Bioscripts

Heatmap

The heatmap may also be combined with clustering methods which group genes and/or samples together based on the similarity of their gene expression pattern.

This can be useful for identifying genes that are commonly regulated, or biological signatures associated with a particular condition.

For heatmap you need pandas modules such as seaborn, pandas, numpy ,sys, matplotlib.

This program will take input file of extension .csv /.xlsx /.xls in which one of the columns must be gene_id which is having ensemble_id/gene symbol (***if not rename it as gene_id) and other columns must be all logFC columns containing logFC values.

To get Heatmap use bellow commands:

Program: python3 heatmap.py input/heatmapintput.xlsx

• python3: version of python
• heatmap.py: code file
• input/heatmapintput.xlsx: folder name and name of the file (path of file with its full name)

Usage: python3 heatmap.py [input file path]

After Executing by Enter you have to provide options on terminal/command prompt

Options:

1. Optional. Enter the colors separated by coma(this is optional ,if you skipped it will take default colors)
2. Optional. Do you want to provide row cluster? (y/n)
3. Optional. Do you want to provide column cluster?(y/n)
4. Optional. Do you want to provide xticklabels? (y/n):(will display label to x axis)
5. Optional. Do you want to provide yticklabels? (y/n):(will display label to y axis)
6. Optional. Do you want to provide row color bar ? (y/n): (y/n):(will display row color bar with heatmap)

Volcano Plot

A volcano plot is a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).

In a volcano plot, the most upregulated genes are towards the right, the most downregulated genes are towards the left, and the most statistically significant genes are towards the top.

For volcano plot you need pandas modules such as bioinfokit, pandas, numpy sys, matplotlib.To get volcano plot use bellow commands:

Program: python3 volcano.py input/data.csv

Usage: python3 volcano.py [input file path]
After Executing by Enter you have to provide options on terminal/command prompt

Options:

1. Compulsory. Name of a column having log or absolute fold change values
2. Compulsory. Name of a column having P-values or adjusted P-values "\t"
3. Compulsory. Name of the column having Ensemble_GeneID
4. Compulsory. gene_name
5. Compulsory. Log or absolute fold change cutoff for up and downregulated genes
6. Compulsory. P-values or adjusted P-values cutoff for up and downregulated genes
7. Optional. Do you want to grid lines on plot with defined log fold change (lfc_thr) and P-value (pv_thr) threshold value(y/n)
8. Compulsory. Name of figure

Wiggle

Wiggle format is line-oriented. Wiggle format is composed of declaration lines and data lines, and require a separate wiggle track definition line. Text files in wiggle format can be uploaded as custom tracks as-is to UCSC for visualization. Wiggle files allow you to plot quantitative data as either shades of color (dense mode) or bars of varying height (full and pack mode) on the genome.

To Execute you need install pandas liberary package as given in How_to_use file in downloaded zip

Program :python3 wiggle.py input/mouse.txt

Usage: python3 [program].py [input file path]

Place the text file into input folder. the file should be txt etension with tab separated and contains ["chr","start","end","Gene symbol"] this must be the first row

Reverse,Complement and Reverese Compliment Of Sequence

Reverse is reversing the order of nucleotides in a sequence

Complement is complementing a sequence means replacing each nucleotide with its complementary nucleotide.Complementing a sequence can be important when determining the base-pairing properties of a sequence

Reverse complement of a sequence combines both reversing and complementing operations

To Execute you need install biopython package as given in How_to_use file in downloaded zip.

For Reverse Program :python3 reverse.py input/sequence.fasta
For Complement Program :python3 complement.py input/sequence.fasta
For Reverse Complement Program :python3 reversecomp.py input/sequence.fasta

Usage: python3 [program].py [input file path]

Feature Count From Fasta Sequence

This program will take input file which has multiple/single fasta sequences and generate count A , Count T, Count C, Count G, Others and also calculate %GC for each fasta sequence and create output in csv format.

To run the file, use python3 ATGC_count.py the file_path is actual path where the file is saved.

Program :python3 ATGC_count.py input/sequence.fasta

Usage: python3 [program].py [input file path]

Fastq To Fasta Format

This program will take fastq file as input and it converts fastq to fasta format file for each record and calculates length of sequence, A,T,G,C count ,GC%, and others for each and store in csv file.

For fastqc report you need pandas,sys modules of python.

To get fastqc report use bellow steps / Read README file which is given in downloaded zip.

To run the file copy the ,use python3 Fastq_to_Fasta.py the file_path is actual path where the file is saved.

python3 Fastq_to_Fasta.py input/mouse.fastq

Usage: python3 Fastq_to_Fasta.py [input file path]