automatic import of python-nanocompopeneuler20.03

3 files changed, 341 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..4befcf3 100644
--- a/.gitignore
+++ b/.gitignore
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+/NanoComp-1.21.0.tar.gz
diff --git a/python-nanocomp.spec b/python-nanocomp.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-NanoComp
+Version:	1.21.0
+Release:	1
+Summary:	Comparing runs of Oxford Nanopore sequencing data and alignments
+License:	MIT
+URL:		https://github.com/wdecoster/NanoComp
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/df/5c/90c269e98d84fddd731ebb897a12ca6d2d793212fa76315e2f0406368996/NanoComp-1.21.0.tar.gz
+BuildArch:	noarch
+
+
+%description
+# NanoComp
+
+
+Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
+
+As of version 1.1.0 NanoComp will also create a static png image for dynamic html plots, as the latter can get quite big and slow to load for big datasets. This however requires that you install [orca](https://github.com/plotly/orca). Without orca the script still works, but no static copies of dynamic plots are created.
+
+[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
+
+
+### INSTALLATION
+`pip install NanoComp`  
+
+This script is written for Python3.
+
+### USAGE
+```
+NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]
+                [--raw] [--readtype {1D,2D,1D2}] [--barcoded]
+                [--split_runs TSV_FILE]
+                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
+                [-n names [names ...]] [--plot {violin,box}] [--title TITLE]
+                (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])
+
+General options:
+  -h, --help            show the help and exit
+  -v, --version         Print version and exit.
+  -t, --threads THREADS
+                        Set the allowed number of threads to be used by the script
+  -o, --outdir OUTDIR   Specify directory in which output has to be created.
+  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
+  --verbose             Write log messages also to terminal.
+  --raw                 Store the extracted data in tab separated file.
+
+Options for filtering or transforming input prior to plotting:
+  --readtype {1D,2D,1D2}
+                        Which read type to extract information about from summary. Options are 1D, 2D,
+                        1D2
+  --barcoded            Barcoded experiment in summary format, splitting per barcode.
+  --split_runs TSV_FILE
+                        File: Split the summary on run IDs and use names in tsv file. Mandatory header
+                        fields are 'NAME' and 'RUN_ID'.
+
+Options for customizing the plots created:
+  -f, --format {'png'(default),'jpg','jpeg','webp','svg','pdf','eps','json'}
+                        Specify the output format of the plots. JSON output allows for customisation by the end-user after plotting the figures (https://plotly.com/python-api-reference/generated/plotly.io.read_json.html).
+  -n, --names names     Specify the names to be used for the datasets.
+  -c, --colors colors   Specify the colors to be used for the datasets.
+  --plot {violin,box,ridge,false}
+                        Which plot type to use: 'box', 'violin' (default), 'ridge' (joyplot) or 'false' (no plots)
+  --title TITLE         Add a title to all plots, requires quoting if using spaces
+
+Input data sources, one of these is required.:
+  --fastq files [files ...]
+                        Data is in (compressed) fastq format.
+  --fasta files [files ...]
+                        Data is in (compressed) fasta format.
+  --summary files [files ...]
+                        Data is in (compressed) summary files generated by albacore or guppy.
+  --bam files [files ...]
+                        Data is in sorted bam files.
+
+```
+
+[Example file for --split_runs](https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv)
+
+
+
+
+
+
+### EXAMPLES
+```
+NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs
+NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
+```
+
+
+### EXAMPLE OUTPUT
+![loglength example](https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png)
+![box percentIdentity example](https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png)
+
+[See more examples](https://github.com/wdecoster/nanocomp/tree/master/examples)
+
+I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanocomp/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
+
+
+## CITATION
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+
+
+%package -n python3-NanoComp
+Summary:	Comparing runs of Oxford Nanopore sequencing data and alignments
+Provides:	python-NanoComp
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-NanoComp
+# NanoComp
+
+
+Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
+
+As of version 1.1.0 NanoComp will also create a static png image for dynamic html plots, as the latter can get quite big and slow to load for big datasets. This however requires that you install [orca](https://github.com/plotly/orca). Without orca the script still works, but no static copies of dynamic plots are created.
+
+[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
+
+
+### INSTALLATION
+`pip install NanoComp`  
+
+This script is written for Python3.
+
+### USAGE
+```
+NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]
+                [--raw] [--readtype {1D,2D,1D2}] [--barcoded]
+                [--split_runs TSV_FILE]
+                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
+                [-n names [names ...]] [--plot {violin,box}] [--title TITLE]
+                (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])
+
+General options:
+  -h, --help            show the help and exit
+  -v, --version         Print version and exit.
+  -t, --threads THREADS
+                        Set the allowed number of threads to be used by the script
+  -o, --outdir OUTDIR   Specify directory in which output has to be created.
+  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
+  --verbose             Write log messages also to terminal.
+  --raw                 Store the extracted data in tab separated file.
+
+Options for filtering or transforming input prior to plotting:
+  --readtype {1D,2D,1D2}
+                        Which read type to extract information about from summary. Options are 1D, 2D,
+                        1D2
+  --barcoded            Barcoded experiment in summary format, splitting per barcode.
