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\documentclass[12pt]{scrartcl}
\usepackage{comment}
\usepackage{fancyhdr}
\usepackage{lastpage}
\usepackage{catchfile}
\pagestyle{fancy}
\CatchFileDef{\RGFAver}{version}{}
\usepackage{array}
\fancyhf{}
\renewcommand{\headrulewidth}{0pt}
\rhead{\bfseries RGFA \RGFAver Cheatsheet (\thepage/\pageref{LastPage})
\hspace{1.1cm}}
\lfoot{\tiny \ \ \ \ \ \ \ \ Copyright (c) 2016, Giorgio Gonnella, ZBH, University of
Hamburg, Germany. This document is under CC-BY-SA license.}
\newcounter{cstablecounter}
\setlength{\footskip}{0in}
\usepackage[top=1in, bottom=0.25in, left=0.1in, right=0.1in]{geometry}
\newcommand{\cstablestart}{
\begin{center}
% \large
% \textbf{RGFA: Cheatsheet
% (\refstepcounter{cstablecounter}\arabic{cstablecounter}/2)
% }\\
%\end{center}
%\vspace*{\fill}
%\begin{table}[h]
\centering
}
\setlength{\baselineskip}{0pt}
\setlength{\textfloatsep}{0pt plus 0pt minus 0pt}
\setlength{\intextsep}{0pt plus 0pt minus 0pt}
\setlength{\floatsep}{0pt plus 0pt minus 0pt}
\newcommand{\cstableend}{
\end{center}
%\end{table}
%\vspace*{\fill}
%\newpage
}
\begin{document}
\cstablestart
\begin{tabular}{|l|>{\ttfamily}l|}
\hline
Create graph & RGFA.new \\
\ldots from GFA file & RGFA.from\_file("filename")\\
\ldots from string & string.to\_rgfa \\
\ldots from string array (e.g.) & \verb/["H\tVN:i:1.0",/ \\
& \hspace{2.3mm}\verb/"S\tA\t*\tLN:i:1200"].to_rgfa/ \\
\hline
Write GFA to file & gfa.to\_file(filename) \\
Write GFA to standard output & puts gfa \\
Create deep copy & gfa.clone \\
Output statistics (normal/compact) & puts gfa.info; puts gfa.info(true) \\
\hline
Turn off validations & gfa.turn\_off\_validations \\
Validate line references & gfa.validate! \\
Enable progress logging & gfa.enable\_progress\_logging \\
\hline
Name of all segments & gfa.segment\_names \\
Name of all paths & gfa.path\_names \\
All segments, links, paths, etc & gfa.segments; gfa.links; gfa.paths; \ldots \\
Iterate over segments, links, etc & gfa.segments.each \verb/{|s|...}/ \\
\hline
Find segment & gfa.segment(segment\_name) \\
\ldots exception if does not exist & gfa.segment!(segment\_name) \\
\hline
Find path & gfa.path(path\_name) \textrm{(or: }path!\textrm{)} \\
All paths through segment & gfa.paths\_with(segment\_name) \\
\hline
Find link & gfa.link(\verb/[:S1,:E]/,\verb/[:S2,:B]/) \textrm{(or: }link!\textrm{)} \\
(or, if multiple may exist) & gfa.links\_between(\verb/[:S1,:E]/,\verb/[:S2,:B]/) \\
All links of segment end & gfa.links\_of(\verb/[:S1,:E]/) \\
(also segment instead of name) &
gfa.links\_of(\verb/[segment!(:S1),:E]/) \\
Target of all links & gfa.neighbours(\verb/[:S1,:E]/) \\
\hline
Find containment & gfa.containment(container,~contained)\\
& gfa.containment!(container,~contained)\\
(or, if multiple may exist) & gfa.containments\_between(c\_ner,~c\_ned)\\
All containments for a segment & gfa.containing(contained)\\
& gfa.contained\_in(container)\\
\hline
Add line (examples) & gfa << "H\verb/\t/VZ:i:1.0" \\
& gfa << "S\verb/\t/a\verb/\t/*\verb/\t/LN:i:1200" \\
Rename segment or path & gfa.rename(:old, :new) \\
\hline
Segment coverage & s.coverage\\
Segment coverage (more accurate) & s.coverage(unit\_length:~avreadlen)\\
