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+/jcvi-1.3.5.tar.gz
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+%global _empty_manifest_terminate_build 0
+Name:		python-jcvi
+Version:	1.3.5
+Release:	1
+Summary:	Python utility libraries on genome assembly, annotation and comparative genomics
+License:	BSD
+URL:		http://github.com/tanghaibao/jcvi
+Source0:	https://mirrors.aliyun.com/pypi/web/packages/54/41/853aa89aac24c68a4576289e3964a0b24be91075c76928323e7bba42d4e7/jcvi-1.3.5.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-CrossMap
+Requires:	python3-PyPDF2
+Requires:	python3-biopython
+Requires:	python3-boto3
+Requires:	python3-brewer2mpl
+Requires:	python3-deap
+Requires:	python3-ete3
+Requires:	python3-ftpretty
+Requires:	python3-gffutils
+Requires:	python3-goatools
+Requires:	python3-graphviz
+Requires:	python3-jinja2
+Requires:	python3-matplotlib
+Requires:	python3-more-itertools
+Requires:	python3-natsort
+Requires:	python3-networkx
+Requires:	python3-numpy
+Requires:	python3-ortools
+Requires:	python3-pybedtools
+Requires:	python3-rich
+Requires:	python3-scikit-image
+Requires:	python3-scipy
+Requires:	python3-seaborn
+Requires:	python3-webcolors
+
+%description
+# JCVI utility libraries
+
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205)
+[![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html?highlight=jcvi)
+[![Github Actions](https://github.com/tanghaibao/jcvi/workflows/build/badge.svg)](https://github.com/tanghaibao/jcvi/actions)
+[![Downloads](https://pepy.tech/badge/jcvi)](https://pepy.tech/project/jcvi)
+
+Collection of Python libraries to parse bioinformatics files, or perform
+computation related to assembly, annotation, and comparative genomics.
+
+|         |                                                                  |
+| ------- | ---------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))         |
+|         | Vivek Krishnakumar ([vivekkrish](https://github.com/vivekkrish)) |
+|         | Jingping Li ([Jingping](https://github.com/Jingping))            |
+|         | Xingtan Zhang ([tangerzhang](https://github.com/tangerzhang))    |
+| Email   | <tanghaibao@gmail.com>                                           |
+| License | [BSD](http://creativecommons.org/licenses/BSD/)                  |
+
+## Citations
+
+- If you use the MCscan pipeline for synteny inference, please cite:
+
+  _Tang et al. (2008) Synteny and Collinearity in Plant Genomes. [Science](https://science.sciencemag.org/content/320/5875/486)_
+
+![MCSCAN example](https://www.dropbox.com/s/9vl3ys3ndvimg4c/grape-peach-cacao.png?raw=1)
+
+- If you use the ALLMAPS pipeline for genome scaffolding, please cite:
+
+  _Tang et al. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1)_
+
+![ALLMAPS animation](https://www.dropbox.com/s/jfs8xavcxix37se/ALLMAPS.gif?raw=1)
+
+- For other uses, please cite the package directly:
+
+  _Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. [10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631)_
+
+![GRABSEEDS example](https://www.dropbox.com/s/yu9ehsi6sqifuaa/bluredges.png?raw=1)
+
+## Contents
+
+Following modules are available as generic Bioinformatics handling
+methods.
+
+- <kbd>algorithms</kbd>
+
+  - Linear programming solver with SCIP and GLPK.
+  - Supermap: find set of non-overlapping anchors in BLAST or NUCMER output.
+  - Longest or heaviest increasing subsequence.
+  - Matrix operations.
+
+- <kbd>apps</kbd>
+
+  - GenBank entrez accession, Phytozome, Ensembl and SRA downloader.
+  - Calculate (non)synonymous substitution rate between gene pairs.
+  - Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and viualization.
+  - Wrapper for BLAST+, LASTZ, LAST, BWA, BOWTIE2, CLC, CDHIT, CAP3, etc.
+
+- <kbd>formats</kbd>
+
+  Currently supports `.ace` format (phrap, cap3, etc.), `.agp`
+  (goldenpath), `.bed` format, `.blast` output, `.btab` format,
+  `.coords` format (`nucmer` output), `.fasta` format, `.fastq`
+  format, `.fpc` format, `.gff` format, `obo` format (ontology),
+  `.psl` format (UCSC blat, GMAP, etc.), `.posmap` format (Celera
+  assembler output), `.sam` format (read mapping), `.contig`
+  format (TIGR assembly format), etc.
