automatic import of python-bgenopeneuler20.03

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+/bgen-1.5.4.tar.gz
diff --git a/python-bgen.spec b/python-bgen.spec
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+%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
diff --git a/sources b/sources
new file mode 100644
index 0000000..a9c2035
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+de7832a9c362f7644030e789cf79dd83  bgen-1.5.4.tar.gz