From adc61877cbc4cccb3e51f198a5a0aa8a60fa5c88 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Wed, 31 May 2023 03:34:31 +0000 Subject: automatic import of python-nanofilt --- python-nanofilt.spec | 297 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 297 insertions(+) create mode 100644 python-nanofilt.spec (limited to 'python-nanofilt.spec') diff --git a/python-nanofilt.spec b/python-nanofilt.spec new file mode 100644 index 0000000..2fdb5a5 --- /dev/null +++ b/python-nanofilt.spec @@ -0,0 +1,297 @@ +%global _empty_manifest_terminate_build 0 +Name: python-NanoFilt +Version: 2.8.0 +Release: 1 +Summary: Filtering and trimming of Oxford Nanopore Sequencing data +License: GPLv3 +URL: https://github.com/wdecoster/nanofilt +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/85/fb/6218b8f18dd3b39569cdfd2803f837730f392cc31df58d5ea927cc14c40c/NanoFilt-2.8.0.tar.gz +BuildArch: noarch + + +%description +# Nanofilt +Filtering and trimming of long read sequencing data. + +[![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) +[![conda badge](https://anaconda.org/bioconda/nanofilt/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanofilt) +[![Build Status](https://travis-ci.org/wdecoster/nanofilt.svg?branch=master)](https://travis-ci.org/wdecoster/nanofilt) + + + +Filtering on quality and/or read length, and optional trimming after passing filters. +Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. + +Intended to be used: +- directly after fastq extraction +- prior to mapping +- in a stream between extraction and mapping + +See also [my post about NanoFilt on my blog Gigabase or gigabyte](https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/). +Due to [a discrepancy](https://gigabaseorgigabyte.wordpress.com/2017/07/14/calculated-average-quality-vs-albacore-summary/) between calculated read quality and the quality as summarized by albacore this script takes since v1.1.0 optionally also a `--summary` argument. Using this argument with the sequencing_summary.txt file from albacore will do the filtering using the quality scores from the summary. It's also faster. + +### INSTALLATION AND UPGRADING: + +`pip install nanofilt` +`pip install nanofilt --upgrade` + +or + +`conda install -c bioconda nanofilt` + +NanoFilt is written for Python 3. + +### USAGE: +``` +NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH] + [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC] + [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP] + [-s SUMMARY] [--readtype {1D,2D,1D2}] + [input] + +Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin. + +General options: + -h, --help show the help and exit + -v, --version Print version and exit. + --logfile LOGFILE Specify the path and filename for the log file. + input input, uncompressed fastq file (optional) + +Options for filtering reads on.: + -l, --length LENGTH Filter on a minimum read length + --maxlength MAXLENGTH Filter on a maximum read length + -q, --quality QUALITY Filter on a minimum average read quality score + --minGC MINGC Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + --maxGC MAXGC Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + +Options for trimming reads.: + --headcrop HEADCROP Trim n nucleotides from start of read + --tailcrop TAILCROP Trim n nucleotides from end of read + +Input options.: + -s, --summary SUMMARY Use albacore or guppy summary file for quality scores + --readtype Which read type to extract information about from summary. Options are 1D, 2D or 1D2 + ``` + +### EXAMPLES +```bash +gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam - +gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz +gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz +``` + +I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanofilt/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-NanoFilt +Summary: Filtering and trimming of Oxford Nanopore Sequencing data +Provides: python-NanoFilt +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-NanoFilt +# Nanofilt +Filtering and trimming of long read sequencing data. + +[![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) +[![conda badge](https://anaconda.org/bioconda/nanofilt/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanofilt) +[![Build Status](https://travis-ci.org/wdecoster/nanofilt.svg?branch=master)](https://travis-ci.org/wdecoster/nanofilt) + + + +Filtering on quality and/or read length, and optional trimming after passing filters. +Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. + +Intended to be used: +- directly after fastq extraction +- prior to mapping +- in a stream between extraction and mapping + +See also [my post about NanoFilt on my blog Gigabase or gigabyte](https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/). +Due to [a discrepancy](https://gigabaseorgigabyte.wordpress.com/2017/07/14/calculated-average-quality-vs-albacore-summary/) between calculated read quality and the quality as summarized by albacore this script takes since v1.1.0 optionally also a `--summary` argument. Using this