+
+- <kbd>graphics</kbd>
+
+  - BLAST or synteny dot plot.
+  - Histogram using R and ASCII art.
+  - Paint regions on set of chromosomes.
+  - Macro-synteny and micro-synteny plots.
+
+- <kbd>utils</kbd>
+  - Grouper can be used as disjoint set data structure.
+  - range contains common range operations, like overlap
+    and chaining.
+  - Miscellaneous cookbook recipes, iterators decorators,
+    table utilities.
+
+Then there are modules that contain domain-specific methods.
+
+- <kbd>assembly</kbd>
+
+  - K-mer histogram analysis.
+  - Preparation and validation of tiling path for clone-based assemblies.
+  - Scaffolding through ALLMAPS, optical map and genetic map.
+  - Pre-assembly and post-assembly QC procedures.
+
+- <kbd>annotation</kbd>
+
+  - Training of _ab initio_ gene predictors.
+  - Calculate gene, exon and intron statistics.
+  - Wrapper for PASA and EVM.
+  - Launch multiple MAKER processes.
+
+- <kbd>compara</kbd>
+  - C-score based BLAST filter.
+  - Synteny scan (de-novo) and lift over (find nearby anchors).
+  - Ancestral genome reconstruction using Sankoff's and PAR method.
+  - Ortholog and tandem gene duplicates finder.
+
+## Applications
+
+Please visit [wiki](https://github.com/tanghaibao/jcvi/wiki) for
+full-fledged applications.
+
+## Dependencies
+
+Following are a list of third-party python packages that are used by
+some routines in the library. These dependencies are _not_ mandatory
+since they are only used by a few modules.
+
+- [Biopython](http://www.biopython.org)
+- [numpy](http://numpy.scipy.org)
+- [matplotlib](http://matplotlib.org/)
+
+There are other Python modules here and there in various scripts. The
+best way is to install them via `pip install` when you see
+`ImportError`.
+
+## Installation
+
+The easiest way is to install it via PyPI:
+
+```console
+pip install jcvi
+```
+
+To install the development version:
+
+```console
+pip install git+git://github.com/tanghaibao/jcvi.git
+```
+
+Alternatively, if you want to install manually:
+
+```console
+cd ~/code  # or any directory of your choice
+git clone git://github.com/tanghaibao/jcvi.git
+pip install -e .
+```
+
+In addition, a few module might ask for locations of external programs,
+if the extended cannot be found in your `PATH`. The external programs
+that are often used are:
+
+- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)
+- [BEDTOOLS](http://code.google.com/p/bedtools/)
+- [EMBOSS](http://emboss.sourceforge.net/)
+
+Most of the scripts in this package contains multiple actions. To use
+the `fasta` example:
+
+```console
+Usage:
+    python -m jcvi.formats.fasta ACTION
+
+
+Available ACTIONs:
+          clean | Remove irregular chars in FASTA seqs
+           diff | Check if two fasta records contain same information
+        extract | Given fasta file and seq id, retrieve the sequence in fasta format
+          fastq | Combine fasta and qual to create fastq file
+         filter | Filter the records by size
+         format | Trim accession id to the first space or switch id based on 2-column mapping file
+        fromtab | Convert 2-column sequence file to FASTA format
+           gaps | Print out a list of gap sizes within sequences
+             gc | Plot G+C content distribution
+      identical | Given 2 fasta files, find all exactly identical records
+            ids | Generate a list of headers
+           info | Run `sequence_info` on fasta files
+          ispcr | Reformat paired primers into isPcr query format
+           join | Concatenate a list of seqs and add gaps in between
+     longestorf | Find longest orf for CDS fasta
+           pair | Sort paired reads to .pairs, rest to .fragments
+    pairinplace | Starting from fragment.fasta, find if adjacent records can form pairs
+           pool | Pool a bunch of fastafiles together and add prefix
+           qual | Generate dummy .qual file based on FASTA file
+         random | Randomly take some records
+         sequin | Generate a gapped fasta file for sequin submission
+       simulate | Simulate random fasta file for testing
+           some | Include or exclude a list of records (also performs on .qual file if available)
+           sort | Sort the records by IDs, sizes, etc.
