bioinfokit documentation
What is bioinfokit?
The bioinfokit toolkit aimed to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments.
How to install?
bioinfokit is developed in Python 3 and tested with Python versions >= 3.6
bioinfokit requires
- NumPy
- scikit-learn
- seaborn
- pandas
- matplotlib
- SciPy
- matplotlib_venn
bioinfokit can be installed using pip, easy_install and git.
latest bioinfokit version: 
Install using pip for Python 3 (easiest way)
# install
pip install bioinfokit
# upgrade to latest version
pip install bioinfokit --upgrade
# uninstall
pip uninstall bioinfokit
Install using easy_install for Python 3 (easiest way)
# install latest version
easy_install bioinfokit
# specific version
easy_install bioinfokit==0.3
# uninstall
pip uninstall bioinfokit
Install using conda
conda install -c bioconda bioinfokit
Install using git
# download and install bioinfokit (Tested on Linux, Mac, Windows)
git clone https://github.com/reneshbedre/bioinfokit.git
cd bioinfokit
python setup.py install
Check the version of bioinfokit
>>> import bioinfokit
>>> bioinfokit.__version__
'0.9.6'
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How to use bioinfokit?
Gene expression analysis
Volcano plot
latest update v0.8.8
bioinfokit.visuz.gene_exp.volcano(df, lfc, pv, lfc_thr, pv_thr, color, valpha, geneid, genenames, gfont, dim, r, ar,
dotsize, markerdot, sign_line, gstyle, show, figtype, axtickfontsize, axtickfontname, axlabelfontsize,
axlabelfontname, axxlabel, axylabel, xlm, ylm, plotlegend, legendpos, figname, legendanchor, legendlabels)
| Parameters | 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 or absolute fold change cutoff for up and downregulated genes [float][default:1.0] |
pv_thr |
P-values or adjusted P-values cutoff for up and downregulated genes [float][default:0.05] |
color |
Tuple of three colors [tuple 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 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 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:”ma”] |
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’]] |
Returns:
Volcano plot image in same directory (volcano.png) Working example
Inverted Volcano plot
latest update v0.8.8
bioinfokit.visuz.gene_exp.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)
| Parameters | Description |
|---|---|
table |
Pandas dataframe table having atleast gene IDs, log fold change, P-values or adjusted P-values |
lfc |
Name of a column having log fold change values [default:logFC] |
pv |
Name of a column having P-values or adjusted P-values [default:p_values] |
lfc_thr |
Log fold change cutoff for up and downregulated genes [default:1] |
pv_thr |
P-values or adjusted P-values cutoff for up and downregulated genes [default:0.05] |
color |
Tuple of three colors [tuple 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 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] |
gstyle |
Style of the text for genenames. 1 for default text and 2 for box text [int][default: 1] |
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”] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (5, 5)] |
r |
Figure resolution in dpi [int][default: 300]. Not compatible with show= True |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
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] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axtickfontsize |
Font size for axis ticks [float][default: 9] |
axtickfontname |
Font name for axis ticks [string][default: ‘Arial’] |
plotlegend |
plot legend on inverted 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”] |
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] |
figname |
name of figure [string ][default:”involcano”] |
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’]] |
ar |
Rotation of X and Y-axis ticks labels [float][default: 90] |
Returns:
Inverted volcano plot image in same directory (involcano.png) Working example
MA plot
latest update v0.8.8
bioinfokit.visuz.gene_exp.ma(df, lfc, ct_count, st_count, lfc_thr, color, dim, dotsize, show, r, valpha, figtype, axxlabel,
axylabel, axlabelfontsize, axtickfontsize, axtickfontname, xlm, ylm, fclines, fclinescolor, legendpos, legendanchor,
figname, legendlabels, plotlegend, ar)
| Parameters | Description |
|---|---|
df |
Pandas dataframe table having atleast gene IDs, log fold change, and normalized counts (control and treatment) columns |
lfc |
Name of a column having log fold change values [default:logFC] |
ct_count |
Name of a column having count values for control sample [default:value1] |
st_count |
Name of a column having count values for treatment sample [default:value2] |
lfc_thr |
Log fold change cutoff for up and downregulated genes [default:1] |
color |
Tuple of three colors [tuple or list][default: (“green”, “grey”, “red”)] |
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”] |
valpha |
