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@@ -23,6 +23,7 @@ Or build from source. | |
| # e.g. get rustup! | ||
| curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh | ||
| # get directly from crates.io | ||
| # currently this is the latest available version 0.2.3XX | ||
| cargo install gfatk | ||
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| # or clone this repo! | ||
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@@ -42,33 +43,29 @@ The features of the toolkit reflect only their usefulness in debugging, visualis | |
| Current help: | ||
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| ``` | ||
| gfatk 0.2.2 | ||
| Max Brown <[email protected]> | ||
| Explore and linearise (mitochondrial) GFA files. | ||
| USAGE: | ||
| gfatk [SUBCOMMAND] | ||
| OPTIONS: | ||
| -h, --help Print help information | ||
| -V, --version Print version information | ||
| SUBCOMMANDS: | ||
| dot Return the dot representation of a GFA. | ||
| extract Extract subgraph from a GFA, given a segment name. | ||
| extract-chloro Extract the plastid from a GFA. | ||
| extract-mito Extract the mitochondria from a GFA. | ||
| fasta Extract a fasta file. | ||
| Almost as simple as: awk '/^S/{print ">"$2"\n"$3}'. | ||
| help Print this message or the help of the given subcommand(s) | ||
| linear Force a linear representation of the graph. | ||
| overlap Extract overlaps from a GFA. | ||
| path Supply an input path to evaluate a linear representation of. Input must be | ||
| a text file of a single comma separated line with node ID's and | ||
| orientations. E.g.: | ||
| 1+,2-,3+ | ||
| stats Some stats about the input GFA. | ||
| trim Trim a GFA to remove nodes of degree < 4 (i.e. only has one neighbour). | ||
| Explore and linearise (plant organellar) GFA files. | ||
| Usage: gfatk [COMMAND] | ||
| Commands: | ||
| overlap Extract overlaps from a GFA. | ||
| extract Extract subgraph from a GFA, given a segment name. | ||
| linear Force a linear representation of the graph. | ||
| fasta Extract a fasta file. | ||
| Almost as simple as: awk '/^S/{print ">"$2"\n"$3}'. | ||
| stats Some stats about the input GFA. | ||
| extract-mito Extract the mitochondria from a GFA. | ||
| extract-chloro Extract the plastid from a GFA. | ||
| dot Return the dot representation of a GFA. | ||
| trim Trim a GFA to remove nodes of degree < 4 (i.e. only has one neighbour). | ||
| path Supply an input path to evaluate a linear representation of. | ||
| Input must be a text file of a single comma separated line with node ID's and orientations. E.g. 1+,2-,3+ | ||
| rename Rename the segment ID's of a GFA. | ||
| help Print this message or the help of the given subcommand(s) | ||
| Options: | ||
| -h, --help Print help | ||
| -V, --version Print version | ||
| ``` | ||
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| To explain each of these briefly: | ||
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@@ -108,7 +105,7 @@ Some unit tests are now provided in the `tests` directory. To run these (you'll | |
| cargo test --release | ||
| ``` | ||
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| For full functionality of the toolkit, two tags are required, node coverage and edge coverage. Other functionality will fail if the CIGAR string is not purely an overlap; i.e. in the format `<integer>M`. Only GFA version 1 supported. Only header (`H`), segment (`S`), and link (`L`) lines are required. Other lines (e.g. path, `P`), will I think be ignored. | ||
| For full functionality of the toolkit, two tags are required, node coverage and edge coverage. Other functionality will fail if the CIGAR string is not purely an overlap; i.e. in the format `<integer>M`. Only GFA version 1 supported. Only header (`H`), segment (`S`), and link (`L`) lines are required. `P` lines are used in `gfatk path --all <GFA>`. | ||
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| ``` | ||
| H VN:Z:1.0 | ||
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| <!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="A module where all the methods of GFA manipulations are defined."><meta name="keywords" content="rust, rustlang, rust-lang, gfa"><title>gfatk::gfa::gfa - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceSerif4-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../FiraSans-Regular.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../FiraSans-Medium.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceCodePro-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceSerif4-Bold.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceCodePro-Semibold.ttf.woff2"><link rel="stylesheet" href="../../../normalize.css"><link rel="stylesheet" href="../../../rustdoc.css" id="mainThemeStyle"><link rel="stylesheet" href="../../../ayu.css" disabled><link rel="stylesheet" href="../../../dark.css" disabled><link rel="stylesheet" href="../../../light.css" id="themeStyle"><script id="default-settings" ></script><script src="../../../storage.js"></script><script defer src="../../../main.js"></script><noscript><link rel="stylesheet" href="../../../noscript.css"></noscript><link rel="alternate icon" type="image/png" href="../../../favicon-16x16.png"><link rel="alternate icon" type="image/png" href="../../../favicon-32x32.png"><link rel="icon" type="image/svg+xml" href="../../../favicon.svg"></head><body class="rustdoc mod"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle">☰</button><a class="sidebar-logo" href="../../../gfatk/index.html"><div class="logo-container"><img class="rust-logo" src="../../../rust-logo.svg" alt="logo"></div></a><h2></h2></nav><nav class="sidebar"><a class="sidebar-logo" href="../../../gfatk/index.html"><div class="logo-container"><img class="rust-logo" src="../../../rust-logo.svg" alt="logo"></div></a><h2 class="location"><a href="#">Module gfa</a></h2><div class="sidebar-elems"><section><ul class="block"><li><a href="#structs">Structs</a></li></ul></section></div></nav><main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><input class="search-input" name="search" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" title="help" tabindex="-1"><a href="../../../help.html">?