path: root/python-bgen.spec

%global _empty_manifest_terminate_build 0
Name:		python-bgen
Version:	1.5.4
Release:	1
Summary:	Package for loading data from bgen files
License:	MIT
URL:		https://github.com/jeremymcrae/bgen
Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/af/8c/03f4e9e6372e87eaad219c190acd240f0051135b1a3263d04339eba1b2b4/bgen-1.5.4.tar.gz

Requires:	python3-numpy

%description
### Another bgen reader
![bgen](https://github.com/jeremymcrae/bgen/workflows/bgen/badge.svg)

This is a package for reading [bgen files](https://www.well.ox.ac.uk/~gav/bgen_format).

This package uses cython to wrap c++ code for parsing bgen files. It's fairly
quick, it can parse genotypes from 500,000 individuals at ~300 variants per
second within a single python process (~450 million probabilities per second
with a 3GHz CPU). Decompressing the genotype probabilities is the slow step,
zlib decompression takes 80% of the total time, using zstd compressed genotypes
would be much faster, maybe 2-3X faster?

This has been optimized for UKBiobank bgen files (i.e. bgen version 1.2 with
zlib compressed 8-bit genotype probabilities, but the other bgen versions and
zstd compression have also been tested using example bgen files).

#### Install
`pip install bgen`

#### Usage
```python
from bgen import BgenReader

bfile = BgenReader(BGEN_PATH)
rsids = bfile.rsids()

# select a variant by indexing
var = bfile[1000]

# pull out genotype probabilities
probs = var.probabilities  # returns 2D numpy array
dosage = var.minor_allele_dosage  # returns 1D numpy array for biallelic variant

# iterate through every variant in the file
with BgenReader(BGEN_PATH, delay_parsing=True) as bfile:
  for var in bfile:
      dosage = var.minor_allele_dosage

# get all variants in a genomic region
variants = bfile.fetch('21', 10000, 5000000)

# or for writing bgen files
import numpy as np
from bgen import BgenWriter

geno = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]).astype(np.float64)
with BgenWriter(BGEN_PATH, n_samples=3) as bfile:
  bfile.add_variant(varid='var1', rsid='rs1', chrom='chr1', pos=1,
                    alleles=['A', 'G'], genotypes=geno)
```

#### API documentation

``` py
class BgenReader(path, sample_path='', delay_parsing=False)
    # opens a bgen file. If a bgenix index exists for the file, the index file
    # will be opened automatically for quicker access of specific variants.
    Arguments:
      path: path to bgen file
      sample_path: optional path to sample file. Samples will be given integer IDs
          if sample file is not given and sample IDs not found in the bgen file
      delay_parsing: True/False option to allow for not loading all variants into
          memory when the BgenFile is opened. This can save time when iterating
          across variants in the file
  
  Attributes:
    samples: list of sample IDs
    header: BgenHeader with info about the bgen version and compression.
  
  Methods:
    slicing: BgenVars can be accessed by slicing the BgenFile e.g. bfile[1000]
    iteration: variants in a BgenFile can be looped over e.g. for x in bfile: print(x)
    fetch(chrom, start=None, stop=None): get all variants within a genomic region
    drop_variants(list[int]): drops variants by index from being used in analyses
    with_rsid(rsid): returns BgenVar with given position
    at_position(pos): returns BgenVar with given rsid
    varids(): returns list of varids for variants in the bgen file.
    rsids(): returns list of rsids for variants in the bgen file.
    chroms(): returns list of chromosomes for variants in the bgen file.
    positions(): returns list of positions for variants in the bgen file.

class BgenVar(handle, offset, layout, compression, n_samples):
  # Note: this isn't called directly, but instead returned from BgenFile methods
  Attributes:
    varid: ID for variant
    rsid: reference SNP ID for variant
    chrom: chromosome variant is on
    pos: nucleotide position variant is at
    alleles: list of alleles for variant
    is_phased: True/False for whether variant has phased genotype data
    ploidy: list of ploidy for each sample. Samples are ordered as per BgenFile.samples
    minor_allele: the least common allele (for biallelic variants)
    minor_allele_dosage: 1D numpy array of minor allele dosages for each sample
    alt_dosage: 1D numpy array of alt allele dosages for each sample
    probabilitiies:  2D numpy array of genotype probabilities, one sample per row
  
  BgenVars can be pickled e.g. pickle.dumps(var)
```


%package -n python3-bgen
Summary:	Package for loading data from bgen files
Provides:	python-bgen
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
BuildRequires:	python3-cffi
BuildRequires:	gcc
BuildRequires:	gdb
%description -n python3-bgen
### Another bgen reader
![bgen](https://github.com/jeremymcrae/bgen/workflows/bgen/badge.svg)

This is a package for reading [bgen files](https://www.well.ox.ac.uk/~gav/bgen_format).

