Merge branch 'master' into logs

Makefile

@@ -14,7 +14,7 @@ style:
 
 ## format:    auto-reformat code with Black
 format:
-	black --line-length=99 *.py lusSTR/scripts/*.py lusSTR/wrappers/*.py lusSTR/tests/test_*.py
+	black --line-length=99 *.py lusSTR/cli/gui.py lusSTR/scripts/*.py lusSTR/wrappers/*.py lusSTR/tests/test_*.py
 
 ## devenv:    configure a development environment
 devenv:

README.md

@@ -5,6 +5,10 @@ lusSTR is a tool written in Python to convert NGS sequence data of forensic STR
 Further, lusSTR can perform filtering and stutter identification using the CE allele, the LUS+ allele, or the bracketed sequence form for autosomal loci and create files for direct input into three probabilistic genotyping software packages, EuroForMix (CE and LUS+), MPSproto (NGS), and STRmix (CE and NGS). 
 
 lusSTR also processes SNP data from the Verogen ForenSeq and Kintelligence panels and create evidence and/or reference files for use in EFM. See the below section ```SNP Data Processing``` for more information.
+____
+
+**lusSTR is available as a command line tool or as a GUI.**
+____
 
 This Python package has been written for use with either:  
 * ForenSeq Signature Prep panel
@@ -42,6 +46,17 @@ make devenv
 
 ## Usage
 
+## *GUI*
+
+Once lusSTR has been installed, the GUI can be started with the command: 
+```
+lusstr gui
+```
+All lusSTR settings for either the STR pipeline or the SNP pipeline can be specified after selecting the desired pipeline tab.
+____
+
+## *Command line interface*
+
 lusSTR accomodates four different input formats:  
 (1) UAS Sample Details Report, UAS Sample Report, and UAS Phenotype Report (for SNP processing) in .xlsx format (a single file or directory containing multiple files)  
 (2) STRait Razor v3 output with one sample per file (a single file or directory containing multiple files)  

lusSTR/cli/__init__.py

@@ -1,33 +1,40 @@
 import argparse
+import importlib.resources
+import streamlit.web.cli as stcli
+import sys
 import lusSTR
 from lusSTR.cli import config
 from lusSTR.cli import strs
 from lusSTR.cli import snps
-import snakemake
-
+from lusSTR.cli import gui
 
 mains = {
     "config": config.main,
     "strs": strs.main,
-    "snps": snps.main
+    "snps": snps.main,
+    "gui": gui.main
 }
 
 subparser_funcs = {
     "config": config.subparser,
     "strs": strs.subparser,
-    "snps": snps.subparser
+    "snps": snps.subparser,
+    "gui": gui.subparser
 }
 
-
 def main(args=None):
-    if args is 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
-
+    elif args.subcmd == "gui":
+        gui_path = importlib.resources.files("lusSTR") / "cli" / "gui.py"
+        sys.argv = ["streamlit", "run", str(gui_path)]
+        sys.exit(stcli.main())
+    else:
+        mainmethod = mains[args.subcmd]
+        result = mainmethod(args)
+        return result
 
 def get_parser():
     parser = argparse.ArgumentParser()
@@ -39,3 +46,6 @@ def get_parser():
     for func in subparser_funcs.values():
         func(subparsers)
     return parser
+
+if __name__ == "__main__":
+    main()