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seqfilter.c

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Seqfilter

Seqfilter is a small tool written in C on top of the excellent klib library by Heng Li. It allows filtering of fasta and fastq files based on sequence IDs and sequence length. The fasta and fastq input files may be gzipped.

Get it!

git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make

Usage

Seqfilter will always try to filter by IDs, since thats its intended purpose. You can however omit the ID file. In that case, you have to specify the ‘-n’ flag for negative filtering if you want to produce output, to allow output of sequences without a “valid” ID.

Negative filtering (‘-n’) means that all sequences without ID matches are kept (subsequently, if no ID file is supplied, all sequences are without ID matches).

# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About

Filter fasta/fastq(.gz) files by ID and/or sequence length

Resources

Readme
MIT license
Activity

Stars

14 stars

Watchers

2 watching

Forks

2 forks
Report repository

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Packages

Contributors

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, '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" + '

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Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
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, '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('^' + ".*" + '

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README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
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('^' + ".*" + '

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Makefile
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README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
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Contributors
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, '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" + '

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klib @ de09fb7
klib @ de09fb7
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Makefile
README.org
README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
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('^' + ".*" + '

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Makefile
README.org
README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
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, '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('^' + ".*" + '

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Makefile
README.org
README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
Resources
Readme
MIT license
Activity
Stars
14 stars
Watchers
2 watching
Forks
2 forks
Report repository
Releases
Packages
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); }
})();
})();

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README.org
seqfilter.c
seqfilter.c
Repository files navigation
Seqfilter
Seqfilter is a small tool written in C on top of the excellent
klib library by Heng Li. It allows filtering of fasta and fastq files
based on sequence IDs and sequence length. The fasta and fastq input
files may be gzipped.
Get it!
git clone --recursive https://github.com/clwgg/seqfilter
cd seqfilter
make
Usage
Seqfilter will always try to filter by IDs, since thats its intended purpose.
You can however omit the ID file. In that case, you have to specify the ‘-n’ flag
for negative filtering if you want to produce output, to allow output
of sequences without a “valid” ID.
Negative filtering (‘-n’) means that all sequences without ID
matches are kept (subsequently, if no ID file is supplied, all
sequences are without ID matches).
# filter by ID file
seqfilter -i in.fq -l ids.txt -o out.fq
#filter by ID file and min length 30
seqfilter -m 30 -i in.fq -l ids.txt -o out.fq
#filter only by min length 30
seqfilter -n -m 30 -i in.fq -o out.fq
#keep only sequence called "mt"
seqfilter -i in.fa -l <(printf "mt\n") -o mt.fa
#remove sequence called "mt" from input
seqfilter -n -i in.fa -l <(printf "mt\n") -o in_no-mt.fa

About
Filter fasta/fastq(.gz) files by ID and/or sequence length
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