Transparency of points on plot [float (between 0 and 1)][default: 1.0] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (5, 5)] |
r |
Figure resolution in dpi [int][default: 300]. Not compatible with show= True |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
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] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axtickfontsize |
Font size for axis ticks [float][default: 9] |
axtickfontname |
Font name for axis ticks [string][default: ‘Arial’] |
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] |
fclines |
draw log fold change threshold lines as defines by lfc [True or False][default:False] |
fclinescolor |
color of fclines [string][default: ‘#2660a4’] |
plotlegend |
plot legend on MA 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”] |
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] |
figname |
name of figure [string ][default:”ma”] |
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’]] |
ar |
Rotation of X and Y-axis ticks labels [float][default: 90] |
Returns:
MA plot image in same directory (ma.png)
Heatmap
latest update v0.8.4
bioinfokit.visuz.gene_exp.hmap(table, cmap='seismic', scale=True, dim=(6, 8), rowclus=True, colclus=True, zscore=None,
xlabel=True, ylabel=True, tickfont=(12, 12), show, r, figtype, figname)
| Parameters | Description |
|---|---|
file |
CSV delimited data file. It should not have NA or missing values |
cmap |
Color Palette for heatmap [string][default: ‘seismic’] |
scale |
Draw a color key with heatmap [boolean (True or False)][default: True] |
dim |
heatmap figure size [tuple of two floats (width, height) in inches][default: (6, 8)] |
rowclus |
Draw hierarchical clustering for rows [boolean (True or False)][default: True] |
colclus |
Draw hierarchical clustering for columns [boolean (True or False)][default: True] |
zscore |
Z-score standardization of row (0) or column (1). It works when clus is True. [None, 0, 1][default: None] |
xlabel |
Plot X-label [boolean (True or False)][default: True] |
ylabel |
Plot Y-label [boolean (True or False)][default: True] |
tickfont |
Fontsize for X and Y-axis tick labels [tuple of two floats][default: (14, 14)] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
r |
Figure resolution in dpi [int][default: 300]. Not compatible with show= True |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
figname |
name of figure [string ][default:”heatmap”] |
Returns:
heatmap plot (heatmap.png, heatmap_clus.png)
Clustering analysis
Scree plot
latest update v0.9.8
bioinfokit.visuz.cluster.screeplot(obj, axlabelfontsize, axlabelfontname, axxlabel, axylabel,
figtype, r, show, dim)
| Parameters | Description |
|---|---|
obj |
list of component name and component variance |
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] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
r |
Figure resolution in dpi [int][default: 300] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
Returns:
Scree plot image (screeplot.png will be saved in same directory)
Principal component analysis (PCA) loadings plots
latest update v0.9.8
bioinfokit.visuz.cluster.pcaplot(x, y, z, labels, var1, var2, var3, axlabelfontsize, axlabelfontname,
figtype, r, show, plotlabels, dim)
| Parameters | Description |
|---|---|
x |
loadings (correlation coefficient) for principal component 1 (PC1) |
y |
loadings (correlation coefficient) for principal component 2 (PC2) |
z |
loadings (correlation coefficient) for principal component 3 (PC2) |
labels |
original variables labels from dataframe used for PCA |
var1 |
Proportion of PC1 variance [float (0 to 1)] |
var2 |
Proportion of PC2 variance [float (0 to 1)] |
var3 |
Proportion of PC3 variance [float (0 to 1)] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axlabelfontname |
Font name for axis labels [string][default: ‘Arial’] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
r |
Figure resolution in dpi [int][default: 300] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
plotlabels |
Plot labels as defined by labels parameter [True or False][default:True] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
Returns:
PCA loadings plot 2D and 3D image (pcaplot_2d.png and pcaplot_3d.png will be saved in same directory)
Principal component analysis (PCA) biplots
latest update v0.9.8
bioinfokit.visuz.cluster.biplot(cscore, loadings, labels, var1, var2, var3, axlabelfontsize, axlabelfontname,
figtype, r, show, markerdot, dotsize, valphadot, colordot, arrowcolor, valphaarrow, arrowlinestyle, arrowlinewidth,
centerlines, colorlist, legendpos, datapoints, dim)
| Parameters | Description |
|---|---|
cscore |
principal component scores (obtained from PCA().fit_transfrom() function in sklearn.decomposition) |
loadings |
loadings (correlation coefficient) for principal components |
labels |
original variables labels from dataframe used for PCA |
var1 |
Proportion of PC1 variance [float (0 to 1)] |
var2 |
Proportion of PC2 variance [float (0 to 1)] |
var3 |
Proportion of PC3 variance [float (0 to 1)] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axlabelfontname |
Font name for axis labels [string][default: ‘Arial’] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
r |
Figure resolution in dpi [int][default: 300] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
markerdot |
Shape of the dot on plot. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: “o”] |
dotsize |
The size of the dots in the plot [float][default: 6] |
valphadot |
Transparency of dots on plot [float (between 0 and 1)][default: 1] |
colordot |
Color of dots on plot [string or list ][default:”#4a4e4d”] |
arrowcolor |
Color of the arrow [string ][default:”#fe8a71”] |
valphaarrow |
Transparency of the arrow [float (between 0 and 1)][default: 1] |
arrowlinestyle |
line style of the arrow. check more styles at https://matplotlib.org/3.1.0/gallery/lines_bars_and_markers/linestyles.html [string][default: ‘-‘] |
arrowlinewidth |
line width of the arrow [float][default: 1.0] |
centerlines |
draw center lines at x=0 and y=0 for 2D plot [bool (True or False)][default: True] |
colorlist |
list of the categories to assign the color [list][default:None] |
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”] |
datapoints |
plot data points on graph [bool (True or False)][default: True] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
Returns:
PCA biplot 2D and 3D image (biplot_2d.png and biplot_3d.png will be saved in same directory)
Normalization
RPM or CPM normalization
latest update v0.8.9
Normalize raw gene expression counts into Reads per million mapped reads (RPM) or Counts per million mapped reads (CPM)
bioinfokit.analys.norm.cpm(df)
| Parameters | Description |
|---|---|
df |
Pandas dataframe containing raw gene expression values. Genes with missing expression values (NA) will be dropped. |
Returns:
RPM or CPM normalized Pandas dataframe as class attributes (cpm_norm)
RPKM or FPKM normalization
latest update v0.9
Normalize raw gene expression counts into Reads per kilo base per million mapped reads (RPKM) or Fragments per kilo base per million mapped reads (FPKM)
bioinfokit.analys.norm.rpkm(df, gl)
| Parameters | Description |
|---|---|
df |
Pandas dataframe containing raw gene expression values. Genes with missing expression or gene length values (NA) will be dropped. |
gl |
Name of a column having gene length in bp [string][default: None] |
Returns:
RPKM or FPKM normalized Pandas dataframe as class attributes (rpkm_norm)
TPM normalization
latest update v0.9.1
Normalize raw gene expression counts into Transcript per million (TPM)
bioinfokit.analys.norm.tpm(df, gl)
| Parameters | Description |
|---|---|
df |
Pandas dataframe containing raw gene expression values. Genes with missing expression or gene length values (NA) will be dropped. |
gl |
Name of a column having gene length in bp [string][default: None] |
Returns:
TPM normalized Pandas dataframe as class attributes (tpm_norm)
Variant analysis
Manhatten plot
latest update v0.9.2
bioinfokit.visuz.marker.mhat(df, chr, pv, color, dim, r, ar, gwas_sign_line, gwasp, dotsize, markeridcol, markernames,
gfont, valpha, show, figtype, axxlabel, axylabel, axlabelfontsize, ylm, gstyle, figname)
| Parameters | Description |
|---|---|
df |
Pandas dataframe object with atleast SNP, chromosome, and P-values columns |
chr |
Name of a column having chromosome numbers [string][default:None] |
pv |
Name of a column having P-values. Must be numeric column [string][default:None] |
color |
List the name of the colors to be plotted. It can accept two alternate colors or the number colors equal to chromosome number. If nothing (None) provided, it will randomly assign the color to each chromosome [list][default:None] |
gwas_sign_line |
Plot statistical significant threshold line defined by option gwasp [bool (True or False)][default: False] |
gwasp |
Statistical significant threshold to identify significant SNPs [float][default: 5E-08] |
dotsize |
The size of the dots in the plot [float][default: 8] |
markeridcol |
Name of a column having SNPs. This is necessary for plotting SNP names on the plot [string][default: None] |
markernames |
The list of the SNPs to display on the plot. These SNP should be present in SNP column. Additionally, it also accepts the dict of SNPs and its associated gene name. If this option set to True, it will label all SNPs with P-value significant score defined by gwasp [string, list, tuple, dict][default: True] |
gfont |
Font size for SNP names to display on the plot [float][default: 8]. gfont not compatible with gstyle=2. |
valpha |
Transparency of points on plot [float (between 0 and 1)][default: 1.0] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
r |
Figure resolution in dpi [int][default: 300] |
ar |
Rotation of X-axis labels [float][default: 90] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
