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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.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
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.1.18-1
+- Package Spec generated