+  --split_runs TSV_FILE
+                        File: Split the summary on run IDs and use names in tsv file. Mandatory header
+                        fields are 'NAME' and 'RUN_ID'.
+
+Options for customizing the plots created:
+  -f, --format {'png'(default),'jpg','jpeg','webp','svg','pdf','eps','json'}
+                        Specify the output format of the plots. JSON output allows for customisation by the end-user after plotting the figures (https://plotly.com/python-api-reference/generated/plotly.io.read_json.html).
+  -n, --names names     Specify the names to be used for the datasets.
+  -c, --colors colors   Specify the colors to be used for the datasets.
+  --plot {violin,box,ridge,false}
+                        Which plot type to use: 'box', 'violin' (default), 'ridge' (joyplot) or 'false' (no plots)
+  --title TITLE         Add a title to all plots, requires quoting if using spaces
+
+Input data sources, one of these is required.:
+  --fastq files [files ...]
+                        Data is in (compressed) fastq format.
+  --fasta files [files ...]
+                        Data is in (compressed) fasta format.
+  --summary files [files ...]
+                        Data is in (compressed) summary files generated by albacore or guppy.
+  --bam files [files ...]
+                        Data is in sorted bam files.
+
+```
+
+[Example file for --split_runs](https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv)
+
+
+
+
+
+
+### EXAMPLES
+```
+NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs
+NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
+```
+
+
+### EXAMPLE OUTPUT
+![loglength example](https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png)
+![box percentIdentity example](https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png)
+
+[See more examples](https://github.com/wdecoster/nanocomp/tree/master/examples)
+
+I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanocomp/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
+
+
+## CITATION
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+
+
+%package help
+Summary:	Development documents and examples for NanoComp
+Provides:	python3-NanoComp-doc
+%description help
+# NanoComp
+
+
+Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
+
+As of version 1.1.0 NanoComp will also create a static png image for dynamic html plots, as the latter can get quite big and slow to load for big datasets. This however requires that you install [orca](https://github.com/plotly/orca). Without orca the script still works, but no static copies of dynamic plots are created.
+
+[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
+
+
+### INSTALLATION
+`pip install NanoComp`  
+
+This script is written for Python3.
+
+### USAGE
+```
+NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]
+                [--raw] [--readtype {1D,2D,1D2}] [--barcoded]
+                [--split_runs TSV_FILE]
+                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
+                [-n names [names ...]] [--plot {violin,box}] [--title TITLE]
+                (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])
+
+General options:
+  -h, --help            show the help and exit
+  -v, --version         Print version and exit.
+  -t, --threads THREADS
+                        Set the allowed number of threads to be used by the script
+  -o, --outdir OUTDIR   Specify directory in which output has to be created.
+  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
+  --verbose             Write log messages also to terminal.
+  --raw                 Store the extracted data in tab separated file.
+
+Options for filtering or transforming input prior to plotting:
+  --readtype {1D,2D,1D2}
+                        Which read type to extract information about from summary. Options are 1D, 2D,
+                        1D2
+  --barcoded            Barcoded experiment in summary format, splitting per barcode.
+  --split_runs TSV_FILE
+                        File: Split the summary on run IDs and use names in tsv file. Mandatory header
+                        fields are 'NAME' and 'RUN_ID'.
+
+Options for customizing the plots created:
+  -f, --format {'png'(default),'jpg','jpeg','webp','svg','pdf','eps','json'}
+                        Specify the output format of the plots. JSON output allows for customisation by the end-user after plotting the figures (https://plotly.com/python-api-reference/generated/plotly.io.read_json.html).
+  -n, --names names     Specify the names to be used for the datasets.
+  -c, --colors colors   Specify the colors to be used for the datasets.
+  --plot {violin,box,ridge,false}
+                        Which plot type to use: 'box', 'violin' (default), 'ridge' (joyplot) or 'false' (no plots)
+  --title TITLE         Add a title to all plots, requires quoting if using spaces
+
+Input data sources, one of these is required.:
+  --fastq files [files ...]
+                        Data is in (compressed) fastq format.
+  --fasta files [files ...]
+                        Data is in (compressed) fasta format.
+  --summary files [files ...]
+                        Data is in (compressed) summary files generated by albacore or guppy.
+  --bam files [files ...]
+                        Data is in sorted bam files.
+
+```
+
+[Example file for --split_runs](https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv)
+
+
+
+
+
+
+### EXAMPLES
+```
+NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs
+NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
+```
+
+
+### EXAMPLE OUTPUT
+![loglength example](https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png)
+![box percentIdentity example](https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png)
+
+[See more examples](https://github.com/wdecoster/nanocomp/tree/master/examples)
+
+I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanocomp/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.
+
+
+## CITATION
+If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+
+
+%prep
+%autosetup -n NanoComp-1.21.0
+
+%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-NanoComp -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 1.21.0-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..ba3da1b
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+4d7dca998a373e036b839c333634ba25  NanoComp-1.21.0.tar.gz