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|
%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.
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanofilt)
[](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.
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanofilt)
[](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.
[](https://twitter.com/wouter_decoster)
[](https://anaconda.org/bioconda/nanofilt)
[](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 <Python_Bot@openeuler.org> - 2.8.0-1
- Package Spec generated
|
