%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. ![Example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/example.png) ## 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: ![User example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1.png) 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). ![User example plot explained](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_explained.png) The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: ![User example circle](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_circ.png) ## 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. ![Example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/example.png) ## 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: ![User example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1.png) 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). ![User example plot explained](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_explained.png) The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: ![User example circle](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_circ.png) ## 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. ![Example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/example.png) ## 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: ![User example plot](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1.png) 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). ![User example plot explained](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_explained.png) The major circularized isoform (exons 2-4; another less prevalent circle appears to include exon 5) is isolated below: ![User example circle](https://github.com/flemingtonlab/SpliceV/blob/master/etc/vta1_circ.png) ## 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 - 0.2.0.0-1 - Package Spec generated