cyvcf2

cython + htslib == fast VCF and BCF processing

https://github.com/brentp/cyvcf2

Science Score: 23.0%

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11 of 43 committers (25.6%) from academic institutions
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Low similarity (12.3%) to scientific vocabulary

Keywords

bioinformatics cython genomics htslib vcf

Keywords from Contributors

tskit trees msprime genetics coalescent argument-parser structural-variation dna genotype alignment

Last synced: 6 months ago · JSON representation

Repository

cython + htslib == fast VCF and BCF processing

Basic Info

Host: GitHub
Owner: brentp
License: mit
Language: Cython
Default Branch: main
Homepage:
Size: 14.4 MB

Statistics

Stars: 411
Watchers: 6
Forks: 75
Open Issues: 47
Releases: 0

Topics

bioinformatics cython genomics htslib vcf

Created over 10 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License

cyvcf2

Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10

The latest documentation for cyvcf2 can be found here:

If you use cyvcf2, please cite the paper

Fast python (2 and 3) parsing of VCF and BCF including region-queries.

cyvcf2 is a cython wrapper around htslib built for fast parsing of 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

CYVCF2HTSLIBMODE=BUILTIN CYTHONIZE=1 python setup.py install

or to use a system htslib.so

CYVCF2HTSLIBMODE=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 PKGCONFIGPATH="/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] 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. ```

Performance

For the performance comparison in the paper, we used thousand genomes chromosome 22 With the full comparison runner here.

Owner

Name: Brent Pedersen
Login: brentp
Kind: user
Location: Oregon, USA

Twitter: brent_p
Repositories: 220
Profile: https://github.com/brentp

Doing genomics

GitHub Events

Total

Issues event: 5
Watch event: 33
Issue comment event: 10
Fork event: 3

Last Year

Issues event: 5
Watch event: 33
Issue comment event: 10
Fork event: 3

Committers

Last synced: over 1 year ago

All Time

Total Commits: 475
Total Committers: 43
Avg Commits per committer: 11.047
Development Distribution Score (DDS): 0.276

Past Year

Commits: 46
Committers: 7
Avg Commits per committer: 6.571
Development Distribution Score (DDS): 0.674

Top Committers

Name	Email	Commits
Brent Pedersen	b**e@g**m	344
Tom White	t**e@g**m	21
graphenn	g**n@g**m	15
indraniel	i**l@g**m	12
Arya Massarat	2****m	7
Jerome Kelleher	jk@w****k	7
Liang-Bo Wang	l**g@w**u	5
Måns Magnusson	m**n@s**e	5
Dave Lawrence	d**w@g**m	4
Marcel Martin	m**n@s**e	4
Sam Lichtenberg	s**e@g**m	4
Nils Homer	n****3	4
Graham Gower	g**r@g**m	3
Michael Hall	m**l@m**h	3
Tim Millar	t****r	2
Elias Kuthe	e**e@t**e	2
LiterallyUniqueLogin	j**e@g**m	2
Sander Bollen	a**n@l**l	2
Wouter De Coster	d**r@g**m	2
arq5x	a**x@v**u	2
cclauss	c**s@b**h	2
chapmanb	c**b@5**m	2
Ben Jeffery	b**y@b**k	1
Ben Jeffery	b**y@g**m	1
Danilo Horta	d**a@p**e	1
Derek Croote	d****e	1
Dave Larson	d**n@g**u	1
Gehring, Julian	j**g@i**m	1
Gilad Mishne	g**d@m**g	1
James Eapen	j**n@g**m	1
and 13 more...

