adding a script to generate the sequencing_speed_over_time plot only

MANIFEST.in

@@ -1,3 +1,4 @@
 include extra/color_options.txt
 include scripts/test.sh
+include scripts/sequencing_speed_only.py
 include README.md

scripts/sequencing_speed_only.py

@@ -0,0 +1,53 @@
+from nanoget import get_input
+from nanoplotter.timeplots import sequencing_speed_over_time
+from argparse import ArgumentParser
+from os import path
+
+
+def main():
+    args = get_args()
+    df = get_input(source="summary", files=args.summary)[["lengths", "start_time", "duration"]]
+    sequencing_speed_over_time(dfs=df,
+                               path=path.join(args.outdir, args.prefix),
+                               figformat=args.format,
+                               title=args.title)
+
+
+def get_args():
+    parser = ArgumentParser(
+        description="Creates sequencing speed over time plot from summary file.".upper(),
+        add_help=False)
+    general = parser.add_argument_group(
+        title='General options')
+    general.add_argument("-h", "--help",
+                         action="help",
+                         help="show the help and exit")
+    general.add_argument("-o", "--outdir",
+                         help="Specify directory in which output has to be created.",
+                         default=".")
+    general.add_argument("-p", "--prefix",
+                         help="Specify an optional prefix to be used for the output files.",
+                         default="",
+                         type=str)
+    general.add_argument("--summary",
+                         help="Data is in one or more summary file(s) from albacore or guppy.",
+                         nargs='+',
+                         metavar="file",
+                         required=True)
+    visual = parser.add_argument_group(
+        title='Options for customizing the plots created')
+    visual.add_argument("-f", "--format",
+                        help="Specify the output format of the plots.",
+                        default="png",
+                        type=str,
+                        choices=['eps', 'jpeg', 'jpg', 'pdf', 'pgf', 'png', 'ps',
+                                 'raw', 'rgba', 'svg', 'svgz', 'tif', 'tiff'])
+    visual.add_argument("--title",
+                        help="Add a title to all plots, requires quoting if using spaces",
+                        type=str,
+                        default=None)
+    return parser.parse_args()
+
+
+if __name__ == '__main__':
+    main()