argument with the sequencing_summary.txt file from albacore will do the filtering using the quality scores from the summary. It's also faster. + +### INSTALLATION AND UPGRADING: + +`pip install nanofilt` +`pip install nanofilt --upgrade` + +or + +`conda install -c bioconda nanofilt` + +NanoFilt is written for Python 3. + +### USAGE: +``` +NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH] + [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC] + [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP] + [-s SUMMARY] [--readtype {1D,2D,1D2}] + [input] + +Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin. + +General options: + -h, --help show the help and exit + -v, --version Print version and exit. + --logfile LOGFILE Specify the path and filename for the log file. + input input, uncompressed fastq file (optional) + +Options for filtering reads on.: + -l, --length LENGTH Filter on a minimum read length + --maxlength MAXLENGTH Filter on a maximum read length + -q, --quality QUALITY Filter on a minimum average read quality score + --minGC MINGC Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + --maxGC MAXGC Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + +Options for trimming reads.: + --headcrop HEADCROP Trim n nucleotides from start of read + --tailcrop TAILCROP Trim n nucleotides from end of read + +Input options.: + -s, --summary SUMMARY Use albacore or guppy summary file for quality scores + --readtype Which read type to extract information about from summary. Options are 1D, 2D or 1D2 + ``` + +### EXAMPLES +```bash +gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam - +gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz +gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz +``` + +I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanofilt/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 NanoFilt +Provides: python3-NanoFilt-doc +%description help +# Nanofilt +Filtering and trimming of long read sequencing data. + +[![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) +[![conda badge](https://anaconda.org/bioconda/nanofilt/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanofilt) +[![Build Status](https://travis-ci.org/wdecoster/nanofilt.svg?branch=master)](https://travis-ci.org/wdecoster/nanofilt) + + + +Filtering on quality and/or read length, and optional trimming after passing filters. +Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. + +Intended to be used: +- directly after fastq extraction +- prior to mapping +- in a stream between extraction and mapping + +See also [my post about NanoFilt on my blog Gigabase or gigabyte](https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/). +Due to [a discrepancy](https://gigabaseorgigabyte.wordpress.com/2017/07/14/calculated-average-quality-vs-albacore-summary/) between calculated read quality and the quality as summarized by albacore this script takes since v1.1.0 optionally also a `--summary` argument. Using this argument with the sequencing_summary.txt file from albacore will do the filtering using the quality scores from the summary. It's also faster. + +### INSTALLATION AND UPGRADING: + +`pip install nanofilt` +`pip install nanofilt --upgrade` + +or + +`conda install -c bioconda nanofilt` + +NanoFilt is written for Python 3. + +### USAGE: +``` +NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH] + [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC] + [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP] + [-s SUMMARY] [--readtype {1D,2D,1D2}] + [input] + +Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin. + +General options: + -h, --help show the help and exit + -v, --version Print version and exit. + --logfile LOGFILE Specify the path and filename for the log file. + input input, uncompressed fastq file (optional) + +Options for filtering reads on.: + -l, --length LENGTH Filter on a minimum read length + --maxlength MAXLENGTH Filter on a maximum read length + -q, --quality QUALITY Filter on a minimum average read quality score + --minGC MINGC Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + --maxGC MAXGC Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if + using summary file. + +Options for trimming reads.: + --headcrop HEADCROP Trim n nucleotides from start of read + --tailcrop TAILCROP Trim n nucleotides from end of read + +Input options.: + -s, --summary SUMMARY Use albacore or guppy summary file for quality scores + --readtype Which read type to extract information about from summary. Options are 1D, 2D or 1D2 + ``` + +### EXAMPLES +```bash +gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam - +gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz +gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz +``` + +I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanofilt/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 NanoFilt-2.8.0 + +%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-NanoFilt -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot - 2.8.0-1 +- Package Spec generated -- cgit v1.2.3