cyvcf2
======
Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
<!-- ghp-import -p docs/build/html/ -->
The latest documentation for cyvcf2 can be found here:
[](http://brentp.github.io/cyvcf2/)
If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
[](https://github.com/brentp/cyvcf2/actions/workflows/build.yml)
cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
Attributes like `variant.gt_ref_depths` work for diploid samples and return a numpy array directly so they are immediately ready for downstream use.
**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
Example
=======
The example below shows much of the use of cyvcf2.
```Python
from cyvcf2 import VCF
for variant in VCF('some.vcf.gz'): # or VCF('some.bcf')
variant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T']
variant.CHROM, variant.start, variant.end, variant.ID, \
variant.FILTER, variant.QUAL
# numpy arrays of specific things we pull from the sample fields.
# gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT
variant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays
variant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array
## INFO Field.
## extract from the info field by it's name:
variant.INFO.get('DP') # int
variant.INFO.get('FS') # float
variant.INFO.get('AC') # float
# convert back to a string.
str(variant)
## sample info...
# Get a numpy array of the depth per sample:
dp = variant.format('DP')
# or of any other format field:
sb = variant.format('SB')
assert sb.shape == (n_samples, 4) # 4-values per
# to do a region-query:
vcf = VCF('some.vcf.gz')
for v in vcf('11:435345-556565'):
if v.INFO["AF"] > 0.1: continue
print(str(v))
```
Installation
============
## pip with bundled htslib
```
pip install cyvcf2
```
## pip with system htslib
Assuming you have already built and installed htslib version 1.12 or higher.
```
CYVCF2_HTSLIB_MODE=EXTERNAL pip install --no-binary cyvcf2 cyvcf2
```
## windows (experimental, only test on MSYS2)
Assuming you have already built and installed htslib.
```
SETUPTOOLS_USE_DISTUTILS=stdlib pip install cyvcf2
```
## github (building htslib and cyvcf2 from source)
```
git clone --recursive https://github.com/brentp/cyvcf2
pip install -r requirements.txt
# sometimes it can be required to remove old files:
# python setup.py clean_ext
CYVCF2_HTSLIB_MODE=BUILTIN CYTHONIZE=1 python setup.py install
# or to use a system htslib.so
CYVCF2_HTSLIB_MODE=EXTERNAL python setup.py install
```
On **OSX**, using brew, you may have to set the following as indicated by the brew install:
```
For compilers to find openssl you may need to set:
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"
For pkg-config to find openssl you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"
```
Testing
=======
Install `pytest`, then tests can be run with:
```
pytest
```
CLI
=======
Run with `cyvcf2 path_to_vcf`
```
$ cyvcf2 --help
Usage: cyvcf2 [OPTIONS] <vcf_file> or -
fast vcf parsing with cython + htslib
Options:
-c, --chrom TEXT Specify what chromosome to include.
-s, --start INTEGER Specify the start of region.
-e, --end INTEGER Specify the end of the region.
--include TEXT Specify what info field to include.
--exclude TEXT Specify what info field to exclude.
--loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
Set the level of log output. [default:
INFO]
--silent Skip printing of vcf.
--help Show this message and exit.
```
See Also
========
Pysam also [has a cython wrapper to htslib](https://github.com/pysam-developers/pysam/blob/master/pysam/libcbcf.pyx) and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.
Performance
===========
For the performance comparison in the paper, we used [thousand genomes chromosome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz)
With the full comparison runner [here](https://github.com/brentp/cyvcf2/blob/main/scripts/compare.sh).
