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sequence_processing

some scripts to process fasta and fastq sequences

remove duplicates

This script takes a fasta file from STDIN, removes duplicated sequences and writes the output to STDOUT.

Sequences will be deleted, if they have an identical header and an identical sequence. This script can also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters are converted to N. This feature can be skipped using the –no-convert option. The script also converts lowercase sequence characters to uppercase. This can be skipped with the –no-up option.

Use one the following commands for help:

./remove_dulicates --help
perldoc ./remove_duplicates

sample from fasta

This script takes a fasta file and a number of sequences (n) to sample. It writes n randomly selected sequences to the output file.

This script can also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters can be converted to N and lowercase sequence characters can be converted to uppercase.

Use the following command for help:

./sample_from_fasta.pl --help

split fasta

This script takes a fasta file and generates a new file for each sequence. The new files are named as <input.fa>.sequenceID

This script will also clean the fasta file: Linebreaks in the sequence as well as empty lines and leading whitespaces in headers (> id) are removed by default. Additionally, non ACGT charachters can be converted to N and lowercase sequence characters can be converted to uppercase.

Use the following command for help:

./sample_from_fasta.pl --help

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some scripts to process fasta and fastq sequences

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, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
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Readme
MIT license
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
1 watching
Forks
1 fork
Report repository
Releases
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
GitHub - nterhoeven/sequence_processing: some scripts to process fasta and fastq sequences · GitHub
Skip to content
BranchesTags
Repository files navigation
sequence_processing
some scripts to process fasta and fastq sequences
remove duplicates
This script takes a fasta file from STDIN, removes duplicated sequences
and writes the output to STDOUT.
Sequences will be deleted, if they have an identical header and an identical sequence.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters are converted to N. This feature can be skipped using the –no-convert
option. The script also converts lowercase sequence characters to uppercase. This can be
skipped with the –no-up option.
Use one the following commands for help:
./remove_dulicates --help
perldoc ./remove_duplicates
sample from fasta
This script takes a fasta file and a number of sequences (n) to sample. It writes n
randomly selected sequences to the output file.
This script can also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
split fasta
This script takes a fasta file and generates a new file for each sequence.
The new files are named as <input.fa>.sequenceID
This script will also clean the fasta file: Linebreaks in the sequence as well as empty
lines and leading whitespaces in headers (> id) are removed by default. Additionally,
non ACGT charachters can be converted to N and lowercase sequence characters can be
converted to uppercase.
Use the following command for help:
./sample_from_fasta.pl --help
About
some scripts to process fasta and fastq sequences
Resources
Readme
MIT license
Activity
Stars
1 star
Watchers
1 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors
Languages