</a></div><div id="settings-menu" tabindex="-1"><a href="../../../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../../../wheel.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1 class="fqn">Module <a href="../../index.html">gfatk</a>::<wbr><a href="../index.html">gfa</a>::<wbr><a class="mod" href="#">gfa</a><button id="copy-path" onclick="copy_path(this)" title="Copy item path to clipboard"><img src="../../../clipboard.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="srclink" href="../../../src/gfatk/gfa/gfa.rs.html#1-647">source</a> · <a id="toggle-all-docs" href="javascript:void(0)" title="collapse all docs">[<span class="inner">−</span>]</a></span></div><details class="rustdoc-toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>A module where all the methods of GFA manipulations are defined.</p> | ||
| <!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1.0"><meta name="generator" content="rustdoc"><meta name="description" content="A module where all the methods of GFA manipulations are defined."><meta name="keywords" content="rust, rustlang, rust-lang, gfa"><title>gfatk::gfa::gfa - Rust</title><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceSerif4-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../FiraSans-Regular.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../FiraSans-Medium.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceCodePro-Regular.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceSerif4-Bold.ttf.woff2"><link rel="preload" as="font" type="font/woff2" crossorigin href="../../../SourceCodePro-Semibold.ttf.woff2"><link rel="stylesheet" href="../../../normalize.css"><link rel="stylesheet" href="../../../rustdoc.css" id="mainThemeStyle"><link rel="stylesheet" href="../../../ayu.css" disabled><link rel="stylesheet" href="../../../dark.css" disabled><link rel="stylesheet" href="../../../light.css" id="themeStyle"><script id="default-settings" ></script><script src="../../../storage.js"></script><script defer src="../../../main.js"></script><noscript><link rel="stylesheet" href="../../../noscript.css"></noscript><link rel="alternate icon" type="image/png" href="../../../favicon-16x16.png"><link rel="alternate icon" type="image/png" href="../../../favicon-32x32.png"><link rel="icon" type="image/svg+xml" href="../../../favicon.svg"></head><body class="rustdoc mod"><!--[if lte IE 11]><div class="warning">This old browser is unsupported and will most likely display funky things.</div><![endif]--><nav class="mobile-topbar"><button class="sidebar-menu-toggle">☰</button><a class="sidebar-logo" href="../../../gfatk/index.html"><div class="logo-container"><img class="rust-logo" src="../../../rust-logo.svg" alt="logo"></div></a><h2></h2></nav><nav class="sidebar"><a class="sidebar-logo" href="../../../gfatk/index.html"><div class="logo-container"><img class="rust-logo" src="../../../rust-logo.svg" alt="logo"></div></a><h2 class="location"><a href="#">Module gfa</a></h2><div class="sidebar-elems"><section><ul class="block"><li><a href="#structs">Structs</a></li></ul></section></div></nav><main><div class="width-limiter"><nav class="sub"><form class="search-form"><span></span><input class="search-input" name="search" autocomplete="off" spellcheck="false" placeholder="Click or press ‘S’ to search, ‘?’ for more options…" type="search"><div id="help-button" title="help" tabindex="-1"><a href="../../../help.html">?</a></div><div id="settings-menu" tabindex="-1"><a href="../../../settings.html" title="settings"><img width="22" height="22" alt="Change settings" src="../../../wheel.svg"></a></div></form></nav><section id="main-content" class="content"><div class="main-heading"><h1 class="fqn">Module <a href="../../index.html">gfatk</a>::<wbr><a href="../index.html">gfa</a>::<wbr><a class="mod" href="#">gfa</a><button id="copy-path" onclick="copy_path(this)" title="Copy item path to clipboard"><img src="../../../clipboard.svg" width="19" height="18" alt="Copy item path"></button></h1><span class="out-of-band"><a class="srclink" href="../../../src/gfatk/gfa/gfa.rs.html#1-646">source</a> · <a id="toggle-all-docs" href="javascript:void(0)" title="collapse all docs">[<span class="inner">−</span>]</a></span></div><details class="rustdoc-toggle top-doc" open><summary class="hideme"><span>Expand description</span></summary><div class="docblock"><p>A module where all the methods of GFA manipulations are defined.</p> | ||
| </div></details><h2 id="structs" class="small-section-header"><a href="#structs">Structs</a></h2><div class="item-table"><div class="item-row"><div class="item-left module-item"><a class="struct" href="struct.GFAtk.html" title="gfatk::gfa::gfa::GFAtk struct">GFAtk</a></div><div class="item-right docblock-short">A wrapper around GFA from the gfa crate | ||
| TODO: make GFAtk generic for any segment name, not just usize.</div></div><div class="item-row"><div class="item-left module-item"><a class="struct" href="struct.Overlap.html" title="gfatk::gfa::gfa::Overlap struct">Overlap</a></div><div class="item-right docblock-short">Overlap from one segment to another.</div></div><div class="item-row"><div class="item-left module-item"><a class="struct" href="struct.Overlaps.html" title="gfatk::gfa::gfa::Overlaps struct">Overlaps</a></div><div class="item-right docblock-short">A vector of <code>Overlap</code> structs.</div></div></div></section></div></main><div id="rustdoc-vars" data-root-path="../../../" data-current-crate="gfatk" data-themes="ayu,dark,light" data-resource-suffix="" data-rustdoc-version="1.66.0 (69f9c33d7 2022-12-12)" ></div></body></html> |
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