pycamverter 0.8.1

Utility for converting searched mass spec data into a format readable by CAMV

# PyCAMVerter

[](https://travis-ci.org/white-lab/pycamverter)
[](https://ci.appveyor.com/project/naderm/pycamverter)
[](https://coveralls.io/r/white-lab/pycamverter?branch=master)
[](https://readthedocs.org/projects/pycamverter/?badge=latest)
[](https://requires.io/github/white-lab/pycamverter/requirements/?branch=master)
[](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).


## 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.
```