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+%global _empty_manifest_terminate_build 0
+Name:		python-InSilicoSeq
+Version:	1.5.4
+Release:	1
+Summary:	a sequencing simulator
+License:	MIT
+URL:		https://github.com/HadrienG/InSilicoSeq
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/cf/35/9af5b2e15e00a76bf1f24a55474665d323ffe7182ccf568eeae6b4ee496d/InSilicoSeq-1.5.4.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-numpy
+Requires:	python3-scipy
+Requires:	python3-biopython
+Requires:	python3-pysam
+Requires:	python3-future
+Requires:	python3-joblib
+Requires:	python3-requests
+
+%description
+# InSilicoSeq
+
+## A sequencing simulator
+
+[![Build Status](https://github.com/HadrienG/InsilicoSeq/workflows/CI/badge.svg)](https://github.com/HadrienG/InSilicoSeq/actions)
+[![Documentation Status](https://readthedocs.org/projects/insilicoseq/badge/?version=latest)](http://insilicoseq.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/InSilicoSeq.svg)](https://badge.fury.io/py/InSilicoSeq)
+[![codecov](https://codecov.io/gh/HadrienG/InSilicoSeq/branch/master/graph/badge.svg)](https://codecov.io/gh/HadrienG/InSilicoSeq)
+[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty630-blue.svg)](https://doi.org/10.1093/bioinformatics/bty630)
+[![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](LICENSE)
+
+InSilicoSeq is a sequencing simulator producing realistic Illumina reads.
+Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
+
+InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.
+
+InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided.
+
+## Installation
+
+Insilicoseq is Available in [bioconda](https://bioconda.github.io/).
+
+To install with conda:
+
+```shell
+conda install -c bioconda insilicoseq
+```
+
+Or with pip:
+
+```shell
+pip install InSilicoSeq
+```
+
+_Note:_ Insilicoseq requires python >= 3.5 
+
+Alternatively, with docker:
+
+```shell
+docker pull hadrieng/insilicoseq:latest
+```
+
+For more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+## Usage
+
+InSilicoSeq has two subcommands: `iss generate` to generate Illumina reads and `iss model` to create an error model from which the reads will take their characteristics.
+
+InSilicoSeq comes with pre-computed error models that should be sufficient for most use cases.
+
+### Generate reads with a pre-computed error model
+
+for generating 1 million reads modelling a MiSeq instrument:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate --genomes SRS121011.fasta --model miseq --output miseq_reads
+```
+
+where `genomes.fasta` should be replaced by a (multi-)fasta file containing the reference genome(s) from which the simulated reads will be generated.
+
+InSilicoSeq comes with 3 error models: `MiSeq`, `HiSeq` and `NovaSeq`.
+
+If you have built your own model, pass the `.npz` file to the `--model` argument to simulate reads from your own error model.
+
+For 10 million reads and a custom error model:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate -g SRS121011.fasta -n 10m --model my_model.npz --output /path/to/my_reads
+```
+
+granted you have built `my_model.npz` with `iss model` (see [below](#create-your-own-error-model))
+
+For more examples and a full list of options, please refer to the full
+[documentation](http://insilicoseq.readthedocs.io)
+
+### Generate reads without input genomes
+
+We can download some for you! InSilicoSeq can download random genomes from the ncbi using the infamous [eutils](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
+
+The command
+
+```shell
+iss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads
+```
+
+will generate 1 million reads from 10 random bacterial genomes.
+
+For more examples and a full list of options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+### Create your own error model
+
+If you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.
+
+Say you have a reference metagenome called `genomes.fasta`, and read pairs `reads_R1.fastq.gz` and `reads_R2.fastq.gz`
+
+Align you reads against the reference:
+
+```shell
+bowtie2-build genomes.fasta genomes
+bowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \
+samtools view -bS | samtools sort -o genomes.bam
+samtools index genomes.bam
+```
+
+then build the model:
+
+```shell
+iss model -b genomes.bam -o genomes
+```
+
+which will create a `genome.npz` file containing your newly built model
+
+## License
+
+Code is under the [MIT](LICENSE) license.
+
+## Issues
+
+Found a bug or have a question? Please open an [issue](https://github.com/HadrienG/InSilicoSeq/issues)
+
+## Contributing
+
+We welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guidelines
+
+## Citation
+
+If you use our software, please cite us!