Committer Domains (Top 20 + Academic)

scilifelab.se: 2 tu-dortmund.de: 2 well.ox.ac.uk: 1 wustl.edu: 1 mbh.sh: 1 lumc.nl: 1 virginia.edu: 1 bluewin.ch: 1 50mail.com: 1 bdi.ox.ac.uk: 1 pm.me: 1 genome.wustl.edu: 1 illumina.com: 1 mishne.org: 1 isb-sib.ch: 1 evolbio.mpg.de: 1 liang2.tw: 1 rivera.za.net: 1 gmx.de: 1 chop.edu: 1 berkeley.edu: 1 medisin.uio.no: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 105
Total pull requests: 52
Average time to close issues: 6 months
Average time to close pull requests: about 1 month
Total issue authors: 71
Total pull request authors: 22
Average comments per issue: 3.96
Average comments per pull request: 2.56
Merged pull requests: 45
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 5
Pull requests: 1
Average time to close issues: 15 days
Average time to close pull requests: 3 days
Issue authors: 5
Pull request authors: 1
Average comments per issue: 2.4
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

tomwhite (15)
davmlaw (5)
grahamgower (3)
vsbuffalo (3)
hammer (3)
jeromekelleher (2)
quattro (2)
nh13 (2)
CholoTook (2)
alanwilter (2)
brentp (2)
gnxsf (2)
graphenn (2)
shubhamsaini (1)
adrienlemeur (1)

Pull Request Authors

tomwhite (20)
graphenn (9)
grahamgower (3)
benjeffery (2)
esrice (2)
nakib103 (2)
EQt (2)
jeromekelleher (2)
Hoeze (2)
horta (1)
kullrich (1)
CholoTook (1)
davmlaw (1)
stefanor (1)
brentp (1)

Top Labels

Issue Labels

enhancement (2) bug (1)

Pull Request Labels

enhancement (1)

Packages

Total packages: 3
Total downloads:
- pypi 82,567 last-month
Total docker downloads: 1,802

Total dependent packages: 45
(may contain duplicates)
Total dependent repositories: 99
(may contain duplicates)
Total versions: 197
Total maintainers: 2

pypi.org: cyvcf2

fast vcf parsing with cython + htslib

Homepage: https://github.com/brentp/cyvcf2/
Documentation: https://cyvcf2.readthedocs.io/
License: MIT
Latest release: 0.31.1
published over 1 year ago

Versions: 95
Dependent Packages: 43
Dependent Repositories: 99
Downloads: 82,567 Last month
Docker Downloads: 1,802

Rankings

Dependent packages count: 0.4%

Docker downloads count: 1.1%

Dependent repos count: 1.5%

Downloads: 1.7%

Average: 2.2%

Stargazers count: 3.5%

Forks count: 5.3%

Maintainers (1)

brentp

Last synced: 6 months ago

proxy.golang.org: github.com/brentp/cyvcf2

Documentation: https://pkg.go.dev/github.com/brentp/cyvcf2#section-documentation
License: mit
Latest release: v0.31.1
published over 1 year ago

Versions: 101
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 6 months ago

spack.io: py-cyvcf2

fast vcf parsing with cython + htslib

Homepage: https://github.com/brentp/cyvcf2
License: []
Latest release: 0.11.7
published almost 4 years ago

Versions: 1
Dependent Packages: 2
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Average: 11.1%

Stargazers count: 12.0%

Forks count: 13.2%

Dependent packages count: 19.0%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

Dependencies

requirements.txt pypi

click *
coloredlogs *
cython >=0.23.3
numpy *

setup.py pypi

click *
coloredlogs *
numpy *

.github/workflows/build.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/wheels.yml actions

actions/checkout v2 composite
actions/download-artifact v2 composite
actions/setup-python v2 composite
actions/upload-artifact v2 composite
mxschmitt/action-tmate v3 composite
pypa/gh-action-pypi-publish release/v1 composite

cyvcf2

Science Score: 23.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

cyvcf2

Example

to do a region-query:

Installation

pip with bundled htslib

pip with system htslib

windows (experimental, only test on MSYS2)

github (building htslib and cyvcf2 from source)

sometimes it can be required to remove old files:

python setup.py clean_ext

or to use a system htslib.so

Testing

CLI

See Also

Performance

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: cyvcf2

Rankings

Maintainers (1)

proxy.golang.org: github.com/brentp/cyvcf2

Rankings

spack.io: py-cyvcf2

Rankings

Maintainers (1)

Dependencies