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cfd and donech scores separated as options
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@ravinpoudel
ravinpoudel committed Sep 26, 2021
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192 changes: 99 additions & 93 deletions coverage.xml
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8 changes: 7 additions & 1 deletion guidemaker/cli.py
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Expand Up @@ -59,7 +59,8 @@ def myparser():
help='List of sequence representing restriction enzymes. Default: None.', default=[])
parser.add_argument('--filter_by_locus', nargs="*",
help='List of locus tag. Default: None.', default=[])
parser.add_argument('--doench_efficiency_score',help='Doench et al. 2016 - only for NGG PAM: None.', action='store_true')
parser.add_argument('--doench_efficiency_score',help='Doench et al. 2016 - only for NGG PAM: Default: None.', action='store_true')
parser.add_argument('--cfd_score',help='CFD score for assessing off-target activity of gRNAs: Default: None.', action='store_true')
parser.add_argument('--keeptemp', help="Option to keep intermediate files be kept", action='store_true')
parser.add_argument('--plot', help="Option to genereate guidemaker plots", action='store_true')
parser.add_argument('--config', help="Path to YAML formatted configuration file, default is " +
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if args.doench_efficiency_score:
logging.info("Creating Efficiency Score based on Doench et al. 2016 - only for NGG PAM...")
prettydf = guidemaker.core.get_doench_efficiency_score(df=prettydf, pam_orientation=args.pam_orientation)

if args.cfd_score:
logging.info("Calculating CFD score for assessing off-target activity of gRNAs")
prettydf = guidemaker.core.cfd_score(df=prettydf)

fd_zero = prettydf['Feature distance'].isin([0]).sum()
logging.info("Number of Guides within a gene coordinates i.e. zero Feature distance: %d", fd_zero)
if not os.path.exists(args.outdir):
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