+
+> Gourlé H, Karlsson-Lindsjö O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. _Bioinformatics_ (2018) doi:10.1093/bioinformatics/bty630
+
+
+
+
+%package -n python3-InSilicoSeq
+Summary:	a sequencing simulator
+Provides:	python-InSilicoSeq
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-InSilicoSeq
+# InSilicoSeq
+
+## A sequencing simulator
+
+[![Build Status](https://github.com/HadrienG/InsilicoSeq/workflows/CI/badge.svg)](https://github.com/HadrienG/InSilicoSeq/actions)
+[![Documentation Status](https://readthedocs.org/projects/insilicoseq/badge/?version=latest)](http://insilicoseq.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/InSilicoSeq.svg)](https://badge.fury.io/py/InSilicoSeq)
+[![codecov](https://codecov.io/gh/HadrienG/InSilicoSeq/branch/master/graph/badge.svg)](https://codecov.io/gh/HadrienG/InSilicoSeq)
+[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty630-blue.svg)](https://doi.org/10.1093/bioinformatics/bty630)
+[![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](LICENSE)
+
+InSilicoSeq is a sequencing simulator producing realistic Illumina reads.
+Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
+
+InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.
+
+InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided.
+
+## Installation
+
+Insilicoseq is Available in [bioconda](https://bioconda.github.io/).
+
+To install with conda:
+
+```shell
+conda install -c bioconda insilicoseq
+```
+
+Or with pip:
+
+```shell
+pip install InSilicoSeq
+```
+
+_Note:_ Insilicoseq requires python >= 3.5 
+
+Alternatively, with docker:
+
+```shell
+docker pull hadrieng/insilicoseq:latest
+```
+
+For more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+## Usage
+
+InSilicoSeq has two subcommands: `iss generate` to generate Illumina reads and `iss model` to create an error model from which the reads will take their characteristics.
+
+InSilicoSeq comes with pre-computed error models that should be sufficient for most use cases.
+
+### Generate reads with a pre-computed error model
+
+for generating 1 million reads modelling a MiSeq instrument:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate --genomes SRS121011.fasta --model miseq --output miseq_reads
+```
+
+where `genomes.fasta` should be replaced by a (multi-)fasta file containing the reference genome(s) from which the simulated reads will be generated.
+
+InSilicoSeq comes with 3 error models: `MiSeq`, `HiSeq` and `NovaSeq`.
+
+If you have built your own model, pass the `.npz` file to the `--model` argument to simulate reads from your own error model.
+
+For 10 million reads and a custom error model:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate -g SRS121011.fasta -n 10m --model my_model.npz --output /path/to/my_reads
+```
+
+granted you have built `my_model.npz` with `iss model` (see [below](#create-your-own-error-model))
+
+For more examples and a full list of options, please refer to the full
+[documentation](http://insilicoseq.readthedocs.io)
+
+### Generate reads without input genomes
+
+We can download some for you! InSilicoSeq can download random genomes from the ncbi using the infamous [eutils](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
+
+The command
+
+```shell
+iss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads
+```
+
+will generate 1 million reads from 10 random bacterial genomes.
+
+For more examples and a full list of options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+### Create your own error model
+
+If you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.
+
+Say you have a reference metagenome called `genomes.fasta`, and read pairs `reads_R1.fastq.gz` and `reads_R2.fastq.gz`
+
+Align you reads against the reference:
+
+```shell
+bowtie2-build genomes.fasta genomes
+bowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \
+samtools view -bS | samtools sort -o genomes.bam
+samtools index genomes.bam
+```
+
+then build the model:
+
+```shell
+iss model -b genomes.bam -o genomes
+```
+
+which will create a `genome.npz` file containing your newly built model
+
+## License
+
+Code is under the [MIT](LICENSE) license.
+
+## Issues
+
+Found a bug or have a question? Please open an [issue](https://github.com/HadrienG/InSilicoSeq/issues)
+
+## Contributing
+
+We welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guidelines
+
+## Citation
+
+If you use our software, please cite us!
