BranchesTags

Repository files navigation

bioscripts

See below for Installation instructions.

Bioinformatics

fastamotifsearch.pl

A simple script to search for a motif in a FASTA file. Specified amino acids or X for any amino acid are allowed.

grabpdb.pl

Grab a PDB file by code from the internet

grabsprot.pl

Grab a SwissProt or FASTA file from UniProtKB by specifying accession or identifier. Can also download the DNA if there is a link to an ENA entry.

indexfasta / getfasta

Index a FASTA file such that an entry can be grabbed quickly

indexswissprot / getswissprot

Index a SwissProt file such that an entry can be grabbed quickly

Weka

arff2csv

Converts a Weka ARFF file to CSV format

csv2arff

Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.

LaTeX

checktex

Checks the nesting of environments and curly brackets in a LaTeX file. Also checks cross-references to tables, figures, etc and reports those that haven't been reference or have been referenced out of order.

fclean

Intelligently lean up intermediate files when using LaTeX.

ftpmirror

A powerful script for mirroring FTP sites

INSTALLATION

Installation places the scripts in a specified directory and then makes links in a binary directory with no extension (so you can just type commands such as "grabpdb")

Edit the Makefile to modify

"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible

Type:

make install

to install the scripts.

indexfasta

The Makefile in the indexfasta directory also allows updating of the indexes for getfasta / getswissprot - i.e. it will run indexfasta and indexswissprot. You will need to edit the Makefile to define the directories containing the SwissProt data and where the index will live.

PREREQUISITES

You need to install the following Perl modules:

LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root) do:

perl -MCPAN -e shell
install LWP::UserAgent

About

Generally useful Bioinformatics scripts

Resources

Readme
GPL-2.0 license
Activity

Stars

3 stars

Watchers

1 watching

Forks

1 fork
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
bioscripts
See below for Installation instructions.
Bioinformatics
fastamotifsearch.pl
A simple script to search for a motif in a FASTA file. Specified amino
acids or X for any amino acid are allowed.
grabpdb.pl
Grab a PDB file by code from the internet
grabsprot.pl
Grab a SwissProt or FASTA file from UniProtKB by specifying accession
or identifier. Can also download the DNA if there is a link to an ENA
entry.
indexfasta / getfasta
Index a FASTA file such that an entry can be grabbed quickly
indexswissprot / getswissprot
Index a SwissProt file such that an entry can be grabbed quickly
Weka
arff2csv
Converts a Weka ARFF file to CSV format
csv2arff
Converts a CSV file to Weka ARFF format with lots of options to select subsets of data, etc.
LaTeX
checktex
Checks the nesting of environments and curly brackets in a LaTeX
file. Also checks cross-references to tables, figures, etc and reports
those that haven't been reference or have been referenced out of
order.
fclean
Intelligently lean up intermediate files when using LaTeX.
ftpmirror
A powerful script for mirroring FTP sites
INSTALLATION
Installation places the scripts in a specified directory and then
makes links in a binary directory with no extension (so you can just
type commands such as "grabpdb")
Edit the Makefile to modify
"dest" - where the scripts will live
"bin" - your binary directory (in your path)

The defaults are sensible
Type:
make install

to install the scripts.
indexfasta
The Makefile in the indexfasta directory also allows updating of the
indexes for getfasta / getswissprot - i.e. it will run
indexfasta and indexswissprot. You will need to edit the
Makefile to define the directories containing the SwissProt data and
where the index will live.
PREREQUISITES
You need to install the following Perl modules:
LWP::UserAgent

Fedora/RedHat/CentOS installs this automatically. Otherwise (as root)
do:
perl -MCPAN -e shell
install LWP::UserAgent

About
Generally useful Bioinformatics scripts
Resources
Readme
GPL-2.0 license
Activity
Stars
3 stars
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages