From 134b8bdb6f391844e64dc1a76ae6915f6590b7ca Mon Sep 17 00:00:00 2001
From: baer0006 <max.baer@unibas.ch>
Date: Mon, 14 Nov 2022 15:18:43 +0100
Subject: [PATCH] reorganising and adding cli which doesn't work - no clue
there
---
CONTRIBUTING.md => Archive/CONTRIBUTING.md | 0
.../PrimingSitePredictor_main_1.0.0.py | 0
.../cli-primingsitepredictor}/.DS_Store | Bin
.../cli-primingsitepredictor}/.gitignore | 0
.../cli-primingsitepredictor}/install.sh | 0
.../pycli/__init__.py | 0
.../pycli/__main__.py | 0
.../pycli/classmodule.py | 0
.../pycli/funcmodule.py | 0
.../cli-primingsitepredictor}/setup.py | 0
my_file1 => Archive/my_file1 | 0
my_file2 => Archive/my_file2 | 0
.../Example_GTF_Output.GTF | 0
.../RIBlast output example.txt | 0
.../Archive/S288C_YKL166C_TPK3_coding.fa | 0
.../Yeast testfiles}/Archive/dbRNA.fa | 0
.../Yeast testfiles}/Archive/queryRNA.fa | 0
.../Yeast testfiles}/dbRNA_test.fa | 0
.../Yeast testfiles}/queryRNA_test.fa | 0
.../README.md => README.md | 0
.../__init__.py | 0
.../__pycache__/__init__.cpython-39.pyc | Bin 0 -> 229 bytes
.../__pycache__/__main__.cpython-39.pyc | Bin 0 -> 547 bytes
primingsitepredictor/classmodule.py | 6 +++++
primingsitepredictor/cli.py | 21 ++++++++++++++++++
primingsitepredictor/funcmodule.py | 3 +++
primingsitepredictor/main.py | 17 ++++++++++++++
setup.py | 15 +++++++++++++
28 files changed, 62 insertions(+)
rename CONTRIBUTING.md => Archive/CONTRIBUTING.md (100%)
rename PrimingSitePredictor_main_1.0.0.py => Archive/PrimingSitePredictor_main_1.0.0.py (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/.DS_Store (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/.gitignore (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/install.sh (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/pycli/__init__.py (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/pycli/__main__.py (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/pycli/classmodule.py (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/pycli/funcmodule.py (100%)
rename {cli-primingsitepredictor => Archive/cli-primingsitepredictor}/setup.py (100%)
rename my_file1 => Archive/my_file1 (100%)
rename my_file2 => Archive/my_file2 (100%)
rename Example_GTF_Output.GTF => In -and- Output examples/Example_GTF_Output.GTF (100%)
rename RIBlast output example.txt => In -and- Output examples/RIBlast output example.txt (100%)
rename {Yeast testfiles => In -and- Output examples/Yeast testfiles}/Archive/S288C_YKL166C_TPK3_coding.fa (100%)
rename {Yeast testfiles => In -and- Output examples/Yeast testfiles}/Archive/dbRNA.fa (100%)
rename {Yeast testfiles => In -and- Output examples/Yeast testfiles}/Archive/queryRNA.fa (100%)
rename {Yeast testfiles => In -and- Output examples/Yeast testfiles}/dbRNA_test.fa (100%)
rename {Yeast testfiles => In -and- Output examples/Yeast testfiles}/queryRNA_test.fa (100%)
rename cli-primingsitepredictor/README.md => README.md (100%)
rename README.txt => primingsitepredictor/__init__.py (100%)
create mode 100644 primingsitepredictor/__pycache__/__init__.cpython-39.pyc
create mode 100644 primingsitepredictor/__pycache__/__main__.cpython-39.pyc
create mode 100644 primingsitepredictor/classmodule.py
create mode 100644 primingsitepredictor/cli.py
create mode 100644 primingsitepredictor/funcmodule.py
create mode 100644 primingsitepredictor/main.py
create mode 100644 setup.py
diff --git a/CONTRIBUTING.md b/Archive/CONTRIBUTING.md
similarity index 100%
rename from CONTRIBUTING.md
rename to Archive/CONTRIBUTING.md