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] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
ylm |
Range of ticks to plot on Y-axis [float tuple (bottom, top, interval)][default: None] |
gstyle |
Style of the text for markernames. 1 for default text and 2 for box text [int][default: 1] |
figname |
name of figure [string][default:”manhatten”] |
Returns:
Manhatten plot image in same directory (manhatten.png)
Variant annotation
latest update v0.9.3
Assign genetic features and function to the variants in VCF file
bioinfokit.analys.marker.vcf_anot(file, id, gff_file, anot_attr)
| Parameters | Description |
|---|---|
file |
VCF file |
id |
chromosome id column in VCF file [string][default=’#CHROM’] |
gff_file |
GFF3 genome annotation file |
anot_attr |
Gene function tag in attributes field of GFF3 file |
Returns:
Tab-delimited text file with annotation (annotated text file will be saved in same directory)
Concatenate VCF files
latest update v0.9.4
Concatenate multiple VCF files into single VCF file (for example, VCF files for each chromosome)
bioinfokit.analys.marker.concatvcf(file)
| Parameters | Description |
|---|---|
file |
Multiple vcf files separated by comma |
Returns:
Concatenated VCF file (concat_vcf.vcf)
Split VCF file
bioinfokit.analys.marker.splitvcf(file)
Split single VCF file containing variants for all chromosomes into individual file containing variants for each chromosome
| Parameters | Description |
|---|---|
file |
VCF file to split |
id |
chromosome id column in VCF file [string][default=’#CHROM’] |
Returns:
VCF files for each chromosome
High-throughput sequence analysis
FASTQ batch downloads from SRA database
latest update v0.9.7
bioinfokit.analys.fastq.sra_bd(file, t, other_opts)
FASTQ files will be downloaded using fasterq-dump. Make sure you have the latest version of the NCBI SRA toolkit
(version 2.10.8) is installed and binaries are added to the system path
| Parameters | Description |
|---|---|
file |
List of SRA accessions for batch download. All accession must be separated by a newline in the file. |
t |
Number of threads for parallel run [int][default=4] |
other_opts |
Provide other relevant options for fasterq-dump [str][default=None] Provide the options as a space-separated string. You can get a detailed option for fasterq-dump using the -help option. |
Returns:
FASTQ files for each SRA accession in the current directory unless specified by other_opts
Description and working example
FASTQ quality format detection
bioinfokit.analys.format.fq_qual_var(file)
| Parameters | Description |
|---|---|
file |
FASTQ file to detect quality format [deafult: None] |
Returns:
Quality format encoding name for FASTQ file (Supports only Sanger, Illumina 1.8+ and Illumina 1.3/1.4)
Sequencing coverage
latest update v0.9.7
bioinfokit.analys.fastq.seqcov(file, gs)
| Parameters | Description |
|---|---|
file |
FASTQ file |
gs |
Genome size in Mbp |
Returns:
Sequencing coverage of the given FASTQ file
Description and Working example
Reverse complement of DNA sequence
latest update v0.9.8
bioinfokit.analys.fasta.rev_com(sequence)
| Parameters | Description |
|---|---|
seq |
DNA sequence to perform reverse complement |
file |
DNA sequence in a fasta file |
Returns:
Reverse complement of original DNA sequence
File format conversions
bioinfokit.analys.format
| Function | Parameters | Description |
|---|---|---|
bioinfokit.analys.format.fqtofa(file) |
FASTQ file |
Convert FASTQ file into FASTA format |
bioinfokit.analys.format.hmmtocsv(file) |
HMM file |
Convert HMM text output (from HMMER tool) to CSV format |
bioinfokit.analys.format.tabtocsv(file) |
TAB file |
Convert TAB file to CSV format |
bioinfokit.analys.format.csvtotab(file) |
CSV file |
Convert CSV file to TAB format |
Returns:
Output will be saved in same directory
GFF3 to GTF file format conversion
latest update v1.0.1
bioinfokit.analys.gff.gff_to_gtf(file, trn_feature_name)
| Parameters | Description |
|---|---|
file |
GFF3 genome annotation file |
trn_feature_name |
Name of the feature (column 3 of GFF3 file) of RNA transcripts if other than ‘mRNA’ or ‘transcript’ |
Returns:
GTF format genome annotation file (file.gtf will be saved in same directory)
Bioinformatics file readers and processing (FASTA, FASTQ, and VCF)
| Function | Parameters | Description |
|---|---|---|
bioinfokit.analys.fasta.fasta_reader(file) |
FASTA file |
FASTA file reader |
bioinfokit.analys.fastq.fastq_reader(file) |
FASTQ file |
FASTQ file reader |
bioinfokit.analys.marker.vcfreader(file) |
VCF file |
VCF file reader |
Returns:
File generator object (can be iterated only once) that can be parsed for the record
Description and working example
Extract subsequence from FASTA files
latest update v0.9.8
bioinfokit.analys.fasta.ext_subseq(file, id, st, end, strand)
Extract the subsequence of specified region from FASTA file. If the target subsequence region is on minus strand. the reverse complementary of subsequence will be printed.
