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@@ -0,0 +1 @@ +/bioinfokit-2.1.0.tar.gz diff --git a/python-bioinfokit.spec b/python-bioinfokit.spec new file mode 100644 index 0000000..b7a70d9 --- /dev/null +++ b/python-bioinfokit.spec @@ -0,0 +1,192 @@ +%global _empty_manifest_terminate_build 0 +Name: python-bioinfokit +Version: 2.1.0 +Release: 1 +Summary: Bioinformatics data analysis and visualization toolkit +License: MIT +URL: https://github.com/reneshbedre/bioinfokit +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/19/2d/4fb9189fcd7d3018aeec6b1940485e90d4c69a30e95b2bdf0405c565cecb/bioinfokit-2.1.0.tar.gz +BuildArch: noarch + + +%description +`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns +`lfc` | Name of a column having log or absolute fold change values [string][default:logFC] +`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values] +`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)] +`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)] +`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")] +`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0] +`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None] +`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None] +`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2. +`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)] +`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True +`ar` | Rotation of X and Y-axis ticks labels [float][default: 90] +`dotsize`| The size of the dots in the plot [float][default: 8] +`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"] +`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False] +`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1] +`show` | Show the figure on console instead of saving in current folder [True or False][default:False] +`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] +`axtickfontsize` | Font size for axis ticks [float][default: 9] +`axtickfontname` | Font name for axis ticks [string][default: 'Arial'] +`axlabelfontsize` | Font size for axis labels [float][default: 9] +`axlabelfontname` | Font name for axis labels [string][default: 'Arial'] +`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None] +`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None] +`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None] +`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None] +`plotlegend` | plot legend on volcano plot [True or False][default:False] +`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"] +`figname` | name of figure [string ][default:"volcano"] +`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None] +`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']] +`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None'] +Returns: +Volcano plot image in same directory (volcano.png) +<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a> +### Inverted Volcano plot +latest update v2.0.8 +`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle, + dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize, + axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)` + +%package -n python3-bioinfokit +Summary: Bioinformatics data analysis and visualization toolkit +Provides: python-bioinfokit +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-bioinfokit +`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns +`lfc` | Name of a column having log or absolute fold change values [string][default:logFC] +`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values] +`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)] +`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)] +`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")] +`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0] +`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None] +`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None] +`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2. +`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)] +`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True +`ar` | Rotation of X and Y-axis ticks labels [float][default: 90] +`dotsize`| The size of the dots in the plot [float][default: 8] +`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"] +`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False] +`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1] +`show` | Show the figure on console instead of saving in current folder [True or False][default:False] +`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] +`axtickfontsize` | Font size for axis ticks [float][default: 9] +`axtickfontname` | Font name for axis ticks [string][default: 'Arial'] +`axlabelfontsize` | Font size for axis labels [float][default: 9] +`axlabelfontname` | Font name for axis labels [string][default: 'Arial'] +`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None] +`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None] +`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None] +`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None] +`plotlegend` | plot legend on volcano plot [True or False][default:False] +`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"] +`figname` | name of figure [string ][default:"volcano"] +`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None] +`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']] +`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None'] +Returns: +Volcano plot image in same directory (volcano.png) +<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a> +### Inverted Volcano plot +latest update v2.0.8 +`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle, + dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize, + axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)` + +%package help +Summary: Development documents and examples for bioinfokit +Provides: python3-bioinfokit-doc +%description help +`df` |Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values columns +`lfc` | Name of a column having log or absolute fold change values [string][default:logFC] +`pv` | Name of a column having P-values or adjusted P-values [string][default:p_values] +`lfc_thr` | Log fold change cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(1.0, 1.0)] +`pv_thr` | p value or adjusted p value cutoff for up and downregulated genes [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default:(0.05, 0.05)] +`color` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of three colors [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) or list][default: color=("green", "grey", "red")] +`valpha` | Transparency of points on volcano plot [float (between 0 and 1)][default: 1.0] +`geneid` | Name of a column having gene Ids. This is necessary for plotting gene label on the points [string][default: None] +`genenames` | [Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of gene Ids to label the points. The gene Ids must be present in the geneid column. If this option set to "deg" it will label all genes defined by lfc_thr and pv_thr [string, tuple, dict][default: None] +`gfont` | Font size for genenames [float][default: 10.0]. gfont not compatible with gstyle=2. +`dim` | Figure size [[Tuple](https://www.reneshbedre.com/blog/python-tuples.html) of two floats (width, height) in inches][default: (5, 5)] +`r` | Figure resolution in dpi [int][default: 300]. Not compatible with `show`= True +`ar` | Rotation of X and Y-axis ticks labels [float][default: 90] +`dotsize`| The size of the dots in the plot [float][default: 8] +`markerdot` | Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: "o"] +`sign_line` | Show grid lines on plot with defined log fold change (`lfc_thr`) and P-value (`pv_thr`) threshold value [True or False][default:False] +`gstyle` | Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1] +`show` | Show the figure on console instead of saving in current folder [True or False][default:False] +`figtype` | Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:'png'] +`axtickfontsize` | Font size for axis ticks [float][default: 9] +`axtickfontname` | Font name for axis ticks [string][default: 'Arial'] +`axlabelfontsize` | Font size for axis labels [float][default: 9] +`axlabelfontname` | Font name for axis labels [string][default: 'Arial'] +`axxlabel` | Label for X-axis. If you provide this option, default label will be replaced [string][default: None] +`axylabel` | Label for Y-axis. If you provide this option, default label will be replaced [string][default: None] +`xlm` | Range of ticks to plot on X-axis [float (left, right, interval)][default: None] +`ylm` | Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None] +`plotlegend` | plot legend on volcano plot [True or False][default:False] +`legendpos` | position of the legend on plot. For more options see loc parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [string ][default:"best"] +`figname` | name of figure [string ][default:"volcano"] +`legendanchor` | position of the legend outside of the plot. For more options see bbox_to_anchor parameter at https://matplotlib.org/3.1.1/api/_as_gen/matplotlib.pyplot.legend.html [list][default:None] +`legendlabels` | legend label names. If you provide custom label names keep the same order of label names as default [list][default:['significant up', 'not significant', 'significant down']] +`theme` | Change background theme. If theme set to `dark`, the dark background will be produced instead of white [string][default:'None'] +Returns: +Volcano plot image in same directory (volcano.png) +<a href="https://reneshbedre.com/blog/volcano.html" target="_blank">Working example</a> +### Inverted Volcano plot +latest update v2.0.8 +`bioinfokit.visuz.GeneExpression.involcano(table, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, gstyle, + dotsize, markerdot, r, dim, show, figtype, axxlabel, axylabel, axlabelfontsize, axtickfontsize, + axtickfontname, plotlegend, legendpos, legendanchor, figname, legendlabels, ar, theme)` + +%prep +%autosetup -n bioinfokit-2.1.0 + +%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-bioinfokit -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 2.1.0-1 +- Package Spec generated @@ -0,0 +1 @@ +ee748f5ff6a8f669708ed9cdbcf13ae7 bioinfokit-2.1.0.tar.gz |