| Name | tmtcrunch JSON |
| Version |
2024.12.18
JSON |
| download |
| home_page | None |
| Summary | Python utility for TMT-based proteomics |
| upload_time | 2024-12-17 21:25:41 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | BSD-3-Clause |
| keywords |
proteomics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# TMTCrunch
TMTCrunch is an open-source Python utility for analysis of tandem mass tag (TMT) proteomics data with the focus on protein isoforms resulting from alternative spicing.
## Istallation
### Installing from PyPI
The latest released version can be installed from the [Python Package Index](https://pypi.org/project/tmtcrunch):
```shell
pip install tmtcrunch
```
### Installing from source
The development version can be installed directly from the source repository:
```shell
pip install https://codeberg.org/makc/tmtcrunch.git
```
## Dependencies
TMTCrunch relies on the following Python packages:
- [numpy](https://pypi.org/project/numpy/)
- [pandas](https://pypi.org/project/pandas/)
- [pyteomics](https://pypi.org/project/pyteomics/)
- [tomli](https://pypi.org/project/tomli/) (required only for Python < 3.11)
and it would use statistics functions from [astropy](https://pypi.org/project/astropy/) package if available.
## Command line options
```
usage: tmtcrunch [-h] [--specimen-tags SPECIMEN_TAGS] [--gis-tags GIS_TAGS]
[--cfg CFG] [--output-dir OUTPUT_DIR] [--output-prefix OUTPUT_PREFIX]
[--keep-columns KEEP_COLUMNS [KEEP_COLUMNS ...]] [--verbose {0,1,2}]
[--version]
file [file ...]
positional arguments:
file Scavager *_PSMs_full.tsv files.
options:
-h, --help show this help message and exit
--specimen-tags SPECIMEN_TAGS
Comma-separated sequence of specimen TMT tags.
--gis-tags GIS_TAGS Comma-separated sequence of GIS TMT tags.
--cfg CFG Path to configuration file.
--output-dir OUTPUT_DIR, --odir OUTPUT_DIR
Existing output directory. Default is current directory.
--output-prefix OUTPUT_PREFIX, --oprefix OUTPUT_PREFIX
Prefix for output files. Default is 'tmtcrunch_'.
--keep-columns KEEP_COLUMNS [KEEP_COLUMNS ...]
Extra columns from input files to keep in output files.
--verbose {0,1,2} Logging verbosity. Default is 1.
--version Output version information and exit.
```
## Configuration file
TMTCrunch stores its configuration in [TOML](https://toml.io) format.
Default TMTCrunch configuration:
```TOML
# Specimen TMT labels.
specimen_tags = ['127C', '127N', '128C', '128N', '129C', '129N', '130C', '130N', '131']
# Global internal standard (GIS) TMT labels.
gis_tags = ['126', '131C']
# Prefix of decoy proteins.
decoy_prefix = 'DECOY_'
# List of column names from input files to save in the output.
keep_columns = []
# If true, perform PSM groupwise analysis.
groupwise = true
# Keys below are only applicable if groupwise analysis is requested.
# Prefixes of target proteins. If not set, `target_prefixes` will be deduced
# from the prefixes of PSM groups.
# target_prefixes = ['alt_', 'canon_']
# PSM group is named after its subkey and defined by three keys:
# `descr` - group description
# `prefixes` - prefixes of target proteins
# `fdr` - groupwise false discovery rate
# Isoform PSMs: protein group of each PSM should consist of proteins
# with 'alt_' prefix only.
[psm_group.isoform]
descr = 'Isoform PSMs'
prefixes = [['alt_']]
fdr = 0.05
# Canonical PSMs: protein group of each PSM should consist of proteins
# with 'canon_' prefix only.
[psm_group.canon]
descr = 'Canonical PSMs'
prefixes = [['canon_']]
fdr = 0.01
# Shared PSMs: protein group of each PSM should consist both of
# 'canon_' and 'alt_' proteins.
[psm_group.shared]
descr = 'Shared PSMs'
prefixes = [['canon_', 'alt_']]
fdr = 0.01
```
## License
TMTCrunch is distributed under a BSD License.
## Related software
- [Pyteomics](https://github.com/levitsky/pyteomics) - Python framework for proteomics data analysis.
- [IdentiPy](https://github.com/levitsky/identipy) - search engine for bottom-up proteomics.
- [Scavager](https://github.com/markmipt/scavager) - proteomics post-search validation tool.
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