| Parameters | Description |
|---|---|
file |
FASTA file [file] |
id |
The ID of sequence from FASTA file to extract the subsequence [string] |
st |
Start integer coordinate of subsequnece [int] |
end |
End integer coordinate of subsequnece [int] |
strand |
Strand of the subsequence [‘plus’ or ‘minus’][default: ‘plus’] |
Returns:
Subsequence to stdout
Extract sequences from FASTA file
latest update v1.0.2
bioinfokit.analys.fasta.extract_seq(file, id)
Extract the sequences from FASTA file based on the list of sequence IDs provided from other file
| Parameters | Description |
|---|---|
file |
FASTA file [file] |
id |
List of sequence IDs separated by new line [file] or Pandas series |
Returns:
Sequences extracted from FASTA file based on the given IDs provided in id file. Output FASTA file will be saved as output.fasta in current working directory.
Functional enrichment analysis
Gene family enrichment analysis (GenFam)
latest update v1.0.0
bioinfokit.analys.genfam.fam_enrich(id_file, species, id_type, stat_sign_test, multi_test_corr, min_map_ids, alpha)
GenFam is a comprehensive classification and enrichment analysis tool for plant genomes. It provides a unique way to characterize the large-scale gene datasets such as those from transcriptome analysis (read GenFam paper for more details)
| Parameters | Description |
|---|---|
id_file |
Text file containing the list of gene IDs to analyze using GenFam. IDs must be separated by newline. |
species |
Plant species ID for GenFam analysis. All plant species ID provided here |
id_type |
Plant species ID type 1: Phytozome locus ID 2: Phytozome transcript ID 3: Phytozome PAC ID |
stat_sign_test |
Statistical significance test for enrichment analysis [default=1]. 1: Fisher exact test 2: Hypergeometric distribution 3: Binomial distribution 4: Chi-squared distribution |
multi_test_corr |
Multiple testing correction test [default=3]. 1: Bonferroni 2: Bonferroni-Holm 3: Benjamini-Hochberg |
min_map_ids |
Minimum number of gene IDs from the user list (id_file) must be mapped to the background database for performing GenFam analysis [default=5] |
alpha |
Significance level [float][default: 0.05] |
Returns:
| Attribute | Description |
|---|---|
| df_enrich | Enriched gene families with p < 0.05 |
| genfam_info | GenFam run information |
| Output files | Output figures and files from GenFam analysis genfam_enrich.png: GenFam figure for enriched gene families fam_enrich_out.txt: List of enriched gene families with mapped gene IDs, GO annotation, and detailed statistics fam_all_out.txt: List of all gene families with mapped gene IDs, GO annotation, and detailed statistics |
Description and working example
Check allowed ID types for plant species for GenFam
latest update v1.0.0
bioinfokit.analys.genfam.check_allowed_ids(species)
| Parameters | Description |
|---|---|
species |
Plant species ID to check for allowed ID type. All plant species ID provided here |
Returns:
Allowed ID types for GenFam
Description and working example
Biostatistical analysis
Correlation matrix plot
bioinfokit.visuz.stat.corr_mat(table, corm, cmap, r, dim, show, figtype, axtickfontsize, axtickfontname)
| Parameters | Description |
|---|---|
table |
Dataframe object with numerical variables (columns) to find correlation. Ideally, you should have three or more variables. Dataframe should not have identifier column. |
corm |
Correlation method [pearson,kendall,spearman] [default:pearson] |
cmap |
Color Palette for heatmap [string][default: ‘seismic’]. More colormaps are available at https://matplotlib.org/3.1.0/tutorials/colors/colormaps.html |
r |
Figure resolution in dpi [int][default: 300]. Not compatible with show= True |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 5)] |
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: 7] |
axtickfontname |
Font name for axis ticks [string][default: ‘Arial’] |
Returns:
Correlation matrix plot image in same directory (corr_mat.png)
Bar-dot plot
latest update v0.8.5
bioinfokit.visuz.stat.bardot(df, colorbar, colordot, bw, dim, r, ar, hbsize, errorbar, dotsize, markerdot, valphabar,
valphadot, show, figtype, axxlabel, axylabel, axlabelfontsize, axlabelfontname, ylm, axtickfontsize, axtickfontname,
yerrlw, yerrcw)
| Parameters | Description |
|---|---|
df |
Pandas dataframe object |
colorbar |
Color of bar graph [string or list][default:”#bbcfff”] |
colordot |
Color of dots on bar [string or list][default:”#ee8972”] |
bw |
Width of bar [float][default: 0.4] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
r |
Figure resolution in dpi [int][default: 300] |
ar |
Rotation of X-axis labels [float][default: 0] |
hbsize |
Horizontal bar size for standard error bars [float][default: 4] |
errorbar |
Draw standard error bars [bool (True or False)][default: True] |
dotsize |
The size of the dots in the plot [float][default: 6] |
markerdot |
Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: “o”] |
valphabar |
Transparency of bars on plot [float (between 0 and 1)][default: 1] |
