Merge pull request #1 from bigbio/dev

Adding commands

.codacy.yml

@@ -0,0 +1,17 @@
+engines:
+  eslint:
+    enabled: true
+  pylint:
+    enabled: true
+
+ignore_patterns:
+  - "tests/*"
+
+eslint:
+  enabled: true
+  config_file: .eslintrc.json
+  exclude_paths:
+    - 'tests/**'
+
+exclude_paths:
+    - 'tests/**'

.github/workflows/python-app.yml

@@ -28,6 +28,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.github/workflows/python-package.yml

@@ -29,6 +29,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        python setup.py install
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+*.tsv
+*.csv
+*_df.csv

README.md

@@ -1,2 +1,45 @@
 # pyquantms
-A python library with script and helpers classes for quantms workflow
+[![Python application](https://github.com/bigbio/pyquantms/actions/workflows/python-app.yml/badge.svg)](https://github.com/bigbio/pyquantms/actions/workflows/python-app.yml)
+[![Python package](https://github.com/bigbio/pyquantms/actions/workflows/python-package.yml/badge.svg)](https://github.com/bigbio/pyquantms/actions/workflows/python-package.yml)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ea6903630b3a4d15b674a16b8ce594a7)](https://app.codacy.com/gh/bigbio/pyquantms/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![PyPI version](https://badge.fury.io/py/pyquantms.svg)](https://badge.fury.io/py/pyquantms)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+Python package with scripts and functions for the [quantms workflow](https://github.com/bigbio/quantms) for the analysis of quantitative proteomics data.
+
+The package is available on PyPI: [pyquantms](https://pypi.org/project/pyquantms/)
+```
+pip install pyquantms
+```
+
+## Available Scripts 
+
+The following functionalities are available in the package:
+
+### Diann scripts
+
+- `dianncfg` - Create a configuration file for Diann including enzymes, modifications, and other parameters.
+- `diann2mztab` - Convert Diann output to mzTab format. In addition, convert DIA-NN output to MSstats, Triqler or mzTab.
+    The output formats are used for quality control and downstream analysis in quantms.
+
+### SDRF scripts
+
+- `openms2sample` - Extra sample information from OpenMS experimental design file. An example of OpenMS experimental design file is available [here](https://github.com/bigbio/pyquantms/blob/dev/tests/test_data/BSA_design_urls.tsv).
+- `checksamplesheet` - Check the sample sheet for errors and inconsistencies. The experimental design coult be an OpenMS experimental design file or and SDRF file. 
+
+### ms2rescore scripts
+
+- `ms2rescore` - Rescore MS2 spectra using the MS2PIP model. The output is a mzML file with the rescored MS2 spectra.
+
+### Features to percolator scripts
+
+- `sage2feature` - The add_sage_feature function enhances an idXML file by appending additional features from a Sage feature table, excluding those generated by 'psm_file'.
+
+### Other scripts
+
+- `psmconvert` - The convert_psm function converts peptide spectrum matches (PSMs) from an idXML file to a CSV file, optionally filtering out decoy matches. It extracts and processes data from both the idXML and an associated spectra file, handling multiple search engines and scoring systems.
+- `mzmlstats` - The `mzmlstats` processes mass spectrometry data files in either `.mzML` or `Bruker .d` formats to extract and compile statistics about the spectra. It supports generating detailed or ID-only CSV files based on the spectra data.
+
+## Contributions and issues
+
+Contributions and issues are welcome. Please, open an issue in the [GitHub repository](https://github.com/bigbio/quantms) or PR in the [GitHub repository](https://github.com/bigbio/pyquantms).

pyproject.toml

@@ -12,7 +12,11 @@ build-backend = "setuptools.build_meta"
 click = ">=7.0"
 pydantic = ">=1.10,<2"
 python = "^3.7"
-sdrf_pipelines = ">=0.0.26"
+sdrf-pipelines = ">=0.0.26"
+pyopenms = ">=2.6.0"
+ms2rescore = ">=3.0.2"
+psm-utils = "==0.8.0"
+pandas = ">=1.0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "*"