diff --git a/PrimingSitePredictor_main_1.0.0.py b/Archive/PrimingSitePredictor_main_1.0.0.py
similarity index 100%
rename from PrimingSitePredictor_main_1.0.0.py
rename to Archive/PrimingSitePredictor_main_1.0.0.py
diff --git a/cli-primingsitepredictor/.DS_Store b/Archive/cli-primingsitepredictor/.DS_Store
similarity index 100%
rename from cli-primingsitepredictor/.DS_Store
rename to Archive/cli-primingsitepredictor/.DS_Store
diff --git a/cli-primingsitepredictor/.gitignore b/Archive/cli-primingsitepredictor/.gitignore
similarity index 100%
rename from cli-primingsitepredictor/.gitignore
rename to Archive/cli-primingsitepredictor/.gitignore
diff --git a/cli-primingsitepredictor/install.sh b/Archive/cli-primingsitepredictor/install.sh
similarity index 100%
rename from cli-primingsitepredictor/install.sh
rename to Archive/cli-primingsitepredictor/install.sh
diff --git a/cli-primingsitepredictor/pycli/__init__.py b/Archive/cli-primingsitepredictor/pycli/__init__.py
similarity index 100%
rename from cli-primingsitepredictor/pycli/__init__.py
rename to Archive/cli-primingsitepredictor/pycli/__init__.py
diff --git a/cli-primingsitepredictor/pycli/__main__.py b/Archive/cli-primingsitepredictor/pycli/__main__.py
similarity index 100%
rename from cli-primingsitepredictor/pycli/__main__.py
rename to Archive/cli-primingsitepredictor/pycli/__main__.py
diff --git a/cli-primingsitepredictor/pycli/classmodule.py b/Archive/cli-primingsitepredictor/pycli/classmodule.py
similarity index 100%
rename from cli-primingsitepredictor/pycli/classmodule.py
rename to Archive/cli-primingsitepredictor/pycli/classmodule.py
diff --git a/cli-primingsitepredictor/pycli/funcmodule.py b/Archive/cli-primingsitepredictor/pycli/funcmodule.py
similarity index 100%
rename from cli-primingsitepredictor/pycli/funcmodule.py
rename to Archive/cli-primingsitepredictor/pycli/funcmodule.py
diff --git a/cli-primingsitepredictor/setup.py b/Archive/cli-primingsitepredictor/setup.py
similarity index 100%
rename from cli-primingsitepredictor/setup.py
rename to Archive/cli-primingsitepredictor/setup.py
diff --git a/my_file1 b/Archive/my_file1
similarity index 100%
rename from my_file1
rename to Archive/my_file1
diff --git a/my_file2 b/Archive/my_file2
similarity index 100%
rename from my_file2
rename to Archive/my_file2
diff --git a/Example_GTF_Output.GTF b/In -and- Output examples/Example_GTF_Output.GTF
similarity index 100%
rename from Example_GTF_Output.GTF
rename to In -and- Output examples/Example_GTF_Output.GTF
diff --git a/RIBlast output example.txt b/In -and- Output examples/RIBlast output example.txt
similarity index 100%
rename from RIBlast output example.txt
rename to In -and- Output examples/RIBlast output example.txt
diff --git a/Yeast testfiles/Archive/S288C_YKL166C_TPK3_coding.fa b/In -and- Output examples/Yeast testfiles/Archive/S288C_YKL166C_TPK3_coding.fa
similarity index 100%
rename from Yeast testfiles/Archive/S288C_YKL166C_TPK3_coding.fa
rename to In -and- Output examples/Yeast testfiles/Archive/S288C_YKL166C_TPK3_coding.fa
diff --git a/Yeast testfiles/Archive/dbRNA.fa b/In -and- Output examples/Yeast testfiles/Archive/dbRNA.fa
similarity index 100%
rename from Yeast testfiles/Archive/dbRNA.fa
rename to In -and- Output examples/Yeast testfiles/Archive/dbRNA.fa
diff --git a/Yeast testfiles/Archive/queryRNA.fa b/In -and- Output examples/Yeast testfiles/Archive/queryRNA.fa
similarity index 100%
rename from Yeast testfiles/Archive/queryRNA.fa
rename to In -and- Output examples/Yeast testfiles/Archive/queryRNA.fa