valphadot |
Transparency of dots on plot [float (between 0 and 1)][default: 1] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
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] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axlabelfontname |
Font name for axis labels [string][default: ‘Arial’] |
ylm |
Range of ticks to plot on Y-axis [float tuple (bottom, top, interval)][default: None] |
axtickfontsize |
Font size for axis ticks [float][default: 9] |
axtickfontname |
Font name for axis ticks [string][default: ‘Arial’] |
yerrlw |
Error bar line width [float][default: None] |
yerrcw |
Error bar cap width [float][default: None] |
Returns:
Bar-dot plot image in same directory (bardot.png)
One sample and two sample (independent and paired) t-tests
latest update v0.9.6
bioinfokit.analys.stat.ttest(df, xfac, res, evar, alpha, test_type, mu)
| Parameters | Description |
|---|---|
df |
Pandas dataframe for appropriate t-test. One sample: It should have atleast dependent (res) variable Two sample independent: It should have independent (xfac) and dependent (res) variables Two sample paired: It should have two dependent (res) variables |
xfac |
Independent group column name with two levels [string][default: None] |
res |
Dependent variable column name [string or list or tuple][default: None] |
evar |
t-test with equal variance [bool (True or False)][default: True] |
alpha |
Significance level for confidence interval (CI). If alpha=0.05, then 95% CI will be calculated [float][default: 0.05] |
test_type |
Type of t-test [int (1,2,3)][default: None]. 1: One sample t-test 2: Two sample independent t-test 3: Two sample paired t-test |
mu |
Population or known mean for the one sample t-test [float][default: None] |
Returns:
Summary output as class attribute (summary)
Description and Working example
Chi-square test
latest update v0.9.5
bioinfokit.analys.stat.chisq(df, p)
| Parameters | Description |
|---|---|
df |
Pandas dataframe. It should be one or two-dimensional contingency table. |
p |
Theoretical expected probabilities for each group. It must be non-negative and sum to 1. If p is provide Goodness of Fit test will be performed [list or tuple][default: None] |
Returns:
Summary and expected counts as class attributes (summary and expected_df)
Linear regression analysis
bioinfokit.visuz.stat.lin_reg(df, x, y)
| Parameters | Description |
|---|---|
df |
Pandas dataframe object |
x |
Name of column having independent X variables [list][default:None] |
y |
Name of column having dependent Y variables [list][default:None] |
Returns:
Regression analysis summary
Regression plot
bioinfokit.visuz.stat.regplot(df, x, y, yhat, dim, colordot, colorline, r, ar, dotsize, markerdot, linewidth,
valphaline, valphadot, show, figtype, axxlabel, axylabel, axlabelfontsize, axlabelfontname, xlm, ylm, axtickfontsize,
axtickfontname)
| Parameters | Description |
|---|---|
df |
Pandas dataframe object |
x |
Name of column having independent X variables [string][default:None] |
y |
Name of column having dependent Y variables [string][default:None] |
yhat |
Name of column having predicted response of Y variable (y_hat) from regression [string][default:None] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (6, 4)] |
r |
Figure resolution in dpi [int][default: 300] |
ar |
Rotation of X-axis labels [float][default: 0] |
dotsize |
The size of the dots in the plot [float][default: 6] |
markerdot |
Shape of the dot marker. See more options at https://matplotlib.org/3.1.1/api/markers_api.html [string][default: “o”] |
valphaline |
Transparency of regression line on plot [float (between 0 and 1)][default: 1] |
valphadot |
Transparency of dots on plot [float (between 0 and 1)][default: 1] |
linewidth |
Width of regression line [float][default: 1] |
figtype |
Format of figure to save. Supported format are eps, pdf, pgf, png, ps, raw, rgba, svg, svgz [string][default:’png’] |
show |
Show the figure on console instead of saving in current folder [True or False][default:False] |
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] |
axlabelfontsize |
Font size for axis labels [float][default: 9] |
axlabelfontname |
Font name for axis labels [string][default: ‘Arial’] |
xlm |
Range of ticks to plot on X-axis [float tuple (bottom, top, interval)][default: None] |
ylm |
Range of ticks to plot on Y-axis [float tuple (bottom, top, interval)][default: None] |
axtickfontsize |
Font size for axis ticks [float][default: 9] |
axtickfontname |
Font name for axis ticks [string][default: ‘Arial’] |
Returns:
Regression plot image in same directory (reg_plot.png)
Tukey HSD test
latest update v1.0.3
bioinfokit.analys.stat.tukey_hsd(df, res_var, xfac_var, anova_model, phalpha, ss_typ)
It performs multiple pairwise comparisons of treatment groups using Tukey’s HSD (Honestly Significant Difference) test to check if group means are significantly different from each other. It uses the Tukey-Kramer approach if the sample sizes are unequal among the groups.
