\documentclass[10pt,a4paper]{article} % Packages \usepackage{fancyhdr} % For header and footer \usepackage{multicol} % Allows multicols in tables \usepackage{tabularx} % Intelligent column widths \usepackage{tabulary} % Used in header and footer \usepackage{hhline} % Border under tables \usepackage{graphicx} % For images \usepackage{xcolor} % For hex colours %\usepackage[utf8x]{inputenc} % For unicode character support \usepackage[T1]{fontenc} % Without this we get weird character replacements \usepackage{colortbl} % For coloured tables \usepackage{setspace} % For line height \usepackage{lastpage} % Needed for total page number \usepackage{seqsplit} % Splits long words. %\usepackage{opensans} % Can't make this work so far. Shame. Would be lovely. \usepackage[normalem]{ulem} % For underlining links % Most of the following are not required for the majority % of cheat sheets but are needed for some symbol support. \usepackage{amsmath} % Symbols \usepackage{MnSymbol} % Symbols \usepackage{wasysym} % Symbols %\usepackage[english,german,french,spanish,italian]{babel} % Languages % Document Info \author{Stephan Fuchs (fuchs)} \pdfinfo{ /Title (covsonar-2.pdf) /Creator (Cheatography) /Author (Stephan Fuchs (fuchs)) /Subject (covSonar 2 Cheat Sheet) } % Lengths and widths \addtolength{\textwidth}{6cm} \addtolength{\textheight}{-1cm} \addtolength{\hoffset}{-3cm} \addtolength{\voffset}{-2cm} \setlength{\tabcolsep}{0.2cm} % Space between columns \setlength{\headsep}{-12pt} % Reduce space between header and content \setlength{\headheight}{85pt} % If less, LaTeX automatically increases it \renewcommand{\footrulewidth}{0pt} % Remove footer line \renewcommand{\headrulewidth}{0pt} % Remove header line \renewcommand{\seqinsert}{\ifmmode\allowbreak\else\-\fi} % Hyphens in seqsplit % This two commands together give roughly % the right line height in the tables \renewcommand{\arraystretch}{1.3} \onehalfspacing % Commands \newcommand{\SetRowColor}[1]{\noalign{\gdef\RowColorName{#1}}\rowcolor{\RowColorName}} % Shortcut for row colour \newcommand{\mymulticolumn}[3]{\multicolumn{#1}{>{\columncolor{\RowColorName}}#2}{#3}} % For coloured multi-cols \newcolumntype{x}[1]{>{\raggedright}p{#1}} % New column types for ragged-right paragraph columns \newcommand{\tn}{\tabularnewline} % Required as custom column type in use % Font and Colours \definecolor{HeadBackground}{HTML}{333333} \definecolor{FootBackground}{HTML}{666666} \definecolor{TextColor}{HTML}{333333} \definecolor{DarkBackground}{HTML}{C10443} \definecolor{LightBackground}{HTML}{FBEFF3} \renewcommand{\familydefault}{\sfdefault} \color{TextColor} % Header and Footer \pagestyle{fancy} \fancyhead{} % Set header to blank \fancyfoot{} % Set footer to blank \fancyhead[L]{ \noindent \begin{multicols}{3} \begin{tabulary}{5.8cm}{C} \SetRowColor{DarkBackground} \vspace{-7pt} {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}} } \end{tabulary} \columnbreak \begin{tabulary}{11cm}{L} \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{covSonar 2 Cheat Sheet}}}} \\ \normalsize{by \textcolor{DarkBackground}{Stephan Fuchs (fuchs)} via \textcolor{DarkBackground}{\uline{cheatography.com/135742/cs/28190/}}} \end{tabulary} \end{multicols}} \fancyfoot[L]{ \footnotesize \noindent \begin{multicols}{3} \begin{tabulary}{5.8cm}{LL} \SetRowColor{FootBackground} \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}} \\ \vspace{-2pt}Stephan Fuchs (fuchs) \\ \uline{cheatography.com/fuchs} \\ \end{tabulary} \vfill \columnbreak \begin{tabulary}{5.8cm}{L} \SetRowColor{FootBackground} \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}} \\ \vspace{-2pt}Published 14th February, 2023.