| Name | varpepdb JSON |
| Version |
1.0.3
JSON |
| download |
| home_page | None |
| Summary | Generate reference database of variant peptides for peptide spectrum matching |
| upload_time | 2024-09-07 05:11:18 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT License Copyright (c) 2024 Jaren sia Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
proteomics
forensics
fasta
peptide
variant
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## Overview
varpepdb is a python package for generating a fasta database of genetically variant peptides for peptide spectrum matching after data acquisition by LC/MS. It takes in a list of amino acid substitutions for a protein sequence and generates all possible variant peptides after enzymatic cleaving. It allows for multiple digestion enzymes and up to 1 miscleavage. It also takes into account the effect of amino acid substitutions on enzyme cleavage.
## Installation
Requires:
* Python version: >= 3.8
* [rpg](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#installation)
You can install varpepdb from PyPI:
```
pip install varpepdb
```
## Usage
```
import varpepdb
import rpg
# Set enzymes to Asp-N and trypsin from the rpg package
varpepdb.setenzyme([rpg.RapidPeptidesGenerator.ALL_ENZYMES[1],
rpg.RapidPeptidesGenerator.ALL_ENZYMES[41]])
# Allow 1 miscleave
varpepdb.miscleave = True
# Set peptide length limits. Default values are 6 and 30.
varpepdb.setpeptidelengths(min_length: 6, max_length: 30)
# Demo inputs. In practice, these will be generated programmatically.
variants = ['O75844:p.Trp11Trp',
'O75844:p.Ala22Lys',
'O75844:p.Glu34Thr',
'O75844:p.Gln41His']
sequence = 'MGMWASLDALWEMPAEKRIFGAVLLFSWTVYLWETFLAQRQRRIYKTTTH'
gene = 'ZMPSTE24'
# Generate variant peptides
peptides = generate_single(variants=variants,
sequence=sequence,
gene=gene)
# Removes variant peptides that do not contain at least 1 amino acid substitution
var_peptides=varpepdb.variant_containing_peptides(peptides)
# Write variant peptides into fasta file
varpepdb.write(path='path/to/output.fasta',
peptides=var_peptides,
include_non_unique=True)
```
Multiple proteins can be processed in parallel using `varpepdb.generate`.
```
peptides = generate(input_list=[(variants1, sequence1, gene1),
(variants2, sequence2, gene3),
(variants3, sequence2, gene3)])
var_peptides=varpepdb.variant_containing_peptides(peptides)
varpepdb.write(path='path/to/output.fasta',
peptides=var_peptides,
include_non_unique=True)
```
## Enzymes
In-silico digestion is performed using the [rpg](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#installation) package. Refer to rpg's [documentation](https://rapid-peptide-generator.readthedocs.io/en/latest/index.html) on which [enzymes are available](https://rapid-peptide-generator.readthedocs.io/en/latest/enzymes.html) and how to [create your own enzyme](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#creating-a-new-enzyme).
## Fasta output
Example of an entry written into the fasta file:
>\>A0A8I5KQE6-v1 RPSA2 129-143 (p.Pro143Arg),p.Thr135Met 0 <br>
ADHQPLMEASYVNLR
**A0A8I5KQE6-v1** is the sequence identifier of the parent protein (in this case the Uniprot ascension number) with <br>
'v{number}' appended to identify it as a peptide of the parent protein. <br>
**RPSA2** is the name of the gene for this protein. <br>
**129-143** is the position of the parent protein sequence from which this peptide is dervied.
**(p.Pro143Arg)** is an amino acid substitution that affected the enzyme cleavage site. Amino acid substitutions that introduce or remove cleavage sites are marked by parenthesis. <br>
**p.Thr135Met** is an amino acid subtstitution that didn't affect enzyne cleavage site. <br>
**0** refers to the number of miscleavages <br>
## Contact
For further information please contact jaren_sia@htx.gov.sg
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"description": "## Overview\nvarpepdb is a python package for generating a fasta database of genetically variant peptides for peptide spectrum matching after data acquisition by LC/MS. It takes in a list of amino acid substitutions for a protein sequence and generates all possible variant peptides after enzymatic cleaving. It allows for multiple digestion enzymes and up to 1 miscleavage. It also takes into account the effect of amino acid substitutions on enzyme cleavage.\n\n## Installation\nRequires:\n* Python version: >= 3.8 \n* [rpg](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#installation) \n\nYou can install varpepdb from PyPI:\n```\npip install varpepdb\n```\n\n## Usage\n```\nimport varpepdb\nimport rpg\n\n# Set enzymes to Asp-N and trypsin from the rpg package\nvarpepdb.setenzyme([rpg.RapidPeptidesGenerator.ALL_ENZYMES[1], \n rpg.RapidPeptidesGenerator.ALL_ENZYMES[41]])\n# Allow 1 miscleave\nvarpepdb.miscleave = True\n# Set peptide length limits. Default values are 6 and 30. \nvarpepdb.setpeptidelengths(min_length: 6, max_length: 30)\n\n# Demo inputs. In practice, these will be generated programmatically.\nvariants = ['O75844:p.Trp11Trp', \n 'O75844:p.Ala22Lys', \n 'O75844:p.Glu34Thr', \n 'O75844:p.Gln41His']\nsequence = 'MGMWASLDALWEMPAEKRIFGAVLLFSWTVYLWETFLAQRQRRIYKTTTH'\ngene = 'ZMPSTE24'\n\n# Generate variant peptides\npeptides = generate_single(variants=variants, \n sequence=sequence, \n gene=gene)\n\n# Removes variant peptides that do not contain at least 1 amino acid substitution\nvar_peptides=varpepdb.variant_containing_peptides(peptides)\n\n# Write variant peptides into fasta file\nvarpepdb.write(path='path/to/output.fasta', \n peptides=var_peptides,\n include_non_unique=True)\n```\n\nMultiple proteins can be processed in parallel using `varpepdb.generate`. \n\n```\npeptides = generate(input_list=[(variants1, sequence1, gene1),\n (variants2, sequence2, gene3),\n (variants3, sequence2, gene3)])\n\nvar_peptides=varpepdb.variant_containing_peptides(peptides)\n\nvarpepdb.write(path='path/to/output.fasta', \n peptides=var_peptides,\n include_non_unique=True)\n```\n\n## Enzymes \nIn-silico digestion is performed using the [rpg](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#installation) package. Refer to rpg's [documentation](https://rapid-peptide-generator.readthedocs.io/en/latest/index.html) on which [enzymes are available](https://rapid-peptide-generator.readthedocs.io/en/latest/enzymes.html) and how to [create your own enzyme](https://rapid-peptide-generator.readthedocs.io/en/latest/userguide.html#creating-a-new-enzyme).\n\n## Fasta output\nExample of an entry written into the fasta file:\n>\\>A0A8I5KQE6-v1 RPSA2 129-143 (p.Pro143Arg),p.Thr135Met 0 <br>\nADHQPLMEASYVNLR\n\n**A0A8I5KQE6-v1** is the sequence identifier of the parent protein (in this case the Uniprot ascension number) with <br>\n'v{number}' appended to identify it as a peptide of the parent protein. <br>\n**RPSA2** is the name of the gene for this protein. <br>\n**129-143** is the position of the parent protein sequence from which this peptide is dervied.\n**(p.Pro143Arg)** is an amino acid substitution that affected the enzyme cleavage site. Amino acid substitutions that introduce or remove cleavage sites are marked by parenthesis. <br>\n**p.Thr135Met** is an amino acid subtstitution that didn't affect enzyne cleavage site. <br>\n**0** refers to the number of miscleavages <br>\n\n\n## Contact\nFor further information please contact jaren_sia@htx.gov.sg\n",
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