<reponame>nick-youngblut/find_differential_primers<gh_stars>10-100
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""subcmd_plot.py

Provides the plot subcommand for pdp

(c) The James Hutton Institute 2017-19

Author: <NAME>
Contact: <EMAIL>

<NAME>,
Information and Computing Sciences,
James Hutton Institute,
Errol Road,
Invergowrie,
Dundee,
DD2 5DA,
Scotland,
UK

The MIT License

Copyright (c) 2017-19 The James Hutton Institute
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

from diagnostic_primers import plot
from diagnostic_primers.scripts.tools import create_output_directory


def subcmd_plot(args, logger):
    """Generate graphical output for pdp."""
    # Create output directory, if required
    create_output_directory(args.outdir, args.pl_force, logger)

    # Plot marker amplicon scatterplot of distance
    if args.markerscatter is not None:
        logger.info("Generating scatterplot of marker distances")
        plot.markerscatter(args.markerscatter, args.outdir)

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""subcmd_plot.py

Provides the plot subcommand for pdp

(c) The James Hutton Institute 2017-19

Author: <NAME>
Contact: <EMAIL>

<NAME>,
Information and Computing Sciences,
James Hutton Institute,
Errol Road,
Invergowrie,
Dundee,
DD2 5DA,
Scotland,
UK

The MIT License

Copyright (c) 2017-19 The James Hutton Institute
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
"""

from diagnostic_primers import plot
from diagnostic_primers.scripts.tools import create_output_directory


def subcmd_plot(args, logger):
    """Generate graphical output for pdp."""
    # Create output directory, if required
    create_output_directory(args.outdir, args.pl_force, logger)

    # Plot marker amplicon scatterplot of distance
    if args.markerscatter is not None:
        logger.info("Generating scatterplot of marker distances")
        plot.markerscatter(args.markerscatter, args.outdir)
#!/usr/bin/env python3 # -*- coding: utf-8 -*- subcmd_plot.py  Provides the plot subcommand for pdp  (c) The James Hutton Institute 2017-19  Author: <NAME> Contact: <EMAIL>  <NAME>, Information and Computing Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, Scotland, UK  The MIT License  Copyright (c) 2017-19 The James Hutton Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Generate graphical output for pdp. # Create output directory, if required # Plot marker amplicon scatterplot of distance