{"id":1114,"date":"2025-12-19T16:55:57","date_gmt":"2025-12-19T11:10:57","guid":{"rendered":"https:\/\/pokharelsugam.com.np\/bioinformatics\/?p=1114"},"modified":"2025-12-28T11:52:49","modified_gmt":"2025-12-28T06:07:49","slug":"bioinformatics-scripts-commands","status":"publish","type":"post","link":"https:\/\/pokharelsugam.com.np\/bioinformatics\/bioinformatics-scripts-commands\/","title":{"rendered":"Bioinformatics Scripts &#038; Commands"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">Python<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Install Python <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Windows:       <a href=\"https:\/\/www.python.org\/downloads\/windows\/\">https:\/\/www.python.org\/downloads\/windows\/<\/a>    (Don&#8217;t forget to tick PATH in first step of installation)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Install Virtual Environment<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Windows:<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install virtualenv<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Virtual Environment Creation<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Windows: Go to the desired folder and open command prompt\/terminal\/powershell  in this folder by pressing &#8220;shift&#8221; key and &#8220;right click&#8221; in mouse then select &#8220;terminal&#8221; or &#8220;powershell&#8221; . Then type following commands<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>virtualenv biopythonenv<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Activate\/Use Virtual Environment : Go to folder that contain env folder then open with terminal like above and enter following commands<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>biopythonenv\\Scripts\\activate<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">Installation of mostly used bioinformatic python library<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Lists of Essential Libraries<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>biopython<\/strong> \u2013 Sequence handling (FASTA, GenBank), BLAST, alignments, phylogenetics<\/li>\n\n\n\n<li><strong>numpy<\/strong> \u2013 Numerical computing, arrays, matrix operations<\/li>\n\n\n\n<li><strong>pandas<\/strong> \u2013 Tabular biological data (expression matrices, metadata)<\/li>\n\n\n\n<li><strong>scipy<\/strong> \u2013 Statistics, clustering, distance metrics<\/li>\n\n\n\n<li><strong>matplotlib<\/strong> \u2013 Core plotting<\/li>\n\n\n\n<li><strong>seaborn<\/strong> \u2013 Statistical &amp; publication-quality plots<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Install all above libraries in activated virtual environment by entering following commands<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install biopython numpy pandas scipy matplotlib seaborn<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>For Genomics, NGS, and Sequence Analysis<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>pyfaidx<\/strong> \u2013 Fast random access to FASTA files<\/li>\n\n\n\n<li><strong>pysam<\/strong> \u2013 Read\/write BAM, SAM, VCF (essential for NGS)<\/li>\n\n\n\n<li><strong>pybedtools<\/strong> \u2013 Genomic interval operations (BED, GTF, GFF)<\/li>\n\n\n\n<li><strong>scikit-bio<\/strong> \u2013 Microbiome, phylogenetics, sequence analysis<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install pysam pyfaidx pybedtools scikit-bio<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Machine Learning &amp; Statistics<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>scikit-learn<\/strong> \u2013 ML (clustering, PCA, classifiers)<\/li>\n\n\n\n<li><strong>statsmodels<\/strong> \u2013 Statistical tests, regression, differential analysis<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install scikit-learn statsmodels<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Structural Biology &amp; Biochemistry<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>biotite<\/strong> \u2013 Structures, alignments, trajectories<\/li>\n\n\n\n<li><strong>mdtraj<\/strong> \u2013 Molecular dynamics trajectory analysis<\/li>\n\n\n\n<li><strong>rdkit<\/strong> \u2013 Cheminformatics (drug discovery)<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install biotite mdtraj rdkit-pypi<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Other Semi Essential Libraries<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Progress meter for Python loops and command-line interfaces<\/strong> (tqdm)<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>pip install requests tqdm<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">Miniconda(Conda Environment )<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Anaconda vs Miniconda: Miniconda is best for low grade computer and easy clean installation and uninstallation<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>How to install miniconda?<\/strong> <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">In windows<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">To install mini conda first need to visit anaconda download  website <a href=\"https:\/\/www.anaconda.com\/download\/success\">https:\/\/www.anaconda.com\/download\/success<\/a>   Then choose miniconda installation file to downlaod<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Installation Guide:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Double click the installation file<\/li>\n\n\n\n<li>Choose installation for user only <\/li>\n\n\n\n<li>Change default installation folder to D or E drive not in C drive for low grade pc and easy unstallation<\/li>\n\n\n\n<li>Do not add PATH and do not use anaconda python default.<\/li>\n\n\n\n<li>Then finish the installation<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">Create conda virtual environment<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Open anaconda PowerShell Prompt from Start Menu in windows<\/li>\n\n\n\n<li>Go to working directory from c drive <\/li>\n\n\n\n<li>Update conda using comand  &#8220;<em><code>conda update conda<\/code><\/em>&#8220;<\/li>\n\n\n\n<li>Create virtual environment using command &#8220;<em><code>conda create -n biocondaenv python=3.10 <\/code><\/em>&#8221; here &#8220;<em><code>biocondaenv<\/code><\/em>&#8221; is the name of virtual environment . You can give any other name also<\/li>\n\n\n\n<li>Use command &#8220;<em><code>conda activate biocondaenv<\/code><\/em>&#8221; to activate virtual environment.<\/li>\n\n\n\n<li>After activating user defined venv the default environment &#8220;<em><code>(base)<\/code><\/em>&#8221; is changed into &#8220;<em><code>(biocondaenv)<\/code><\/em>&#8220;<\/li>\n\n\n\n<li>After finishing data analysis and research you can deactivate conda using command &#8220;<em><code>conda deactivate<\/code><\/em>&#8221; .<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Update Conda Channel Configuration (in default  &#8216;base&#8217; environment)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Run these commands one by one in conda terminal<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>conda config --add channels bioconda\nconda config --add channels conda-forge\nconda config --set channel_priority strict<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">Verify setup by command &#8221; <em><code>conda config --show channels<\/code><\/em> &#8221; This should show following order<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">channels:<br>                     -conda-forge<br>                    -bioconda<br>                    -defaults<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Now your computer is ready to install bioconda libraries<\/strong> <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Enter the give command in biocondaenv virtual environment<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>conda install -c conda-forge -c bioconda fastqc multiqc samtools bcftools bedtools bwa bowtie2 hisat2 blast mafft muscle clustalo biopython snakemake seqkit<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Install mamba in user created virtual environment because mamba is faster than conda in low grade computer<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Create virtual environment using command &#8220;<em><code>conda create -n biomambaaenv python=3.10 <\/code><\/em>&#8221; here &#8220;<em><code>biomambaenv<\/code><\/em>&#8221; is the name of virtual environment . You can give any other name also<\/li>\n\n\n\n<li>Activate miomambaenve<\/li>\n\n\n\n<li>Then install mamba like below<\/li>\n<\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>conda install -c conda-forge mamba<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code>mamba  --version<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Python Install Python Windows: https:\/\/www.python.org\/downloads\/windows\/ (Don&#8217;t forget to tick PATH in first step of installation) Install Virtual Environment Windows: Virtual [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":null,"ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":null,"ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":null,"ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":null,"stick-header-meta":null,"header-above-stick-meta":null,"header-main-stick-meta":null,"header-below-stick-meta":null,"astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"categories":[8,6,11],"tags":[],"class_list":["post-1114","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-general-bioinformatics","category-programming"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Bioinformatics Scripts &amp; 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