| Parameters | Description |
|---|---|
df |
Pandas dataframe with the variables mentioned in the res_var, xfac_var and anova_model options. It should not have missing data. The missing data will be omitted. |
res_var |
Name of a column having response variable [string][default: None] |
xfac_var |
Name of a column having factor or group for pairwise comparison [string][default: None] |
anova_model |
ANOVA model (calculated using statsmodels ols function) [string][default: None] |
phalpha |
Significance level [float][default: 0.05] |
ss_typ |
Type of sum of square to perform ANOVA [int][default: 2] |
Returns:
| Attribute | Description |
|---|---|
tukey_summary |
Pairwise comparisons for main and interaction effects by Tukey HSD test |
Description and Working example
Bartlett’s test
latest update v1.0.3
bioinfokit.analys.stat.bartlett(df, xfac_var, res_var)
It performs Bartlett’s test to check the homogeneity of variances among the treatment groups. It accepts the input table in a stacked format. More details https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.bartlett.html
| Parameters | Description |
|---|---|
df |
Pandas dataframe containing response (res_var) and independent variables (xfac_var) in a stacked format. It should not have missing data. The missing data will be omitted. |
res_var |
Name of a column having response variable [string][default: None] |
xfac_var |
Name of a column having treatment groups (independent variables) [string or list][default: None] |
Returns:
| Attribute | Description |
|---|---|
bartlett_summary |
Pandas dataframe containing Bartlett’s test statistics, degree of freedom, and p value |
Description and Working example
Levene’s test
latest update v1.0.3
bioinfokit.analys.stat.levene(df, xfac_var, res_var)
It performs Levene’s test to check the homogeneity of variances among the treatment groups. It accepts the input table in a stacked format. More details https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.levene.html
| Parameters | Description |
|---|---|
df |
Pandas dataframe containing response (res_var) and independent variables (xfac_var) in a stacked format. It should not have missing data. The missing data will be omitted. |
res_var |
Name of a column having response variable [string][default: None] |
xfac_var |
Name of a column having treatment groups (independent variables) [string or list][default: None] |
center |
Choice for the Levene’s test [string (median, mean, trimmed)] [default: median] median: Brown-Forsythe Levene-type test mean: original Levene’s test trimmed: Brown-Forsythe Levene-type test |
Returns:
| Attribute | Description |
|---|---|
levene_summary |
Pandas dataframe containing Levene’s test statistics, degree of freedom, and p value |
Description and Working example
ROC plot
Receiver operating characteristic (ROC) curve for visualizing classification performance
latest update v1.0.4
bioinfokit.visuz.stat.roc(fpr, tpr, c_line_style, c_line_color, c_line_width, diag_line, diag_line_style,
diag_line_width, diag_line_color, auc, shade_auc, shade_auc_color, axxlabel, axylabel, axtickfontsize,
axtickfontname, axlabelfontsize, axlabelfontname, plotlegend, legendpos, legendanchor, legendcols, legendfontsize,
legendlabelframe, legend_columnspacing, dim, show, figtype, figname, r, ylm)
| Parameters | Description |
|---|---|
fpr |
Increasing false positive rates obtained from sklearn.metrics.roc_curve [list][default:None] |
tpr |
Increasing true positive rates obtained from sklearn.metrics.roc_curve [list][default:None] |
c_line_style |
Line style for ROC curve [string][default:’-‘] |
c_line_color |
Line color for ROC curve [string][default:’#f05f21’] |
c_line_width |
Line width for ROC curve [float][default:1] |
diag_line |
Plot reference line [True or False][default: True] |
diag_line_style |
Line style for reference line [string][default:’–’] |
diag_line_width |
Line width for reference line [float][default:1] |
diag_line_color |
Line color for reference line [string][default:’b’] |
