| Name | viramp-hub JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | |
| Summary | VirAmp-Hub lets you manipulate/convert viral amplicon/primer scheme information. |
| upload_time | 2023-07-10 10:34:45 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.6 |
| license | MIT License Copyright (c) 2023 Wolfgang Maier 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 |
virology
tiled-amplicon
primer schemes
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# VirAmp-Hub
A tool that lets you manipulate/convert viral amplicon/primer scheme information.
## What is it for?
The layout of (tiled-) amplicon schemes for amplifying and sequencing viral
genomes is typically specified through one of a number of non-standardized
scheme files. These can, generally, not be used interchangeably with downstream
analysis tools.
VirAmp-Hub can convert between commonly used scheme file formats, such as used,
e.g., by the [ARTIC network](https://github.com/artic-network/primer-schemes),
the [ivar](https://github.com/andersen-lab/ivar) and
[cojac](https://github.com/cbg-ethz/cojac) suites of tools, and
[Galaxy](https://galaxyproject.org/) tools and workflows for viral sequencing
data analysis.
## Usage
After installation (`pip install viramp-hub`), use the package via the
`scheme-convert` command.
For help run:
scheme-convert --help
Prepare an existing primer scheme file for use with ivar:
scheme-convert primer_scheme.bed --to bed --bed-type ivar -o ivar.bed
Generate an amplicon insert scheme file for cojac:
scheme-convert primer_scheme.bed --to bed --bed-type cojac -o cojac_insert.bed
Generate an amplicon info file for use with ivar inside Galaxy:
scheme-convert primer_scheme.bed --to amplicon-info -o info.tsv
Amplicon info files are simple tab-separated files listing primers contributing
to the same amplicon on a single line. For nested primer schemes, you can
control, which primers to report in the info file.
List only the inner primers:
scheme-convert primer_scheme.bed --to amplicon-info -r inner -o info.tsv
List only the outer primers:
scheme-convert primer_scheme.bed --to amplicon-info -r outer -o info.tsv
VirAmp-Hub tries to autodetect primer to amplicon assignments using the Python
re pattern: `r'(?P<prefix>(.*_)*)(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)'`.
If this fails for any given primer scheme, it is possible to override
autodetection by providing an amplicon info file directly, e.g.:
scheme-convert primer_scheme.bed -a amplicon_info.tsv --to bed --bed-type cojac -o cojac_insert.bed
or:
scheme-convert primer_scheme.bed -a amplicon_info.tsv --to amplicon-info -r inner -o info.tsv
Raw data
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"description": "# VirAmp-Hub\n\nA tool that lets you manipulate/convert viral amplicon/primer scheme information.\n\n## What is it for?\n\nThe layout of (tiled-) amplicon schemes for amplifying and sequencing viral\ngenomes is typically specified through one of a number of non-standardized\nscheme files. These can, generally, not be used interchangeably with downstream\nanalysis tools.\n\nVirAmp-Hub can convert between commonly used scheme file formats, such as used,\ne.g., by the [ARTIC network](https://github.com/artic-network/primer-schemes),\nthe [ivar](https://github.com/andersen-lab/ivar) and\n[cojac](https://github.com/cbg-ethz/cojac) suites of tools, and\n[Galaxy](https://galaxyproject.org/) tools and workflows for viral sequencing\ndata analysis.\n\n## Usage\n\nAfter installation (`pip install viramp-hub`), use the package via the\n`scheme-convert` command.\n\nFor help run:\n\n scheme-convert --help\n\nPrepare an existing primer scheme file for use with ivar:\n\n scheme-convert primer_scheme.bed --to bed --bed-type ivar -o ivar.bed\n\nGenerate an amplicon insert scheme file for cojac:\n\n scheme-convert primer_scheme.bed --to bed --bed-type cojac -o cojac_insert.bed\n\nGenerate an amplicon info file for use with ivar inside Galaxy:\n\n scheme-convert primer_scheme.bed --to amplicon-info -o info.tsv\n\nAmplicon info files are simple tab-separated files listing primers contributing\nto the same amplicon on a single line. For nested primer schemes, you can\ncontrol, which primers to report in the info file.\n\nList only the inner primers:\n\n scheme-convert primer_scheme.bed --to amplicon-info -r inner -o info.tsv\n\nList only the outer primers:\n\n scheme-convert primer_scheme.bed --to amplicon-info -r outer -o info.tsv\n\nVirAmp-Hub tries to autodetect primer to amplicon assignments using the Python\nre pattern: `r'(?P<prefix>(.*_)*)(?P<num>\\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)'`.\nIf this fails for any given primer scheme, it is possible to override\nautodetection by providing an amplicon info file directly, e.g.:\n\n scheme-convert primer_scheme.bed -a amplicon_info.tsv --to bed --bed-type cojac -o cojac_insert.bed\n\nor:\n\n scheme-convert primer_scheme.bed -a amplicon_info.tsv --to amplicon-info -r inner -o info.tsv\n\n",
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