+        summary | Report the real no of bases and N's in fasta files
+           tidy | Normalize gap sizes and remove small components in fasta
+      translate | Translate CDS to proteins
+           trim | Given a cross_match screened fasta, trim the sequence
+      trimsplit | Split sequences at lower-cased letters
+           uniq | Remove records that are the same
+```
+
+Then you need to use one action, you can just do:
+
+```console
+python -m jcvi.formats.fasta extract
+```
+
+This will tell you the options and arguments it expects.
+
+**Feel free to check out other scripts in the package, it is not just
+for FASTA.**
+
+
+
+
+%package -n python3-jcvi
+Summary:	Python utility libraries on genome assembly, annotation and comparative genomics
+Provides:	python-jcvi
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-jcvi
+# JCVI utility libraries
+
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205)
+[![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html?highlight=jcvi)
+[![Github Actions](https://github.com/tanghaibao/jcvi/workflows/build/badge.svg)](https://github.com/tanghaibao/jcvi/actions)
+[![Downloads](https://pepy.tech/badge/jcvi)](https://pepy.tech/project/jcvi)
+
+Collection of Python libraries to parse bioinformatics files, or perform
+computation related to assembly, annotation, and comparative genomics.
+
+|         |                                                                  |
+| ------- | ---------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))         |
+|         | Vivek Krishnakumar ([vivekkrish](https://github.com/vivekkrish)) |
+|         | Jingping Li ([Jingping](https://github.com/Jingping))            |
+|         | Xingtan Zhang ([tangerzhang](https://github.com/tangerzhang))    |
+| Email   | <tanghaibao@gmail.com>                                           |
+| License | [BSD](http://creativecommons.org/licenses/BSD/)                  |
+
+## Citations
+
+- If you use the MCscan pipeline for synteny inference, please cite:
+
+  _Tang et al. (2008) Synteny and Collinearity in Plant Genomes. [Science](https://science.sciencemag.org/content/320/5875/486)_
+
+![MCSCAN example](https://www.dropbox.com/s/9vl3ys3ndvimg4c/grape-peach-cacao.png?raw=1)
+
+- If you use the ALLMAPS pipeline for genome scaffolding, please cite:
+
+  _Tang et al. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1)_
+
+![ALLMAPS animation](https://www.dropbox.com/s/jfs8xavcxix37se/ALLMAPS.gif?raw=1)
+
+- For other uses, please cite the package directly:
+
+  _Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. [10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631)_
+
+![GRABSEEDS example](https://www.dropbox.com/s/yu9ehsi6sqifuaa/bluredges.png?raw=1)
+
+## Contents
+
+Following modules are available as generic Bioinformatics handling
+methods.
+
+- <kbd>algorithms</kbd>
+
+  - Linear programming solver with SCIP and GLPK.
+  - Supermap: find set of non-overlapping anchors in BLAST or NUCMER output.
+  - Longest or heaviest increasing subsequence.
+  - Matrix operations.
+
+- <kbd>apps</kbd>
+
+  - GenBank entrez accession, Phytozome, Ensembl and SRA downloader.
+  - Calculate (non)synonymous substitution rate between gene pairs.
+  - Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and viualization.
+  - Wrapper for BLAST+, LASTZ, LAST, BWA, BOWTIE2, CLC, CDHIT, CAP3, etc.
+
+- <kbd>formats</kbd>
+
+  Currently supports `.ace` format (phrap, cap3, etc.), `.agp`
+  (goldenpath), `.bed` format, `.blast` output, `.btab` format,
+  `.coords` format (`nucmer` output), `.fasta` format, `.fastq`
+  format, `.fpc` format, `.gff` format, `obo` format (ontology),
+  `.psl` format (UCSC blat, GMAP, etc.), `.posmap` format (Celera
+  assembler output), `.sam` format (read mapping), `.contig`
+  format (TIGR assembly format), etc.
+
+- <kbd>graphics</kbd>
+
+  - BLAST or synteny dot plot.
+  - Histogram using R and ASCII art.
+  - Paint regions on set of chromosomes.
+  - Macro-synteny and micro-synteny plots.
+
+- <kbd>utils</kbd>
+  - Grouper can be used as disjoint set data structure.
