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|
%global _empty_manifest_terminate_build 0
Name: python-jla-tailer
Version: 0.1.18
Release: 1
Summary: Tool to find 3' tailing of non-coding RNAs
License: MIT License
URL: https://github.com/TimNicholsonShaw/tailer
Source0: https://mirrors.aliyun.com/pypi/web/packages/07/34/c749189431cf822392c4f80fb154921c8a7fd058f23d8668d39c5b8adfee/jla-tailer-0.1.18.tar.gz
BuildArch: noarch
Requires: python3-pysam
Requires: python3-Bio
Requires: python3-gffutils
Requires: python3-tqdm
Requires: python3-requests
%description
# Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data
## Requirements
- ``Python >= 3.6``
- ``pysam``
- ``Bio``
- ``gffuitls``
- ``requests``
- ``tqdm``
## Installation
```bash
pip install jla-tailer
```
## Usage
Global alignment with a GTF annotation and SAM/BAM formatted files
```bash
Tailer -a [GTF Annotation] [SAM or BAM Files]
```
Required Arguments
* ``-a, --annotation``
- GTF formatted database to be used to infer 3' ends. Ensembl GTFs have worked well for this pipeline
* ``[SAM or BAM Files]``
- Space separated list of sam/bam formatted file locations to perform 3' end tail analysis
Local alignment with with FASTA/Q and specific Ensembl IDs of interest or reference fasta
```bash
Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Tailer -f fasta_reference_file.fasta [FASTA/Q files]
```
Required Arguments
* ``-e, --ensids``
- Comma separated list of ensembl IDs. Either -e or -f inputs are required.
* ``-f, --fasta``
- FASTA formatted file to align reads against. Either -f or -e inputs are required
* ``[Trimmed FASTQ files]``
- Space separated FASTQ file locations for analysis.
Optional arguments
* ``-t, --threshold [int, default=100]``
- Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
* ``-x, --trim [int, default=0]``
- Helper for local mode only, can remove X nucleotides from adapter on the 3' end
* ``-read, --read [int, default=1]``
- Paired end only. 1 or 2 to signify which end contains the 3' end information.
* ``-r, --rev_comp``
- If set, will reverse complement the reads. Necessary for some library prep methods
* ``-f, --fasta``
- Use a fasta file as a reference instead of building one from ensembl IDs (Local Only)
* ``-s, --sequence``
- Output sequence in the tail file. Useful for debugging.
miRNA tailing (in development)
```bash
Tailer --miRNA [sam files]
```
Determines tails using an alignment file (SAM/BAM) that was aligned to a fasta genome of mature miRNAs
Optional arguments
* ``--rpad [int, default=0]``
- Number of downstream nucleotides added to distinguish between post-transcriptional and genome-encoded tails
%package -n python3-jla-tailer
Summary: Tool to find 3' tailing of non-coding RNAs
Provides: python-jla-tailer
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-jla-tailer
# Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data
## Requirements
- ``Python >= 3.6``
- ``pysam``
- ``Bio``
- ``gffuitls``
- ``requests``
- ``tqdm``
## Installation
```bash
pip install jla-tailer
```
## Usage
Global alignment with a GTF annotation and SAM/BAM formatted files
```bash
Tailer -a [GTF Annotation] [SAM or BAM Files]
```
Required Arguments
* ``-a, --annotation``
- GTF formatted database to be used to infer 3' ends. Ensembl GTFs have worked well for this pipeline
* ``[SAM or BAM Files]``
- Space separated list of sam/bam formatted file locations to perform 3' end tail analysis
Local alignment with with FASTA/Q and specific Ensembl IDs of interest or reference fasta
```bash
Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Tailer -f fasta_reference_file.fasta [FASTA/Q files]
```
Required Arguments
* ``-e, --ensids``
- Comma separated list of ensembl IDs. Either -e or -f inputs are required.
* ``-f, --fasta``
- FASTA formatted file to align reads against. Either -f or -e inputs are required
* ``[Trimmed FASTQ files]``
- Space separated FASTQ file locations for analysis.
Optional arguments
* ``-t, --threshold [int, default=100]``
- Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
* ``-x, --trim [int, default=0]``
- Helper for local mode only, can remove X nucleotides from adapter on the 3' end
* ``-read, --read [int, default=1]``
- Paired end only. 1 or 2 to signify which end contains the 3' end information.
* ``-r, --rev_comp``
- If set, will reverse complement the reads. Necessary for some library prep methods
* ``-f, --fasta``
- Use a fasta file as a reference instead of building one from ensembl IDs (Local Only)
* ``-s, --sequence``
- Output sequence in the tail file. Useful for debugging.
miRNA tailing (in development)
```bash
Tailer --miRNA [sam files]
```
Determines tails using an alignment file (SAM/BAM) that was aligned to a fasta genome of mature miRNAs
Optional arguments
* ``--rpad [int, default=0]``
- Number of downstream nucleotides added to distinguish between post-transcriptional and genome-encoded tails
%package help
Summary: Development documents and examples for jla-tailer
Provides: python3-jla-tailer-doc
%description help
# Tailer: A tool for 3' end analysis of non-polyadenylated RNAs from 3' sequencing data
## Requirements
- ``Python >= 3.6``
- ``pysam``
- ``Bio``
- ``gffuitls``
- ``requests``
- ``tqdm``
## Installation
```bash
pip install jla-tailer
```
## Usage
Global alignment with a GTF annotation and SAM/BAM formatted files
```bash
Tailer -a [GTF Annotation] [SAM or BAM Files]
```
Required Arguments
* ``-a, --annotation``
- GTF formatted database to be used to infer 3' ends. Ensembl GTFs have worked well for this pipeline
* ``[SAM or BAM Files]``
- Space separated list of sam/bam formatted file locations to perform 3' end tail analysis
Local alignment with with FASTA/Q and specific Ensembl IDs of interest or reference fasta
```bash
Tailer -e [comma separated list of EnsIDs no spaces] [FASTA/Q files]
Tailer -f fasta_reference_file.fasta [FASTA/Q files]
```
Required Arguments
* ``-e, --ensids``
- Comma separated list of ensembl IDs. Either -e or -f inputs are required.
* ``-f, --fasta``
- FASTA formatted file to align reads against. Either -f or -e inputs are required
* ``[Trimmed FASTQ files]``
- Space separated FASTQ file locations for analysis.
Optional arguments
* ``-t, --threshold [int, default=100]``
- Any alignment identified further than this distance in nucleotides from the mature end will be considered spurious and discarded
* ``-x, --trim [int, default=0]``
- Helper for local mode only, can remove X nucleotides from adapter on the 3' end
* ``-read, --read [int, default=1]``
- Paired end only. 1 or 2 to signify which end contains the 3' end information.
* ``-r, --rev_comp``
- If set, will reverse complement the reads. Necessary for some library prep methods
* ``-f, --fasta``
- Use a fasta file as a reference instead of building one from ensembl IDs (Local Only)
* ``-s, --sequence``
- Output sequence in the tail file. Useful for debugging.
miRNA tailing (in development)
```bash
Tailer --miRNA [sam files]
```
Determines tails using an alignment file (SAM/BAM) that was aligned to a fasta genome of mature miRNAs
Optional arguments
* ``--rpad [int, default=0]``
- Number of downstream nucleotides added to distinguish between post-transcriptional and genome-encoded tails
%prep
%autosetup -n jla-tailer-0.1.18
%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-jla-tailer -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.18-1
- Package Spec generated
|
