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miraligner input files require fixed names #98

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miraligner input files require fixed names#98
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greatfireball
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@greatfireball
greatfireball
opened on Mar 22, 2018

According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.

The names have to be:

  • hairpin.fa
  • miRNA.str

Therefore, we need to ensure, that files with that names are provided.

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    , 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
     blocks
(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" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
    Skip to content
    miraligner input files require fixed names #98
    Closed
    Closed
    miraligner input files require fixed names#98
    Assignees
    greatfireball
    Labels
    bug
    Description
    @greatfireball
    greatfireball
    opened on Mar 22, 2018
    According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
    The names have to be:
    • hairpin.fa
    • miRNA.str
    Therefore, we need to ensure, that files with that names are provided.
    Metadata
    Metadata
    Assignees
    Labels
    bug
    Type
    No type
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    No projects
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      No milestone
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      No branches or pull requests
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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('^' + ".*" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
      Skip to content
      miraligner input files require fixed names #98
      Closed
      Closed
      miraligner input files require fixed names#98
      Assignees
      greatfireball
      Labels
      bug
      Description
      @greatfireball
      greatfireball
      opened on Mar 22, 2018
      According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
      The names have to be:
      • hairpin.fa
      • miRNA.str
      Therefore, we need to ensure, that files with that names are provided.
      Metadata
      Metadata
      Assignees
      Labels
      bug
      Type
      No type
      Projects
      No projects
        Milestone
        No milestone
        Relationships
        None yet
        Development
        No branches or pull requests
        Issue actions
        
, '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('^' + ".*" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
        Skip to content
        miraligner input files require fixed names #98
        Closed
        Closed
        miraligner input files require fixed names#98
        Assignees
        greatfireball
        Labels
        bug
        Description
        @greatfireball
        greatfireball
        opened on Mar 22, 2018
        According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
        The names have to be:
        • hairpin.fa
        • miRNA.str
        Therefore, we need to ensure, that files with that names are provided.
        Metadata
        Metadata
        Assignees
        Labels
        bug
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, '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" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
          Skip to content
          miraligner input files require fixed names #98
          Closed
          Closed
          miraligner input files require fixed names#98
          Assignees
          greatfireball
          Labels
          bug
          Description
          @greatfireball
          greatfireball
          opened on Mar 22, 2018
          According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
          The names have to be:
          • hairpin.fa
          • miRNA.str
          Therefore, we need to ensure, that files with that names are provided.
          Metadata
          Metadata
          Assignees
          Labels
          bug
          Type
          No type
          Projects
          No projects
            Milestone
            No milestone
            Relationships
            None yet
            Development
            No branches or pull requests
            Issue actions
            
, '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('^' + ".*" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
            Skip to content
            miraligner input files require fixed names #98
            Closed
            Closed
            miraligner input files require fixed names#98
            Assignees
            greatfireball
            Labels
            bug
            Description
            @greatfireball
            greatfireball
            opened on Mar 22, 2018
            According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
            The names have to be:
            • hairpin.fa
            • miRNA.str
            Therefore, we need to ensure, that files with that names are provided.
            Metadata
            Metadata
            Assignees
            Labels
            bug
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, '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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
              Skip to content
              miraligner input files require fixed names #98
              Closed
              Closed
              miraligner input files require fixed names#98
              Assignees
              greatfireball
              Labels
              bug
              Description
              @greatfireball
              greatfireball
              opened on Mar 22, 2018
              According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
              The names have to be:
              • hairpin.fa
              • miRNA.str
              Therefore, we need to ensure, that files with that names are provided.
              Metadata
              Metadata
              Assignees
              Labels
              bug
              Type
              No type
              Projects
              No projects
                Milestone
                No milestone
                Relationships
                None yet
                Development
                No branches or pull requests
                Issue actions
                
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
miraligner input files require fixed names · Issue #98 · microPIECE-team/microPIECE · GitHub
                Skip to content
                miraligner input files require fixed names #98
                Closed
                Closed
                miraligner input files require fixed names#98
                Assignees
                greatfireball
                Labels
                bug
                Description
                @greatfireball
                greatfireball
                opened on Mar 22, 2018
                According to http://seqcluster.readthedocs.io/mirna_annotation.html and @DanielAmselmiraligner.jar requires fixed names for the input files.
                The names have to be:
                • hairpin.fa
                • miRNA.str
                Therefore, we need to ensure, that files with that names are provided.
                Metadata
                Metadata
                Assignees
                Labels
                bug
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions