Merge pull request #117 from briney/development

Development

.gitignore

@@ -56,5 +56,7 @@ docs/_build/
 # PyBuilder
 target/
 
+.vscode
+
 *.sublime-*
 .DS_Store

MANIFEST.in

@@ -32,6 +32,7 @@ include abstar/assigners/germline_dbs/tcr/human/*
 include abstar/assigners/germline_dbs/tcr/human/blast/*
 include abstar/assigners/germline_dbs/tcr/human/ungapped/*
 include abstar/assigners/germline_dbs/tcr/human/imgt_gapped/*
+include abstar/preprocess/*
 include abstar/test_data/*
 include abstar/utils/*
 include abstar/utils/queue/*

abstar/__init__.py

@@ -1,8 +1,9 @@
 import warnings
 from Bio import BiopythonWarning
-warnings.simplefilter('ignore', BiopythonWarning)
 
-from .core.abstar import run, run_standalone, main, parse_arguments, validate_args
+warnings.simplefilter("ignore", BiopythonWarning)
+
+from .core.abstar import run, run_standalone, main, create_parser, validate_args
 from .preprocess import fastqc, adapter_trim, quality_trim
 
 from .version import __version__

abstar/_preprocess/qc.py

@@ -0,0 +1,23 @@
+#!/usr/bin/python
+# filename: qc.py
+
+#
+# Copyright (c) 2023 Bryan Briney
+# License: The MIT license (http://opensource.org/licenses/MIT)
+#
+# 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.
+#
+

abstar/_preprocess/trimming.py

@@ -0,0 +1,23 @@
+#!/usr/bin/python
+# filename: trimming.py
+
+#
+# Copyright (c) 2023 Bryan Briney
+# License: The MIT license (http://opensource.org/licenses/MIT)
+#
+# 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.
+#
+