BranchesTags

Latest commit

History

1 Commit

Folders and files

NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py

Repository files navigation

Hello!

We're going to run fastp to trim any adaptors and filter any low quality reads. While I understand it's possible to run a process on all files in a directory using wildcards like so:

fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed! I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.

We can run BWA later in paired end read mode, so we won't merge reads. Make sure to place yourself in the folder with all your gzipped fastq paired end reads first. Also, make a folder called fastp inside that folder. I could probably tell python to make it for you, but let's meet eachother halfway! .°(ಗдಗ。)°.

I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python). I would also refer to the link if you want to try using python to automate getting data from SRA.

Dependencies:

  • Python and modules os and subprocess
  • fastp
  • multiqc

Have fun!

About

Automating fastp over a directory followed by multiqc

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

Packages

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
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
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
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 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('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
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
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 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('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
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
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 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); }
})();
})();

Skip to content
BranchesTags
Latest commit
History
1 Commit
Folders and files
NameName
Last commit message
Last commit date
README.md
README.md
fastp_pe.py
fastp_pe.py
Repository files navigation
Hello!
We're going to run fastp to trim any adaptors and filter any low quality reads.
While I understand it's possible to run a process on all files in a directory using wildcards like so:
fastp -i ./*pass_1.fastq.gz #...

I'm not sure how to automatically make the output file names the same as the input file names, thus this script was needed!
I believe this might be a way : https://itectec.com/unixlinux/bash-how-to-write-output-to-a-file-of-the-same-name-as-the-input/ but for want of time I'm going with python.
We can run BWA later in paired end read mode, so we won't merge reads.
Make sure to place yourself in the folder with all your gzipped fastq paired end reads first.
Also, make a folder called fastp inside that folder.
I could probably tell python to make it for you, but let's meet eachother halfway!
.°(ಗдಗ。)°.
I heavily referenced the approach of Erick Lu (https://erilu.github.io/python-fastq-downloader/#automating-downloads-using-python).
I would also refer to the link if you want to try using python to automate getting data from SRA.
Dependencies:
  • Python and modules os and subprocess
  • fastp
  • multiqc
Have fun!
About
Automating fastp over a directory followed by multiqc
Resources
Readme
Activity
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages