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bcf-extras-0.2.0
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مشاهده بیشترتوضیحات
A set of variant file helper utilities built on top of bcftools and htslib.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bcf-extras-0.2.0 |
| نام | bcf-extras |
| نسخه کتابخانه | 0.2.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | David Lougheed |
| ایمیل نویسنده | david.lougheed@gmail.com |
| آدرس صفحه اصلی | https://github.com/davidlougheed/bcf_extras |
| آدرس اینترنتی | https://pypi.org/project/bcf-extras/ |
| مجوز | GPLv3 |
# bcf_extras
Extra variant file helper utilities built on top of `bcftools` and `htslib`.
## License
`bcf_extras` is licensed under GPLv3. See [the license](./LICENSE) for more
information.
## Dependencies
The package requires that `bcftools` and `htslib` are installed on your
operating system.
For the `str` extra, `TRtools` is required as a pip dependency. This should be
handled automatically upon installation, but I have encountered installation
issues before (especially when copies of `htslib` interfere with one another.)
Feel free to file an issue to ask about this.
## Installation
One can use pip to install either the base `bcf-extras` or `bcf-extras[str]`,
which has additional dependencies and adds some more utilities related to STR
calling.
```bash
pip install bcf-extras
# or
pip install bcf-extras[str]
```
## What's Included (Base)
### `copy-compress-index`
Creates `.vcf.gz` files with a corresponding tabix indices from one or more
VCFs, sorting the VCFs if necessary.
For example, the following would generate `sample-1.vcf.gz` and `sample-1.vcf.gz.tbi`:
```bash
bcf-extras copy-compress-index sample-1.vcf
```
### `add-header-lines`
Adds header lines from a text file to a particular position in the VCF header.
Useful for e.g. inserting missing `##contig` lines to a bunch of VCFs at once
(taking advantage of this + something like GNU parallel.)
For the `##contig` lines example, inserting the contents of
[`tests/vcfs/new_lines.txt`](tests/vcfs/new_lines.txt), we could run the
following command on [`tests/vcfs/ahl.vcf`](tests/vcfs/ahl.vcf), replacing the
file with a new copy:
```bash
bcf-extras add-header-lines tests/vcfs/ahl.vcf tests/vcfs/new_lines.txt
```
There is also a flag, `--tmp-dir`, for specifying a temporary folder location
into which header artifacts will be placed. This is especially useful when
running jobs on clusters, which may have specific locations for temporary I/O.
Using GNU parallel, we can do multiple VCFs at once, e.g.:
```bash
parallel 'bcf-extras add-header-lines {} tests/vcfs/new_lines.txt --keep-old' ::: /path/to/my/vcfs/*.vcf
```
The `--keep-old` flag keeps the original VCFs as a copy.
### `arg-join`
Some bioinformatics utilities take in comma-separated file lists rather than
the more standard whitespace-separated lists that something like a glob
(`*.vcf.gz`) generates.
This command can be run by itself, e.g.:
```bash
bcf-extras arg-join --sep ";" *.vcf
# Outputs e.g. sample1.vcf;sample2.vcf
```
It can be used embedded in another command, e.g. with `mergeSTR`,
[a tool for merging STR caller VCFs](https://github.com/gymreklab/TRTools)
which takes as input a *comma-separated* list of files:
```bash
mergeSTR --vcfs $(bcf-extras arg-join *.vcf) --out my_merge
```
The default separator (specified via `--sep`) is `,`.
### `filter-gff3`
This command can filter a GFF3 (or similarly formatted) file and filter it
by various columns using regular expressions.
It prints the filtered lines to `stdout`, which can then be redirected to a
file or piped to another process.
Currently, you can filter by the `seqid`, `source`, `type`, `strand`, and
`phrase` columns using Python-formatted regular expressions, e.g. the
following, which filters `type` to be either `gene` or `exon` and stores that
in a new file:
```bash
bcf-extras filter-gff3 --type '^(gene|exon)$' example.gff3 > example-genes-exons.gff3
```
For help, run the sub-command with no arguments:
```bash
bcf-extras filter-gff3
```
### `reformat-vcf-contigs`
TODO
## What's Included (STR)
### `parallel-mergeSTR`
[mergeSTR](https://github.com/gymreklab/TRTools) is a tool by the Gymrek lab
used to merge STR call VCFs. It proceeds linearly over a list of files, which
cannot easily take advantage of multiple cores. This utility merges VCFs in a
tree fashion to produce a final merged result, and is handy when merging 100s
of STR call VCFs at once.
```bash
bcf-extras parallel-mergeSTR *.vcf.gz --out my_merge --ntasks 10
```
In a dataset of 148 single-sample gangSTR call VCFs, merging with
`parallel-mergeSTR` on 10 cores resulted in an 60% speedup versus
running on a single core (~2 hours versus ~5 hours.)
Speedup is not linear with number of cores used, so it only makes sense to use
this if turnaround time is important and resources are available.
To not over-allocate resources on a cluster, the process can be split further
into first a parallelized task, and then a task which only uses one core:
```bash
# Runs on multiple cores
bcf-extras parallel-mergeSTR *.vcf.gz --ntasks 10 --out my_merge --step1-only
# Intermediate files generated by the first step will feed into the second step.
# Bottlenecked single process step; the ntasks argument is still needed to
# calculate the names of the intermediate output files (but sub-processes are
# not spawned) - thus, the provided value must match the value above.
bcf-extras parallel-mergeSTR --ntasks 10 --out my_merge --step2-only
```
نیازمندی
| مقدار | نام |
|---|---|
| - | trtools |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| ~=3.7 | Python |
نحوه نصب
نصب پکیج whl bcf-extras-0.2.0:
pip install bcf-extras-0.2.0.whl
نصب پکیج tar.gz bcf-extras-0.2.0:
pip install bcf-extras-0.2.0.tar.gz