initial

.gitignore

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+.vscode/*
+venv/*
+LargeDataSet.mz.sqlite
+*.png
+*.svg
+*.html

README.md

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+PSM Validation Tool
+===================
+
+The PSM validation tool verifies PSM scans against the ion fragmentation of the associated peptide squence.
+
+Inputs
+------
+
+- MZSQLite database generated in a Galaxy workflow
+- Tabular file of peptide sequences
+
+By default the tool will fragment peptde into
+
+- b and y ions
+- b-H2O, b-NH3, y-H2O, y-NH3
+- Internals
+
+You can disable internals and neutral loss ions.
+
+Output
+------
+
+A self-contained HTML report that includes:
+
+- All PSMs for peptides of interest with PSM identifiers
+- PSM PeptideShaker scores are presented
+- MSMS interactive graphs with
+    - PSM scan mz and intensities
+    - All matching ion fragments
+- Ion fragment table 
+    - Color coded for matching fragments
+    - Internal values and color coded for internal matches

requirements.txt

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+appdirs==1.4.4
+certifi==2020.6.20
+cycler==0.10.0
+jedi==0.17.2
+kiwisolver==1.2.0
+lxml==4.5.2
+numpy==1.19.2
+parso==0.7.1
+Pillow==7.2.0
+plotly==4.10.0
+prompt-toolkit==3.0.7
+ptpython==3.0.5
+Pygments==2.7.0
+pyparsing==2.4.7
+pyteomics==4.3.2
+python-dateutil==2.8.1
+retrying==1.3.3
+six==1.15.0
+wcwidth==0.2.5

setup.py

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+import setuptools
+
+_pkg_version = "1.0.0"
+_author = "Thomas McGowan"
+_author_email = "[email protected]"
+_license = "MIT"
+_repo = "https://github.umn.edu/mcgo0092/psm_fragments.git"
+
+
+setuptools.setup(
+    name="psm_fragments",
+    version=f"{_pkg_version}",
+    packages=["psmfragmentation"],
+    install_requires=["pyteomics", "plotly"],
+    description="Score PSMs with fragmentation quality check",
+    author=f"{_author}",
+    author_email=f"{_author_email}",
+    url="f{_repo}",
+    download_url=f"{_repo}/archive/v_{_pkg_version}.tar.gz",
+    license=f"{_license}",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+        "Intended Audience :: Science/Research",
+    ],
+    python_requires=">=3.6",
+)

tests/data/peptide_sequences.txt

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+YLGTGPEAGLPYGANK
+MAGNGGDAALALLLLDR
+RGPEQTQGNFGDQELIR
+KQQTVTLLPAADLDDFSK
+IGMEVTPSGTWLTYTGAIK
+GQGVPINTNSSPDDQIGYYRR
+RPQGLPNNTASWFTALTQHGK
+MAGNGGDAALALLLLDRLNQLESK
+RPQGLPNNTASWFTALTQHGKEDLKFPR