Utility for converting searched mass spec data into a format readable by CAMV
Project description
# PyCAMVerter
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[![Requirements Status](https://requires.io/github/white-lab/pycamverter/requirements.svg?branch=master)](https://requires.io/github/white-lab/pycamverter/requirements/?branch=master)
[![PyPI](https://img.shields.io/pypi/v/pycamverter.svg)](https://pypi.python.org/pypi/pycamverter)
Utility for converting searched mass spec data into a format readable by [CAMV](https://github.com/white-lab/pycamverter/blob/master/README.md).
![pycamverter demo](https://zippy.gfycat.com/CleverGrotesqueErmine.gif)
## Installation
To download a completely packaged Windows executable, visit our [releases page](https://github.com/white-lab/pycamverter/releases)
To install the core pycamverter python library, run the following command:
```
pip install pycamverter
```
## Usage
To use pycamverter, select your raw data file, your search files (either MASCOT .xml or ProteomeDiscoverer .msf), and an optional excel listing scan numbers in a file browser. Then simply drag-and-drop them onto PyCAMVerter.exe.
After a few minutes of processing, you should see the output .camv.gz file in the same directory as your raw file.
For a full list of arguments, run PyCAMVerter.exe from the command line:
```
usage: PyCAMVerter [-h] [-v] [-q] [-V] [--cpus CPUS] [--reprocess]
[--no-auto-maybe] [--raw-paths RAW_PATHS [RAW_PATHS ...]]
[--search-path SEARCH_PATH] [--scans-path SCANS_PATH]
[--scans [SCANS [SCANS ...]]]
[--mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]]
[--out-path OUT_PATH]
[files [files ...]]
Aww yeah, mass specs!
positional arguments:
files Raw, search, or scan list files, determined by file
extension.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Increase verbosity of output.
-q, --quiet Decrease verbosity of output.
-V, --version show program's version number and exit
--cpus CPUS Limit the number of concurrent processes.
--reprocess Reprocess a set of scans, without limiting ptm
combinations.
--no-auto-maybe Don't auto-assign all peptides with best MASCOT rank
as 'maybe'
--raw-paths RAW_PATHS [RAW_PATHS ...]
Raw data file(s) containing mass spec data.
--search-path SEARCH_PATH
MASCOT or ProteomeDiscoverer search files.
--scans-path SCANS_PATH
.xlsx or .csv file listing scans to select for
validation.
--scans [SCANS [SCANS ...]]
Individual scans to select for validation.
--mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]
Path to CAMV-Matlab session files.
--out-path OUT_PATH Output path for CAMV export.
```
[![Build Status](https://img.shields.io/travis/white-lab/pycamverter.svg)](https://travis-ci.org/white-lab/pycamverter)
[![Build status](https://ci.appveyor.com/api/projects/status/0uew150mwdh2qesx?svg=true)](https://ci.appveyor.com/project/naderm/pycamverter)
[![Coverage Status](https://img.shields.io/coveralls/white-lab/pycamverter.svg)](https://coveralls.io/r/white-lab/pycamverter?branch=master)
[![Documentation Status](https://readthedocs.org/projects/pycamverter/badge/?version=latest)](https://readthedocs.org/projects/pycamverter/?badge=latest)
[![Requirements Status](https://requires.io/github/white-lab/pycamverter/requirements.svg?branch=master)](https://requires.io/github/white-lab/pycamverter/requirements/?branch=master)
[![PyPI](https://img.shields.io/pypi/v/pycamverter.svg)](https://pypi.python.org/pypi/pycamverter)
Utility for converting searched mass spec data into a format readable by [CAMV](https://github.com/white-lab/pycamverter/blob/master/README.md).
![pycamverter demo](https://zippy.gfycat.com/CleverGrotesqueErmine.gif)
## Installation
To download a completely packaged Windows executable, visit our [releases page](https://github.com/white-lab/pycamverter/releases)
To install the core pycamverter python library, run the following command:
```
pip install pycamverter
```
## Usage
To use pycamverter, select your raw data file, your search files (either MASCOT .xml or ProteomeDiscoverer .msf), and an optional excel listing scan numbers in a file browser. Then simply drag-and-drop them onto PyCAMVerter.exe.
After a few minutes of processing, you should see the output .camv.gz file in the same directory as your raw file.
For a full list of arguments, run PyCAMVerter.exe from the command line:
```
usage: PyCAMVerter [-h] [-v] [-q] [-V] [--cpus CPUS] [--reprocess]
[--no-auto-maybe] [--raw-paths RAW_PATHS [RAW_PATHS ...]]
[--search-path SEARCH_PATH] [--scans-path SCANS_PATH]
[--scans [SCANS [SCANS ...]]]
[--mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]]
[--out-path OUT_PATH]
[files [files ...]]
Aww yeah, mass specs!
positional arguments:
files Raw, search, or scan list files, determined by file
extension.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Increase verbosity of output.
-q, --quiet Decrease verbosity of output.
-V, --version show program's version number and exit
--cpus CPUS Limit the number of concurrent processes.
--reprocess Reprocess a set of scans, without limiting ptm
combinations.
--no-auto-maybe Don't auto-assign all peptides with best MASCOT rank
as 'maybe'
--raw-paths RAW_PATHS [RAW_PATHS ...]
Raw data file(s) containing mass spec data.
--search-path SEARCH_PATH
MASCOT or ProteomeDiscoverer search files.
--scans-path SCANS_PATH
.xlsx or .csv file listing scans to select for
validation.
--scans [SCANS [SCANS ...]]
Individual scans to select for validation.
--mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]
Path to CAMV-Matlab session files.
--out-path OUT_PATH Output path for CAMV export.
```
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