EasyPQP: Simple library generation for OpenSWATH
EasyPQP is a Python package that provides simplified and fast peptide query parameter generation for OpenSWATH. It can process input from MSFragger, Sage or other database search engines in pepXML/idXML/tsv format. Statistical validation can be conducted either using PyProphet or PeptideProphet/iProphet. Retention times and ion mobilities are calibrated using an internal or external standard. In addition to a cumulative library, run-specific libraries are generated for non-linear RT alignment in OpenSWATH. For generation of PTM specific libraries that utilizes a unimod.xml database, you can further restrict the unimod.xml database file for modifications and site-specificities of interest. It also supports in-silico library generation.
Installation
We strongly advice to install EasyPQP in a Python virtualenv. EasyPQP is compatible with Python 3.
Install the development version of easypqp from GitHub:
$ pip install git+https://github.com/grosenberger/easypqp.git@master
Full Installation
To install all optional features:
$ pip install easypqp[all]
This will install the easypqp_rs package, which provides the in-silico library generation feature and pyprophet for statistical validation.
Running EasyPQP
EasyPQP is not only a Python package, but also a command line tool:
$ easypqp --help
or:
$ easypqp convert --help
$ easypqp convertpsm --help
$ easypqp convertsage --help
$ easypqp library --help
$ easypqp insilico-library --help
$ easypqp reduce --help
$ easypqp filter-unimod --help
$ easypqp openswath-assay-generator --help
$ easypqp openswath-decoy-generator --help
$ easypqp targeted-file-converter --help
Generating an In-Silico Library
The in-silico library generation feature is included if you installed EasyPQP with the [all] or [rust] extras (to install the easypqp_rs package).
To generate an in-silico library, you can use the insilico-library command. For example:
$ easypqp insilico-library --fasta your_proteome.fasta --output_file insilico_library.tsv
For more information on the parameters and JSON configuration file, see the Configuration Reference
If you want just a standalone portable rust binary, you can download one from the easypqp-rs releases page.
Docker
EasyPQP is also available from Docker (automated builds):
Pull the development version of easypqp from DockerHub (synced with GitHub):
$ docker pull grosenberger/easypqp:latest
1 maintainer
Metadata
1 maintainer
Release files for easypqp 0.1.60
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| easypqp-0.1.60.tar.gz | 242.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| easypqp-0.1.60-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 493.5 kB
Release files / easypqp-0.1.60.tar.gz
| Download URL | easypqp-0.1.60.tar.gz |
|---|---|
| Size | 242.8 kB |
| Tags | Source |
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Release files / easypqp-0.1.60-py3-none-any.whl
| Download URL | easypqp-0.1.60-py3-none-any.whl |
|---|---|
| Size | 250.7 kB |
| Tags | Python 3 |
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