auc |
Area under ROC. It can be obtained from sklearn.metrics.roc_auc_score [float][default: None] |
shade_auc |
Shade are for AUC [True or False][default: False] |
shade_auc_color |
Shade color for AUC [string][default: ‘#f48d60’] |
axxlabel |
Label for X-axis [string][default: ‘False Positive Rate (1 - Specificity)’] |
axylabel |
Label for Y-axis [string][default: ‘True Positive Rate (Sensitivity)’] |
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’] |
plotlegend |
plot legend [True or False][default:True] |
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:’lower right’] |
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] |
legendcols |
Number of columns for legends [int][default: 1] |
legendfontsize |
Font size for the legends [float][default:8] |
legendlabelframe |
Box frame for the legend [True or False][default: False] |
legend_columnspacing |
Spacing between the legends [float][default: None] |
dim |
Figure size [tuple of two floats (width, height) in inches][default: (5, 4)] |
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’] |
figname |
name of figure [string ][default:’roc’] |
r |
Figure resolution in dpi [int][default: 300]. Not compatible with show= True |
ylm |
Range of ticks to plot on Y-axis [float (bottom, top, interval)][default: None] |
Returns:
ROC plot image in same directory (roc.png) Working example
How to cite bioinfokit?
- Renesh Bedre. (2020, July 29). reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit. Zenodo. http://doi.org/10.5281/zenodo.3965241
- Additionally check Zenodo to cite specific version of bioinfokit
References:
- Travis E. Oliphant. A guide to NumPy, USA: Trelgol Publishing, (2006).
- John D. Hunter. Matplotlib: A 2D Graphics Environment, Computing in Science & Engineering, 9, 90-95 (2007), DOI:10.1109/MCSE.2007.55 (publisher link)
- Fernando Pérez and Brian E. Granger. IPython: A System for Interactive Scientific Computing, Computing in Science & Engineering, 9, 21-29 (2007), DOI:10.1109/MCSE.2007.53 (publisher link)
- Michael Waskom, Olga Botvinnik, Joel Ostblom, Saulius Lukauskas, Paul Hobson, MaozGelbart, … Constantine Evans. (2020, January 24). mwaskom/seaborn: v0.10.0 (January 2020) (Version v0.10.0). Zenodo. http://doi.org/10.5281/zenodo.3629446
- Fabian Pedregosa, Gaël Varoquaux, Alexandre Gramfort, Vincent Michel, Bertrand Thirion, Olivier Grisel, Mathieu Blondel, Peter Prettenhofer, Ron Weiss, Vincent Dubourg, Jake Vanderplas, Alexandre Passos, David Cournapeau, Matthieu Brucher, Matthieu Perrot, Édouard Duchesnay. Scikit-learn: Machine Learning in Python, Journal of Machine Learning Research, 12, 2825-2830 (2011)
- David C. Howell. Multiple Comparisons With Unequal Sample Sizes. https://www.uvm.edu/~statdhtx/StatPages/MultipleComparisons/unequal_ns_and_mult_comp.html
- Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. (2020) SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17(3), 261-272.
bioinfokit cited by:
- Liang L, Darbandi SF, Pochareddy S, Gulden FO, Gilson MC, Sheppard BK, Sahagun A, An JY, Werling DM, Rubenstein JL, Sestan N. Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse neocortex. bioRxiv. 2020 Jan 1.
- Irigoyen S, Ramasamy M, Pant S, Niraula P, Bedre R, Gurung M, Rossi D, Laughlin C, Gorman Z, Achor D, Levy A. Plant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp. Nature Communications. 2020 Nov 16;11(1):1-4.
- Lu J, Wilfred P, Korbie D, Trau M. Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation. Cancers. 2020 Nov;12(11):3199.
- Jennifer Gribble, Andrea J. Pruijssers, Maria L. Agostini, Jordan Anderson-Daniels, James D. Chappell, Xiaotao Lu, Laura J. Stevens, Andrew L. Routh, Mark R. Denison bioRxiv 2020.04.23.057786; doi: https://doi.org/10.1101/2020.04.23.057786
- Aarts J, Bijma P, Xia S, Textor J, de Vries A. A GWAS about the wingsize of Nasonia Vitripennis.
- Greaney AM, Adams TS, Raredon MS, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing. Cell Reports. 2020 Mar 24;30(12):4250-65.
Last updated: November 24, 2020