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"description": "cyvcf2\n======\n\nNote: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10\n\n<!-- ghp-import -p docs/build/html/ -->\nThe latest documentation for cyvcf2 can be found here:\n\n[](http://brentp.github.io/cyvcf2/)\n\nIf you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)\n\n\nFast python **(2 and 3)** parsing of VCF and BCF including region-queries.\n\n\n[](https://github.com/brentp/cyvcf2/actions/workflows/build.yml)\n\ncyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.\n\nAttributes like `variant.gt_ref_depths` work for diploid samples and return a numpy array directly so they are immediately ready for downstream use.\n**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.\nTo persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.\n\nExample\n=======\n\nThe example below shows much of the use of cyvcf2.\n\n```Python\nfrom cyvcf2 import VCF\n\nfor variant in VCF('some.vcf.gz'): # or VCF('some.bcf')\n variant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T']\n\n variant.CHROM, variant.start, variant.end, variant.ID, \\\n variant.FILTER, variant.QUAL\n\n # numpy arrays of specific things we pull from the sample fields.\n # gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT\n variant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays\n variant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array\n\n ## INFO Field.\n ## extract from the info field by it's name:\n variant.INFO.get('DP') # int\n variant.INFO.get('FS') # float\n variant.INFO.get('AC') # float\n\n # convert back to a string.\n str(variant)\n\n\n ## sample info...\n\n # Get a numpy array of the depth per sample:\n dp = variant.format('DP')\n # or of any other format field:\n sb = variant.format('SB')\n assert sb.shape == (n_samples, 4) # 4-values per\n\n# to do a region-query:\n\nvcf = VCF('some.vcf.gz')\nfor v in vcf('11:435345-556565'):\n if v.INFO[\"AF\"] > 0.1: continue\n print(str(v))\n```\n\nInstallation\n============\n\n## pip with bundled htslib\n```\npip install cyvcf2\n```\n\n## pip with system htslib\n\nAssuming you have already built and installed htslib version 1.12 or higher.\n```\nCYVCF2_HTSLIB_MODE=EXTERNAL pip install --no-binary cyvcf2 cyvcf2\n```\n\n## windows (experimental, only test on MSYS2)\n\nAssuming you have already built and installed htslib.\n```\nSETUPTOOLS_USE_DISTUTILS=stdlib pip install cyvcf2\n```\n\n## github (building htslib and cyvcf2 from source)\n\n```\ngit clone --recursive https://github.com/brentp/cyvcf2\npip install -r requirements.txt\n# sometimes it can be required to remove old files:\n# python setup.py clean_ext\nCYVCF2_HTSLIB_MODE=BUILTIN CYTHONIZE=1 python setup.py install\n# or to use a system htslib.so\nCYVCF2_HTSLIB_MODE=EXTERNAL python setup.py install\n```\n\nOn **OSX**, using brew, you may have to set the following as indicated by the brew install:\n\n```\nFor compilers to find openssl you may need to set:\n export LDFLAGS=\"-L/usr/local/opt/openssl/lib\"\n export CPPFLAGS=\"-I/usr/local/opt/openssl/include\"\n\nFor pkg-config to find openssl you may need to set:\n export PKG_CONFIG_PATH=\"/usr/local/opt/openssl/lib/pkgconfig\"\n```\n\nTesting\n=======\n\nInstall `pytest`, then tests can be run with:\n\n```\npytest\n```\n\nCLI\n=======\nRun with `cyvcf2 path_to_vcf`\n\n```\n$ cyvcf2 --help\nUsage: cyvcf2 [OPTIONS] <vcf_file> or -\n\n fast vcf parsing with cython + htslib\n\nOptions:\n -c, --chrom TEXT Specify what chromosome to include.\n -s, --start INTEGER Specify the start of region.\n -e, --end INTEGER Specify the end of the region.\n --include TEXT Specify what info field to include.\n --exclude TEXT Specify what info field to exclude.\n --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]\n Set the level of log output. [default:\n INFO]\n --silent Skip printing of vcf.\n --help Show this message and exit.\n```\n\n\nSee Also\n========\n\nPysam also [has a cython wrapper to htslib](https://github.com/pysam-developers/pysam/blob/master/pysam/libcbcf.pyx) and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.\n\nPerformance\n===========\n\nFor the performance comparison in the paper, we used [thousand genomes chromosome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz)\nWith the full comparison runner [here](https://github.com/brentp/cyvcf2/blob/main/scripts/compare.sh).\n",
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