%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.nju.edu.cn/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 * Tue May 30 2023 Python_Bot - 0.1.18-1 - Package Spec generated