergy.add_argument(
"--aa", help='path to file produced from "rust_amino"', required=True
)
synergy.add_argument(
"--tri", help='path to file produced from "rust_tripeptide"', required=True
)
synergy.add_argument(
"-P",
"--Path",
help='path to outputfile, default is "synergy"',
default="synergy",
)
synergy.set_defaults(mode="synergy")
plot = subparsers.add_parser(
"plot", help="Plot observed and predicted ribosome profiles"
)
plot.add_argument(
"-t",
"--transcriptome",
help="fasta file of transcripts, CDS start and end may be provided on description line using tab separation e.g. >NM_0001 10 5000, otherwise it searches for longest ORF"
", required=True",
)
plot.add_argument(
"-a",
"--alignment",
help="sorted bam file of transcriptome alignments",
required=True,
)
plot.add_argument("-o", "--offset", help="nucleotide offset to A-site", type=int)
plot.add_argument(
"-l",
"--lengths",
help="lengths of footprints included, for example 28:32 is 28,29,30,31,32",
)
plot.add_argument(
"-P", "--Path", help='path to outputfile, default is "amino"', default="plot"
)
plot.add_argument(
"-i",
"--identifier",
help='Specific transcript to plot (Use of unique identifier is sufficient for example "NM_031946"',
required=True,
)
plot.add_argument(
"-r",
"--rustfile",
help='path to file produced from "rust_codon"',
required=True,
)
plot.set_defaults(mode="plot")
parser.add_argument("-v", "--version", action="version", version="%(prog)s 1.3.0")
args = parser.parse_args()
return args
def main():
args = parser()
if args.mode == "amino":
RUST.amino.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "codon":
RUST.codon.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "nucleotide":
RUST.nucleotide.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "dipeptide":
RUST.dipeptide.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "tripeptide":
RUST.tripeptide.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "predict":
RUST.predict_profiles.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "synergy":
RUST.synergy.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
elif args.mode == "plot":
RUST.plot_transcript.main(args)
print(f"RUST successfully ran and outputted to {args.Path}")
else:
raise Exception(
"Weird. RUST ran to end of program without triggering a pipeline or raising an error"
)
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