+  - range contains common range operations, like overlap
+    and chaining.
+  - Miscellaneous cookbook recipes, iterators decorators,
+    table utilities.
+
+Then there are modules that contain domain-specific methods.
+
+- <kbd>assembly</kbd>
+
+  - K-mer histogram analysis.
+  - Preparation and validation of tiling path for clone-based assemblies.
+  - Scaffolding through ALLMAPS, optical map and genetic map.
+  - Pre-assembly and post-assembly QC procedures.
+
+- <kbd>annotation</kbd>
+
+  - Training of _ab initio_ gene predictors.
+  - Calculate gene, exon and intron statistics.
+  - Wrapper for PASA and EVM.
+  - Launch multiple MAKER processes.
+
+- <kbd>compara</kbd>
+  - C-score based BLAST filter.
+  - Synteny scan (de-novo) and lift over (find nearby anchors).
+  - Ancestral genome reconstruction using Sankoff's and PAR method.
+  - Ortholog and tandem gene duplicates finder.
+
+## Applications
+
+Please visit [wiki](https://github.com/tanghaibao/jcvi/wiki) for
+full-fledged applications.
+
+## Dependencies
+
+Following are a list of third-party python packages that are used by
+some routines in the library. These dependencies are _not_ mandatory
+since they are only used by a few modules.
+
+- [Biopython](http://www.biopython.org)
+- [numpy](http://numpy.scipy.org)
+- [matplotlib](http://matplotlib.org/)
+
+There are other Python modules here and there in various scripts. The
+best way is to install them via `pip install` when you see
+`ImportError`.
+
+## Installation
+
+The easiest way is to install it via PyPI:
+
+```console
+pip install jcvi
+```
+
+To install the development version:
+
+```console
+pip install git+git://github.com/tanghaibao/jcvi.git
+```
+
+Alternatively, if you want to install manually:
+
+```console
+cd ~/code  # or any directory of your choice
+git clone git://github.com/tanghaibao/jcvi.git
+pip install -e .
+```
+
+In addition, a few module might ask for locations of external programs,
+if the extended cannot be found in your `PATH`. The external programs
+that are often used are:
+
+- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)
+- [BEDTOOLS](http://code.google.com/p/bedtools/)
+- [EMBOSS](http://emboss.sourceforge.net/)
+
+Most of the scripts in this package contains multiple actions. To use
+the `fasta` example:
+
+```console
+Usage:
+    python -m jcvi.formats.fasta ACTION
+
+
+Available ACTIONs:
+          clean | Remove irregular chars in FASTA seqs
+           diff | Check if two fasta records contain same information
+        extract | Given fasta file and seq id, retrieve the sequence in fasta format
+          fastq | Combine fasta and qual to create fastq file
+         filter | Filter the records by size
+         format | Trim accession id to the first space or switch id based on 2-column mapping file
+        fromtab | Convert 2-column sequence file to FASTA format
+           gaps | Print out a list of gap sizes within sequences
+             gc | Plot G+C content distribution
+      identical | Given 2 fasta files, find all exactly identical records
+            ids | Generate a list of headers
+           info | Run `sequence_info` on fasta files
+          ispcr | Reformat paired primers into isPcr query format
+           join | Concatenate a list of seqs and add gaps in between
+     longestorf | Find longest orf for CDS fasta
+           pair | Sort paired reads to .pairs, rest to .fragments
+    pairinplace | Starting from fragment.fasta, find if adjacent records can form pairs
+           pool | Pool a bunch of fastafiles together and add prefix
+           qual | Generate dummy .qual file based on FASTA file
+         random | Randomly take some records
+         sequin | Generate a gapped fasta file for sequin submission
+       simulate | Simulate random fasta file for testing
+           some | Include or exclude a list of records (also performs on .qual file if available)
+           sort | Sort the records by IDs, sizes, etc.
+        summary | Report the real no of bases and N's in fasta files
+           tidy | Normalize gap sizes and remove small components in fasta
+      translate | Translate CDS to proteins
+           trim | Given a cross_match screened fasta, trim the sequence
+      trimsplit | Split sequences at lower-cased letters
+           uniq | Remove records that are the same
+```
+
+Then you need to use one action, you can just do:
+
+```console
+python -m jcvi.formats.fasta extract
+```
+
+This will tell you the options and arguments it expects.