diff --git a/Yeast testfiles/dbRNA_test.fa b/In -and- Output examples/Yeast testfiles/dbRNA_test.fa
similarity index 100%
rename from Yeast testfiles/dbRNA_test.fa
rename to In -and- Output examples/Yeast testfiles/dbRNA_test.fa
diff --git a/Yeast testfiles/queryRNA_test.fa b/In -and- Output examples/Yeast testfiles/queryRNA_test.fa
similarity index 100%
rename from Yeast testfiles/queryRNA_test.fa
rename to In -and- Output examples/Yeast testfiles/queryRNA_test.fa
diff --git a/cli-primingsitepredictor/README.md b/README.md
similarity index 100%
rename from cli-primingsitepredictor/README.md
rename to README.md
diff --git a/README.txt b/primingsitepredictor/__init__.py
similarity index 100%
rename from README.txt
rename to primingsitepredictor/__init__.py
diff --git a/primingsitepredictor/__pycache__/__init__.cpython-39.pyc b/primingsitepredictor/__pycache__/__init__.cpython-39.pyc
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diff --git a/primingsitepredictor/classmodule.py b/primingsitepredictor/classmodule.py
new file mode 100644
index 0000000..31fea4f
--- /dev/null
+++ b/primingsitepredictor/classmodule.py
@@ -0,0 +1,6 @@
+class MyClass():
+ def __init__(self, name):
+ self.name = name
+
+ def say_name(self):
+ print('name is {}'.format(self.name))
diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py
new file mode 100644
index 0000000..cae6bb2
--- /dev/null
+++ b/primingsitepredictor/cli.py
@@ -0,0 +1,21 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Nov 14 14:49:50 2022
+
+@author: baerma
+"""
+import argparse
+
+
+parser = argparse.ArgumentParser(description='Process some integers.')
+parser.add_argument('integers', metavar='N', type=int, nargs='+',
+ help='an integer for the accumulator')
+parser.add_argument('--sum', dest='accumulate', action='store_const',
+ const=sum, default=max,
+ help='sum the integers (default: find the max)')
+
+args = parser.parse_args()
+print(args.accumulate(args.integers))
+
+
+
diff --git a/primingsitepredictor/funcmodule.py b/primingsitepredictor/funcmodule.py
new file mode 100644
index 0000000..180f0d4
--- /dev/null
+++ b/primingsitepredictor/funcmodule.py
@@ -0,0 +1,3 @@
+def my_function(text_to_display):
+ print('text from my_function :: {}'.format(text_to_display))
+
diff --git a/primingsitepredictor/main.py b/primingsitepredictor/main.py
new file mode 100644
index 0000000..e1488c3
--- /dev/null
+++ b/primingsitepredictor/main.py
@@ -0,0 +1,17 @@
+import sys
+#from .classmodule import MyClass
+#from .funcmodule import my_function
+
+def main():
+ print('in main')
+ args = sys.argv[1:]
+ print('count of args :: {}'.format(len(args)))
+ for arg in args:
+ print('passed argument :: {}'.format(arg))
+
+ #my_function('Hello World')
+ #my_object = MyClass('Robin')
+ #my_object.say_name()
+
+if __name__ == '__main__':
+ main()
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..6c3b041
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,15 @@
+from setuptools import setup
+setup(
+ name = 'cli-primingsitepredictor',
+ url = 'https://git.scicore.unibas.ch/zavolan_group/tools/priming-site-predictor/-/tree/main/CLI',
+ author = 'Robin Christen & Max Baer',
+ author_email = 'robin.christen@stud.unibas.ch & max.baer@swisstph.ch',
+ description = 'Command-Line Interface',
+ license = 'MIT,',
+ version = '0.1.0',
+ packages = ['primingsitepredictor'],
+ entry_points = {
+ 'console_scripts': [
+ 'primingsitepredictor = primingsitepredictor.main:main'
+ ]
+ })
--
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