Isolated command-line interface from the __main__.py file.

nmrstarlib/cli.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+nmrstarlib command-line interface
+
+Usage:
+    nmrstarlib -h | --help
+    nmrstarlib --version
+    nmrstarlib convert (<from_path> <to_path>) [--from_format=<format>] [--to_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose]
+    nmrstarlib csview <starfile_path> [--amino_acids=<aa>] [--atoms=<at>] [--csview_outfile=<path>] [--csview_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose]
+    nmrstarlib plsimulate (<from_path> <to_path> <spectrum>) [--from_format=<format>] [--to_format=<format>] [--plsplit=<%>] [--distribution=<func>] [--H=<value>] [--C=<value>] [--N=<value>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--spectrum_descriptions=<path>] [--verbose]
+
+Options:
+    -h, --help                      Show this screen.
+    --version                       Show version.
+    --verbose                       Print what files are processing.
+    --from_format=<format>          Input file format, available formats: nmrstar, json [default: nmrstar].
+    --to_format=<format>            Output file format, available formats: nmrstar, json [default: json].
+    --nmrstar_version=<version>     Version of NMR-STAR format to use, available: 2, 3 [default: 3].
+    --bmrb_url=<url>                URL to BMRB REST interface [default: http://rest.bmrb.wisc.edu/bmrb/NMR-STAR3/].
+    --amino_acids=<aa>              Comma-separated amino acid three-letter codes.
+    --atoms=<at>                    Comma-separated BMRB atom codes.
+    --csview_outfile=<path>         Where to save chemical shifts table.
+    --csview_format=<format>        Format to which save chemical shift table [default: svg].
+    --plsplit=<%>                   How to split peak list into chunks by percent [default: 100].
+    --spectrum_descriptions=<path>  Path to custom spectrum descriptions file.
+    --distribution=<func>           Statistical distribution function [default: normal].
+    --H=<value>                     Statistical distribution parameter(s) for H dimension.
+    --C=<value>                     Statistical distribution parameter(s) for C dimension.
+    --N=<value>                     Statistical distribution parameter(s) for N dimension.
+"""
+
+import collections
+
+from . import nmrstarlib
+from . import converter
+from . import csviewer
+from . import noise
+from . import translator
+
+
+def cli(cmdargs):
+
+    nmrstarlib.BMRB_REST = cmdargs["--bmrb_url"]
+    nmrstarlib.VERBOSE = cmdargs["--verbose"]
+    nmrstarlib.NMRSTAR_VERSION = cmdargs["--nmrstar_version"]
+
+    if cmdargs["convert"]:
+
+        nmrstar_file_translator = translator.StarFileToStarFile(from_path=cmdargs["<from_path>"],
+                                                                to_path=cmdargs["<to_path>"],
+                                                                from_format=cmdargs["--from_format"],
+                                                                to_format=cmdargs["--to_format"])
+
+        nmrstar_converter = converter.Converter(file_generator=nmrstar_file_translator)
+        nmrstar_converter.convert()
+
+    elif cmdargs["csview"]:
+        aminoacids = cmdargs["--amino_acids"].split(",") if cmdargs["--amino_acids"] else []
+        atoms = cmdargs["--atoms"].split(",") if cmdargs["--atoms"] else []
+
+        chemshift_viewer = csviewer.CSViewer(from_path=cmdargs["<starfile_path>"],
+                                             amino_acids=aminoacids,
+                                             atoms=atoms,
+                                             filename=cmdargs["--csview_outfile"],
+                                             csview_format=cmdargs["--csview_format"])
+        chemshift_viewer.csview(view=True)
+
+    elif cmdargs["plsimulate"]:
+        if cmdargs["--spectrum_descriptions"]:
+            nmrstarlib.update_constants(spectrum_descriptions_cfg=cmdargs["--spectrum_descriptions"])
+
+        plsplit = tuple(float(i) for i in cmdargs["--plsplit"].split(","))
+        distribution_name = cmdargs["--distribution"]
+        distribution_parameter_names = noise.distributions[distribution_name]["parameters"]
+
+        if not distribution_parameter_names:
+            parameters = None
+        else:
+            parameters = collections.defaultdict(list)
+
+            for dim in ("H", "N", "C"):
+                params = cmdargs["--{}".format(dim)]
+                if params is None:
+                    for param_name in distribution_parameter_names:
+                        parameters["{}_{}".format(dim, param_name)].append(None)
+                else:
+                    params = params.split(",")
+                    if len(params) > len(distribution_parameter_names):
+                        raise ValueError("Inconsistent number of parameters provided.")
+
+                    for param, param_name in zip(params, distribution_parameter_names):
+                        parameters["{}_{}".format(dim, param_name)].extend([float(val) if val else None for val in param.split(":")])
+
+            # fill with None values for parameters that have missing values
+            for param_name, param_values in parameters.items():
+                given_values = list(param_values)
+                missing_values = [None for _ in range(len(plsplit) - len(param_values))]
+                param_values = given_values + missing_values
+                parameters[param_name] = tuple(param_values)
+
+        noise_generator = noise.NoiseGenerator(parameters=parameters, distribution_name=distribution_name)
+
+        peaklist_file_translator = translator.StarFileToPeakList(from_path=cmdargs["<from_path>"],
+                                                                 to_path=cmdargs["<to_path>"],
+                                                                 from_format=cmdargs["--from_format"],
+                                                                 to_format=cmdargs["--to_format"],
+                                                                 spectrum_name=cmdargs["<spectrum>"],
+                                                                 plsplit=plsplit,
+                                                                 noise_generator=noise_generator,
+                                                                 nmrstar_version=cmdargs["--nmrstar_version"])
+
+        nmrstar_to_peaklist_converter = converter.Converter(file_generator=peaklist_file_translator)
+        nmrstar_to_peaklist_converter.convert()
+
+#
+# args = docopt.docopt(__doc__, version=__version__)
+# cli(args)