+
+**Feel free to check out other scripts in the package, it is not just
+for FASTA.**
+
+
+
+
+%package help
+Summary:	Development documents and examples for jcvi
+Provides:	python3-jcvi-doc
+%description help
+# JCVI utility libraries
+
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205)
+[![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi)
+[![bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/jcvi/README.html?highlight=jcvi)
+[![Github Actions](https://github.com/tanghaibao/jcvi/workflows/build/badge.svg)](https://github.com/tanghaibao/jcvi/actions)
+[![Downloads](https://pepy.tech/badge/jcvi)](https://pepy.tech/project/jcvi)
+
+Collection of Python libraries to parse bioinformatics files, or perform
+computation related to assembly, annotation, and comparative genomics.
+
+|         |                                                                  |
+| ------- | ---------------------------------------------------------------- |
+| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))         |
+|         | Vivek Krishnakumar ([vivekkrish](https://github.com/vivekkrish)) |
+|         | Jingping Li ([Jingping](https://github.com/Jingping))            |
+|         | Xingtan Zhang ([tangerzhang](https://github.com/tangerzhang))    |
+| Email   | <tanghaibao@gmail.com>                                           |
+| License | [BSD](http://creativecommons.org/licenses/BSD/)                  |
+
+## Citations
+
+- If you use the MCscan pipeline for synteny inference, please cite:
+
+  _Tang et al. (2008) Synteny and Collinearity in Plant Genomes. [Science](https://science.sciencemag.org/content/320/5875/486)_
+
+![MCSCAN example](https://www.dropbox.com/s/9vl3ys3ndvimg4c/grape-peach-cacao.png?raw=1)
+
+- If you use the ALLMAPS pipeline for genome scaffolding, please cite:
+
+  _Tang et al. (2015) ALLMAPS: robust scaffold ordering based on multiple maps. [Genome Biology](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0573-1)_
+
+![ALLMAPS animation](https://www.dropbox.com/s/jfs8xavcxix37se/ALLMAPS.gif?raw=1)
+
+- For other uses, please cite the package directly:
+
+  _Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo. [10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631)_
+
+![GRABSEEDS example](https://www.dropbox.com/s/yu9ehsi6sqifuaa/bluredges.png?raw=1)
+
+## Contents
+
+Following modules are available as generic Bioinformatics handling
+methods.
+
+- <kbd>algorithms</kbd>
+
+  - Linear programming solver with SCIP and GLPK.
+  - Supermap: find set of non-overlapping anchors in BLAST or NUCMER output.
+  - Longest or heaviest increasing subsequence.
+  - Matrix operations.
+
+- <kbd>apps</kbd>
+
+  - GenBank entrez accession, Phytozome, Ensembl and SRA downloader.
+  - Calculate (non)synonymous substitution rate between gene pairs.
+  - Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and viualization.
+  - Wrapper for BLAST+, LASTZ, LAST, BWA, BOWTIE2, CLC, CDHIT, CAP3, etc.
+
+- <kbd>formats</kbd>
+
+  Currently supports `.ace` format (phrap, cap3, etc.), `.agp`
+  (goldenpath), `.bed` format, `.blast` output, `.btab` format,
+  `.coords` format (`nucmer` output), `.fasta` format, `.fastq`
+  format, `.fpc` format, `.gff` format, `obo` format (ontology),
+  `.psl` format (UCSC blat, GMAP, etc.), `.posmap` format (Celera
+  assembler output), `.sam` format (read mapping), `.contig`
+  format (TIGR assembly format), etc.
+
+- <kbd>graphics</kbd>
+
+  - BLAST or synteny dot plot.
+  - Histogram using R and ASCII art.
+  - Paint regions on set of chromosomes.
+  - Macro-synteny and micro-synteny plots.
+
+- <kbd>utils</kbd>
+  - Grouper can be used as disjoint set data structure.
+  - range contains common range operations, like overlap
+    and chaining.
+  - Miscellaneous cookbook recipes, iterators decorators,
+    table utilities.
+
+Then there are modules that contain domain-specific methods.
+
+- <kbd>assembly</kbd>
+
+  - K-mer histogram analysis.
+  - Preparation and validation of tiling path for clone-based assemblies.
+  - Scaffolding through ALLMAPS, optical map and genetic map.
