%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