Snakemake workflow (#52)

MANIFEST.in

@@ -1,10 +1,12 @@
 include versioneer.py
 include lusSTR/_version.py
-include lusSTR/filters.json
-include lusSTR/str_markers.json
-include lusSTR/snp_data.json
-include lusSTR/filters.json
+include lusSTR/data/filters.json
+include lusSTR/data/str_markers.json
+include lusSTR/data/snp_data.json
+include lusSTR/data/config.yaml
 include lusSTR/tests/data/*
+include lusSTR/workflows/*
+include lusSTR/wrappers/*
 include lusSTR/tests/data/STRait_Razor_test_output/*
 include lusSTR/tests/data/UAS_bulk_input/*
 include lusSTR/tests/data/snps/*

Makefile

@@ -6,15 +6,15 @@ help: Makefile
 
 ## test:      run the automated test suite and print coverage information
 test:
-	pytest --cov=lusSTR --doctest-modules lusSTR/annot.py lusSTR/tests/test_*.py
+	pytest -m "not snps" --cov=lusSTR --doctest-modules lusSTR/tests/test_*.py
 
 ## style:     check code style
 style:
-	black --line-length=99 --check *.py lusSTR/*.py lusSTR/tests/test_*.py
+	black --line-length=99 --check *.py lusSTR/scripts/*.py lusSTR/wrappers/*.py lusSTR/tests/test_*.py
 
 ## format:    auto-reformat code with Black
 format:
-	black --line-length=99 *.py lusSTR/*.py lusSTR/tests/test_*.py
+	black --line-length=99 *.py lusSTR/scripts/*.py lusSTR/wrappers/*.py lusSTR/tests/test_*.py
 
 ## devenv:    configure a development environment
 devenv:

lusSTR/__init__.py

@@ -10,14 +10,17 @@
 # Development Center.
 # -------------------------------------------------------------------------------------------------
 
-from lusSTR import annot
-from lusSTR import marker
-from lusSTR import repeat
-from lusSTR import format
-from lusSTR import snps
-from lusSTR import filter
+from pkg_resources import resource_filename
 from lusSTR import cli
-from ._version import get_versions
+from lusSTR._version import get_versions
 
 __version__ = get_versions()["version"]
 del get_versions
+
+
+def snakefile(workflow="strs"):
+    return resource_filename("lusSTR", f"workflows/{workflow}.smk")
+
+
+def wrapper(label):
+    return resource_filename("lusSTR", f"wrappers/{label}.py")

lusSTR/cli/__init__.py

@@ -0,0 +1,41 @@
+import argparse
+import lusSTR
+from lusSTR.cli import config
+from lusSTR.cli import strs
+from lusSTR.cli import snps
+import snakemake
+
+
+mains = {
+    "config": config.main,
+    "strs": strs.main,
+    "snps": snps.main
+}
+
+subparser_funcs = {
+    "config": config.subparser,
+    "strs": strs.subparser,
+    "snps": snps.subparser
+}
+
+
+def main(args=None):
+    if args is None: 
+        args = get_parser().parse_args()
+    if args.subcmd is None:
+        get_parser().parse_args(["-h"])
+    mainmethod = mains[args.subcmd]
+    result = mainmethod(args)
+    return result
+
+
+def get_parser():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-v", "--version", action="version", version="lusSTR v" + lusSTR.__version__
+    )
+    subcommandstr = ", ".join(sorted(subparser_funcs.keys()))
+    subparsers = parser.add_subparsers(dest="subcmd", metavar="subcmd", help=subcommandstr)
+    for func in subparser_funcs.values():
+        func(subparsers)
+    return parser