Segment K-mer coverage & s.coverage(count\_tag:~:KC)\\
Segment length & s.length\\
Other end of a link & link.other\_end([s1,:E])\\
Other end of other end of link &
link.other\_end([s1,:E])\\
& \hspace{2.8cm}.revert\_end\_type\\
\hline
Read req.field/tag value & segment.from; segment.LN \\
\ldots raise if tag not available & segment.LN! \\
\ldots tag string & segment.field\_to\_s(:LN) \\
\hline
Set/create custom tag (ab, Z type) & segment.ab = "value" \\
\ldots of i or B/i type & s.ab = 12; \ \ \ s.ab = [1,2,3]\\
\ldots of f or B/f type & s.ab = 12.0; \ s.ab = [1.2,2.3,3.0] \\
\ldots of J type (hash/array) & s.ab = \{"a" => 12\}; s.ab = ["a","b",1] \\
\hline
\end{tabular}
\cstableend
\cstablestart
\begin{tabular}{|l|>{\ttfamily}l|}
\hline
Delete segment (and its links, etc) & gfa.rm("a") \\
Delete path & gfa.rm("path1") \\
Delete link/containment & gfa.rm(gfa.link(\ldots)) \\
Delete all headers & gfa.rm(:headers) \\
Delete sequences (set all to \texttt{*}) & gfa.rm(:sequences) \\
\hline
\textit{(rm with a method)} &\\
Delete links of segment end & gfa.rm(\verb/:links_of,[:S1,"E]/) \\
Delete link targets & gfa.rm(\verb/:neighbours,[:S1,"E]/) \\
Delete paths of segment & gfa.rm(\verb/:paths_with,:S1/) \\
Delete segments contained in s & gfa.rm(\verb/:contained_in,:s/) \\
Delete s1-E links except to s2-B & gfa.delete\_other\_links(\verb/[s1,:E],[s2,:B]/)\\
\hline
Access headers field & gfa.header.xx \\
Add new header field & gfa.header.add(:xx, 12)\\
\hline
Sum of read counts & \verb/gfa.segments.map(&:RC).inject(:+)/ \\
Highest coverage & \verb/gfa.segments.map(&:coverage).max/ \\
Delete low coverage segments & \verb/gfa.rm(gfa.segments.select {|s|/ \\
& \hspace{2.7cm}\verb/s.coverage < mincov })/ \\
Delete isolated segments & \verb/gfa.rm(gfa.segments.select {|s|/ \\
& \hspace{1cm}\verb/gfa.connectivity(s) == [0,0] })/ \\
\hline
Muliply segment & gfa.multiply("A", 4) \\
Detect linear paths & gfa.linear\_paths \\
Detect and merge linear paths & gfa.merge\_linear\_paths \\
Compute connected components & gfa.connected\_components \\
Component of a segment & gfa.segment\_connected\_component(s) \\
Split components & gfa.split\_connected\_components \\
Number of dead ends & gfa.n\_dead\_ends \\
\hline
\textit{(require "rgfatools")} & \\
Muliply segment, distribute links & gfa.multiply("A", 4) \\
Compute copy numbers & gfa.compute\_copy\_numbers \\
Apply copy numbers & gfa.apply\_copy\_numbers \\
Orient invertible segments & gfa.randomly\_orient\_invertibles \\
Enforce mandatory links & gfa.enforce\_mandatory\_links \\
Remove p-bubbles & gfa.remove\_p\_bubbles \\
Remove small components & gfa.remove\_small\_components(minlen) \\
\hline
\textit{(Command line tools)} & \\
Compare two GFA files & gfadiff 1.gfa 2.gfa \\
\ldots only segments and links & gfadiff -s -l 1.gfa 2.gfa \\
\ldots output as ruby script & gfadiff -script 1.gfa 2.gfa \\
Merge linear paths in graph & rgfa-mergelinear 2.gfa > 3.gfa \\
\hline
\textit{(Case studies CLI tools)} & \\
Simulate de Bruijn graph & rgfa-simdebruijn 27 gnm.fas > 1.gfa \\
\ldots and find CRISPRs candidates & rgfa-findcrisprs 1.gfa \\
\hline
\end{tabular}
\cstableend
\end{document}
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