+
+> Gourlé H, Karlsson-Lindsjö O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. _Bioinformatics_ (2018) doi:10.1093/bioinformatics/bty630
+
+
+
+
+%package help
+Summary:	Development documents and examples for InSilicoSeq
+Provides:	python3-InSilicoSeq-doc
+%description help
+# InSilicoSeq
+
+## A sequencing simulator
+
+[![Build Status](https://github.com/HadrienG/InsilicoSeq/workflows/CI/badge.svg)](https://github.com/HadrienG/InSilicoSeq/actions)
+[![Documentation Status](https://readthedocs.org/projects/insilicoseq/badge/?version=latest)](http://insilicoseq.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/InSilicoSeq.svg)](https://badge.fury.io/py/InSilicoSeq)
+[![codecov](https://codecov.io/gh/HadrienG/InSilicoSeq/branch/master/graph/badge.svg)](https://codecov.io/gh/HadrienG/InSilicoSeq)
+[![doi](https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbty630-blue.svg)](https://doi.org/10.1093/bioinformatics/bty630)
+[![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](LICENSE)
+
+InSilicoSeq is a sequencing simulator producing realistic Illumina reads.
+Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
+
+InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data.
+
+InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided.
+
+## Installation
+
+Insilicoseq is Available in [bioconda](https://bioconda.github.io/).
+
+To install with conda:
+
+```shell
+conda install -c bioconda insilicoseq
+```
+
+Or with pip:
+
+```shell
+pip install InSilicoSeq
+```
+
+_Note:_ Insilicoseq requires python >= 3.5 
+
+Alternatively, with docker:
+
+```shell
+docker pull hadrieng/insilicoseq:latest
+```
+
+For more installation options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+## Usage
+
+InSilicoSeq has two subcommands: `iss generate` to generate Illumina reads and `iss model` to create an error model from which the reads will take their characteristics.
+
+InSilicoSeq comes with pre-computed error models that should be sufficient for most use cases.
+
+### Generate reads with a pre-computed error model
+
+for generating 1 million reads modelling a MiSeq instrument:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate --genomes SRS121011.fasta --model miseq --output miseq_reads
+```
+
+where `genomes.fasta` should be replaced by a (multi-)fasta file containing the reference genome(s) from which the simulated reads will be generated.
+
+InSilicoSeq comes with 3 error models: `MiSeq`, `HiSeq` and `NovaSeq`.
+
+If you have built your own model, pass the `.npz` file to the `--model` argument to simulate reads from your own error model.
+
+For 10 million reads and a custom error model:
+
+```shell
+curl -O -J -L https://osf.io/thser/download  # download the example data
+iss generate -g SRS121011.fasta -n 10m --model my_model.npz --output /path/to/my_reads
+```
+
+granted you have built `my_model.npz` with `iss model` (see [below](#create-your-own-error-model))
+
+For more examples and a full list of options, please refer to the full
+[documentation](http://insilicoseq.readthedocs.io)
+
+### Generate reads without input genomes
+
+We can download some for you! InSilicoSeq can download random genomes from the ncbi using the infamous [eutils](https://www.ncbi.nlm.nih.gov/books/NBK25501/)
+
+The command
+
+```shell
+iss generate --ncbi bacteria -u 10 --model MiSeq --output ncbi_reads
+```
+
+will generate 1 million reads from 10 random bacterial genomes.
+
+For more examples and a full list of options, please refer to the full [documentation](http://insilicoseq.readthedocs.io)
+
+### Create your own error model
+
+If you do not wish to use the pre-computed error models provided with InSilicoSeq, it is possible to create your own.
+
+Say you have a reference metagenome called `genomes.fasta`, and read pairs `reads_R1.fastq.gz` and `reads_R2.fastq.gz`
+
+Align you reads against the reference:
+
+```shell
+bowtie2-build genomes.fasta genomes
+bowtie2 -x genomes -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz | \
+samtools view -bS | samtools sort -o genomes.bam
+samtools index genomes.bam
+```
+
+then build the model:
+
+```shell
+iss model -b genomes.bam -o genomes
+```
+
+which will create a `genome.npz` file containing your newly built model
+
+## License
+
+Code is under the [MIT](LICENSE) license.
+
+## Issues
+
+Found a bug or have a question? Please open an [issue](https://github.com/HadrienG/InSilicoSeq/issues)
+
+## Contributing
+
+We welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guidelines
+
+## Citation
+
+If you use our software, please cite us!
+
+> Gourlé H, Karlsson-Lindsjö O, Hayer J and Bongcam+Rudloff E, Simulating Illumina data with InSilicoSeq. _Bioinformatics_ (2018) doi:10.1093/bioinformatics/bty630
+
+
+
+
+%prep
+%autosetup -n InSilicoSeq-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-InSilicoSeq -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.5.4-1
+- Package Spec generated