+  - Pre-assembly and post-assembly QC procedures.
+
+- <kbd>annotation</kbd>
+
+  - Training of _ab initio_ gene predictors.
+  - Calculate gene, exon and intron statistics.
+  - Wrapper for PASA and EVM.
+  - Launch multiple MAKER processes.
+
+- <kbd>compara</kbd>
+  - C-score based BLAST filter.
+  - Synteny scan (de-novo) and lift over (find nearby anchors).
+  - Ancestral genome reconstruction using Sankoff's and PAR method.
+  - Ortholog and tandem gene duplicates finder.
+
+## Applications
+
+Please visit [wiki](https://github.com/tanghaibao/jcvi/wiki) for
+full-fledged applications.
+
+## Dependencies
+
+Following are a list of third-party python packages that are used by
+some routines in the library. These dependencies are _not_ mandatory
+since they are only used by a few modules.
+
+- [Biopython](http://www.biopython.org)
+- [numpy](http://numpy.scipy.org)
+- [matplotlib](http://matplotlib.org/)
+
+There are other Python modules here and there in various scripts. The
+best way is to install them via `pip install` when you see
+`ImportError`.
+
+## Installation
+
+The easiest way is to install it via PyPI:
+
+```console
+pip install jcvi
+```
+
+To install the development version:
+
+```console
+pip install git+git://github.com/tanghaibao/jcvi.git
+```
+
+Alternatively, if you want to install manually:
+
+```console
+cd ~/code  # or any directory of your choice
+git clone git://github.com/tanghaibao/jcvi.git
+pip install -e .
+```
+
+In addition, a few module might ask for locations of external programs,
+if the extended cannot be found in your `PATH`. The external programs
+that are often used are:
+
+- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)
+- [BEDTOOLS](http://code.google.com/p/bedtools/)
+- [EMBOSS](http://emboss.sourceforge.net/)
+
+Most of the scripts in this package contains multiple actions. To use
+the `fasta` example:
+
+```console
+Usage:
+    python -m jcvi.formats.fasta ACTION
+
+
+Available ACTIONs:
+          clean | Remove irregular chars in FASTA seqs
+           diff | Check if two fasta records contain same information
+        extract | Given fasta file and seq id, retrieve the sequence in fasta format
+          fastq | Combine fasta and qual to create fastq file
+         filter | Filter the records by size
+         format | Trim accession id to the first space or switch id based on 2-column mapping file
+        fromtab | Convert 2-column sequence file to FASTA format
+           gaps | Print out a list of gap sizes within sequences
+             gc | Plot G+C content distribution
+      identical | Given 2 fasta files, find all exactly identical records
+            ids | Generate a list of headers
+           info | Run `sequence_info` on fasta files
+          ispcr | Reformat paired primers into isPcr query format
+           join | Concatenate a list of seqs and add gaps in between
+     longestorf | Find longest orf for CDS fasta
+           pair | Sort paired reads to .pairs, rest to .fragments
+    pairinplace | Starting from fragment.fasta, find if adjacent records can form pairs
+           pool | Pool a bunch of fastafiles together and add prefix
+           qual | Generate dummy .qual file based on FASTA file
+         random | Randomly take some records
+         sequin | Generate a gapped fasta file for sequin submission
+       simulate | Simulate random fasta file for testing
+           some | Include or exclude a list of records (also performs on .qual file if available)
+           sort | Sort the records by IDs, sizes, etc.
+        summary | Report the real no of bases and N's in fasta files
+           tidy | Normalize gap sizes and remove small components in fasta
+      translate | Translate CDS to proteins
+           trim | Given a cross_match screened fasta, trim the sequence
+      trimsplit | Split sequences at lower-cased letters
+           uniq | Remove records that are the same
+```
+
+Then you need to use one action, you can just do:
+
+```console
+python -m jcvi.formats.fasta extract
+```
+
+This will tell you the options and arguments it expects.
+
+**Feel free to check out other scripts in the package, it is not just
+for FASTA.**
+
+
+
+
+%prep
+%autosetup -n jcvi-1.3.5
+
+%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-jcvi -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Fri Jun 09 2023 Python_Bot <Python_Bot@openeuler.org> - 1.3.5-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..73675df
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+5ad1c361202bb37a44ab38e6f8183d10  jcvi-1.3.5.tar.gz