This package uses cython to wrap c++ code for parsing bgen files. It's fairly
quick, it can parse genotypes from 500,000 individuals at ~300 variants per
second within a single python process (~450 million probabilities per second
with a 3GHz CPU). Decompressing the genotype probabilities is the slow step,
zlib decompression takes 80% of the total time, using zstd compressed genotypes
would be much faster, maybe 2-3X faster?

This has been optimized for UKBiobank bgen files (i.e. bgen version 1.2 with
zlib compressed 8-bit genotype probabilities, but the other bgen versions and
zstd compression have also been tested using example bgen files).

#### Install
`pip install bgen`

#### Usage
```python
from bgen import BgenReader

bfile = BgenReader(BGEN_PATH)
rsids = bfile.rsids()

# select a variant by indexing
var = bfile[1000]

# pull out genotype probabilities
probs = var.probabilities  # returns 2D numpy array
dosage = var.minor_allele_dosage  # returns 1D numpy array for biallelic variant

# iterate through every variant in the file
with BgenReader(BGEN_PATH, delay_parsing=True) as bfile:
  for var in bfile:
      dosage = var.minor_allele_dosage

# get all variants in a genomic region
variants = bfile.fetch('21', 10000, 5000000)

# or for writing bgen files
import numpy as np
from bgen import BgenWriter

geno = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]).astype(np.float64)
with BgenWriter(BGEN_PATH, n_samples=3) as bfile:
  bfile.add_variant(varid='var1', rsid='rs1', chrom='chr1', pos=1,
                    alleles=['A', 'G'], genotypes=geno)
```

#### API documentation

``` py
class BgenReader(path, sample_path='', delay_parsing=False)
    # opens a bgen file. If a bgenix index exists for the file, the index file
    # will be opened automatically for quicker access of specific variants.
    Arguments:
      path: path to bgen file
      sample_path: optional path to sample file. Samples will be given integer IDs
          if sample file is not given and sample IDs not found in the bgen file
      delay_parsing: True/False option to allow for not loading all variants into
          memory when the BgenFile is opened. This can save time when iterating
          across variants in the file
  
  Attributes:
    samples: list of sample IDs
    header: BgenHeader with info about the bgen version and compression.
  
  Methods:
    slicing: BgenVars can be accessed by slicing the BgenFile e.g. bfile[1000]
    iteration: variants in a BgenFile can be looped over e.g. for x in bfile: print(x)
    fetch(chrom, start=None, stop=None): get all variants within a genomic region
    drop_variants(list[int]): drops variants by index from being used in analyses
    with_rsid(rsid): returns BgenVar with given position
    at_position(pos): returns BgenVar with given rsid
    varids(): returns list of varids for variants in the bgen file.
    rsids(): returns list of rsids for variants in the bgen file.
    chroms(): returns list of chromosomes for variants in the bgen file.
    positions(): returns list of positions for variants in the bgen file.

class BgenVar(handle, offset, layout, compression, n_samples):
  # Note: this isn't called directly, but instead returned from BgenFile methods
  Attributes:
    varid: ID for variant
    rsid: reference SNP ID for variant
    chrom: chromosome variant is on
    pos: nucleotide position variant is at
    alleles: list of alleles for variant
    is_phased: True/False for whether variant has phased genotype data
    ploidy: list of ploidy for each sample. Samples are ordered as per BgenFile.samples
    minor_allele: the least common allele (for biallelic variants)
    minor_allele_dosage: 1D numpy array of minor allele dosages for each sample
    alt_dosage: 1D numpy array of alt allele dosages for each sample
    probabilitiies:  2D numpy array of genotype probabilities, one sample per row
  
  BgenVars can be pickled e.g. pickle.dumps(var)
```


%package help
Summary:	Development documents and examples for bgen
Provides:	python3-bgen-doc
%description help
### Another bgen reader
![bgen](https://github.com/jeremymcrae/bgen/workflows/bgen/badge.svg)

This is a package for reading [bgen files](https://www.well.ox.ac.uk/~gav/bgen_format).

