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diff --git a/python-splicev.spec b/python-splicev.spec new file mode 100644 index 0000000..2765042 --- /dev/null +++ b/python-splicev.spec @@ -0,0 +1,261 @@ +%global _empty_manifest_terminate_build 0 +Name: python-SpliceV +Version: 0.2.0.0 +Release: 1 +Summary: Visualize splice junctions, backsplice junctions (circleRNA) and coverage from RNA-Seq datasets +License: GNU General Public License v3 (GPLv3) +URL: https://github.com/flemingtonlab/SpliceV +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/37/33/e33fcc13b73fe050b5c315cdabe27798ce95285b54d2407090db7c5c1ef6/SpliceV-0.2.0.0.tar.gz +BuildArch: noarch + +Requires: python3-matplotlib +Requires: python3-numpy +Requires: python3-pysam + +%description +# SpliceV # +Visualize coverage, canonical, and backsplice junctions. + + + +## Documentation ## +See https://splicev.readthedocs.io/en/master/ + +## Example pipeline ## +See https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf + +This will generate figure 1B and 1C from our manuscript (DOI pending) + +## Requirements ## +SpliceV works with Python 2.7 and 3.0+. +## Dependencies ## +* Matplotlib +* Numpy +* pysam +## Installation ## +To install SpliceV: + +``` +pip install SpliceV +``` + +Or: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git +``` + +## Example ## +To run the example dataset: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git + +cd SpliceV/example + +python ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3 + +``` + +The sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample. + +These example commands will generate the following plot: + + +This plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color). + + + +The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: + + + + +## Authors ## +Created by Nathan Ungerleider and Erik Flemington + + + + +%package -n python3-SpliceV +Summary: Visualize splice junctions, backsplice junctions (circleRNA) and coverage from RNA-Seq datasets +Provides: python-SpliceV +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-SpliceV +# SpliceV # +Visualize coverage, canonical, and backsplice junctions. + + + +## Documentation ## +See https://splicev.readthedocs.io/en/master/ + +## Example pipeline ## +See https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf + +This will generate figure 1B and 1C from our manuscript (DOI pending) + +## Requirements ## +SpliceV works with Python 2.7 and 3.0+. +## Dependencies ## +* Matplotlib +* Numpy +* pysam +## Installation ## +To install SpliceV: + +``` +pip install SpliceV +``` + +Or: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git +``` + +## Example ## +To run the example dataset: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git + +cd SpliceV/example + +python ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3 + +``` + +The sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample. + +These example commands will generate the following plot: + + +This plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color). + + + +The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: + + + + +## Authors ## +Created by Nathan Ungerleider and Erik Flemington + + + + +%package help +Summary: Development documents and examples for SpliceV +Provides: python3-SpliceV-doc +%description help +# SpliceV # +Visualize coverage, canonical, and backsplice junctions. + + + +## Documentation ## +See https://splicev.readthedocs.io/en/master/ + +## Example pipeline ## +See https://github.com/flemingtonlab/SpliceV/blob/master/docs/example.pdf + +This will generate figure 1B and 1C from our manuscript (DOI pending) + +## Requirements ## +SpliceV works with Python 2.7 and 3.0+. +## Dependencies ## +* Matplotlib +* Numpy +* pysam +## Installation ## +To install SpliceV: + +``` +pip install SpliceV +``` + +Or: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git +``` + +## Example ## +To run the example dataset: + +``` +git clone https://github.com/flemingtonlab/SpliceV.git + +cd SpliceV/example + +python ../bin/SpliceV -b example.vta1.bam -gtf vta1.gtf -sj example.canonical.bed -bsj example.circles.bed -g VTA1 -f 3 -is 3 + +``` + +The sample data comes from Akata cells (a B Cell Lymphoma line) that were treated with the exonuclease RNase R prior to sequencing. RNase R exclusively digests RNA with a free end, helping enrich circularized RNA abundance in the sample. + +These example commands will generate the following plot: + + +This plot reveals a prominant circle from exon 2 through exon 4 (evidenced by the back-splice junction reads which are plotted as curves below the axis. This is also demonstrated by the higher level of coverage in exon 2-4, shown by the relative intensity of color). + + + +The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: + + + + +## Authors ## +Created by Nathan Ungerleider and Erik Flemington + + + + +%prep +%autosetup -n SpliceV-0.2.0.0 + +%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-SpliceV -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.0.0-1 +- Package Spec generated |