This package uses cython to wrap c++ code for parsing bgen files. It's fairly
quick, it can parse genotypes from 500,000 individuals at ~300 variants per
second within a single python process (~450 million probabilities per second
with a 3GHz CPU). Decompressing the genotype probabilities is the slow step,
zlib decompression takes 80% of the total time, using zstd compressed genotypes
would be much faster, maybe 2-3X faster?

This has been optimized for UKBiobank bgen files (i.e. bgen version 1.2 with
zlib compressed 8-bit genotype probabilities, but the other bgen versions and
zstd compression have also been tested using example bgen files).

#### Install
`pip install bgen`

#### Usage
```python
from bgen import BgenReader

bfile = BgenReader(BGEN_PATH)
rsids = bfile.rsids()

# select a variant by indexing
var = bfile[1000]

# pull out genotype probabilities
probs = var.probabilities  # returns 2D numpy array
dosage = var.minor_allele_dosage  # returns 1D numpy array for biallelic variant

# iterate through every variant in the file
with BgenReader(BGEN_PATH, delay_parsing=True) as bfile:
  for var in bfile:
      dosage = var.minor_allele_dosage

# get all variants in a genomic region
variants = bfile.fetch('21', 10000, 5000000)

# or for writing bgen files
import numpy as np
from bgen import BgenWriter

geno = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]).astype(np.float64)
with BgenWriter(BGEN_PATH, n_samples=3) as bfile:
  bfile.add_variant(varid='var1', rsid='rs1', chrom='chr1', pos=1,
                    alleles=['A', 'G'], genotypes=geno)
```

#### API documentation

``` py
class BgenReader(path, sample_path='', delay_parsing=False)
    # opens a bgen file. If a bgenix index exists for the file, the index file
    # will be opened automatically for quicker access of specific variants.
    Arguments:
      path: path to bgen file
      sample_path: optional path to sample file. Samples will be given integer IDs
          if sample file is not given and sample IDs not found in the bgen file
      delay_parsing: True/False option to allow for not loading all variants into
          memory when the BgenFile is opened. This can save time when iterating
          across variants in the file
  
  Attributes:
    samples: list of sample IDs
    header: BgenHeader with info about the bgen version and compression.
  
  Methods:
    slicing: BgenVars can be accessed by slicing the BgenFile e.g. bfile[1000]
    iteration: variants in a BgenFile can be looped over e.g. for x in bfile: print(x)
    fetch(chrom, start=None, stop=None): get all variants within a genomic region
    drop_variants(list[int]): drops variants by index from being used in analyses
    with_rsid(rsid): returns BgenVar with given position
    at_position(pos): returns BgenVar with given rsid
    varids(): returns list of varids for variants in the bgen file.
    rsids(): returns list of rsids for variants in the bgen file.
    chroms(): returns list of chromosomes for variants in the bgen file.
    positions(): returns list of positions for variants in the bgen file.

class BgenVar(handle, offset, layout, compression, n_samples):
  # Note: this isn't called directly, but instead returned from BgenFile methods
  Attributes:
    varid: ID for variant
    rsid: reference SNP ID for variant
    chrom: chromosome variant is on
    pos: nucleotide position variant is at
    alleles: list of alleles for variant
    is_phased: True/False for whether variant has phased genotype data
    ploidy: list of ploidy for each sample. Samples are ordered as per BgenFile.samples
    minor_allele: the least common allele (for biallelic variants)
    minor_allele_dosage: 1D numpy array of minor allele dosages for each sample
    alt_dosage: 1D numpy array of alt allele dosages for each sample
    probabilitiies:  2D numpy array of genotype probabilities, one sample per row
  
  BgenVars can be pickled e.g. pickle.dumps(var)
```


%prep
%autosetup -n bgen-1.5.4

%build
%py3_build

%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .

%files -n python3-bgen -f filelist.lst
%dir %{python3_sitearch}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.5.4-1
- Package Spec generated