\\ Updated 15th February, 2023.\\ Page {\thepage} of \pageref{LastPage}. \end{tabulary} \vfill \columnbreak \begin{tabulary}{5.8cm}{L} \SetRowColor{FootBackground} \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}} \\ \SetRowColor{white} \vspace{-5pt} %\includegraphics[width=48px,height=48px]{dave.jpeg} Measure your website readability!\\ www.readability-score.com \end{tabulary} \end{multicols}} \begin{document} \raggedright \raggedcolumns % Set font size to small. Switch to any value % from this page to resize cheat sheet text: % www.emerson.emory.edu/services/latex/latex_169.html \footnotesize % Small font. \begin{multicols*}{3} \begin{tabularx}{5.377cm}{x{2.43873 cm} x{2.53827 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Database Setup}} \tn % Row 0 \SetRowColor{LightBackground} \mymulticolumn{2}{x{5.377cm}}{{\bf{sonar setup}}} \tn % Row Count 1 (+ 1) % Row 1 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify the name of the new database \tn % Row Count 3 (+ 2) % Row 2 \SetRowColor{LightBackground} \{\{ar\}\}-{}-gbk {\emph{FILE}} & set a custom reference based on the specified Genbank file {\emph{{[}opt.{]}}} \tn % Row Count 7 (+ 4) % Row 3 \SetRowColor{white} \{\{ar\}\}-a\{\{nl\}\}\{\{nobreak\}\}-{}-auto-create & add pre-defined sample properties to the new database {\emph{{[}opt.{]}}} \tn % Row Count 11 (+ 4) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{x{1.89126 cm} x{3.08574 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Show Infos}} \tn % Row 0 \SetRowColor{LightBackground} \mymulticolumn{2}{x{5.377cm}}{\{\{nobreak\}\}{\bf{sonar info}}} \tn % Row Count 1 (+ 1) % Row 1 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 3 (+ 2) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Sample Management}} \tn % Row 0 \SetRowColor{LightBackground} \{\{nobreak\}\}{\bf{sonar import}} & {\emph{to import data}} \tn % Row Count 2 (+ 2) % Row 1 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 4 (+ 2) % Row 2 \SetRowColor{LightBackground} \{\{ar\}\}\{\{nobreak\}\}-{}-fasta {\emph{FILE {[}FILE, ...{]}}} & specify fasta file to import sequences {[}opt{]} \tn % Row Count 7 (+ 3) % Row 3 \SetRowColor{white} \{\{ar\}\}-{}-tsv {\emph{FILE {[}FILE, ...{]}}} & specify tab-delimited text file to import meta information {[}opt{]} \tn % Row Count 11 (+ 4) % Row 4 \SetRowColor{LightBackground} \{\{ar\}\}-{}-cols {\emph{STR {[}STR, ...{]}}} & link properties with tsv columns in the form of\{\{nl\}\}{\emph{prop\_name=col\_header}} {[}opt{]} \tn % Row Count 16 (+ 5) % Row 5 \SetRowColor{white} \{\{ar\}\}-{}-no-autodetect & do not auto-link properties with tsv columns based on identical names {[}opt{]} \tn % Row Count 20 (+ 4) % Row 6 \SetRowColor{LightBackground} \{\{ar\}\}-{}-no-update & skip data of existing samples {[}opt{]} \tn % Row Count 22 (+ 2) % Row 7 \SetRowColor{white} \{\{ar\}\}-{}-cache {\emph{DIR}} & specify a folder to cache import data {[}opt{]} \tn % Row Count 25 (+ 3) % Row 8 \SetRowColor{LightBackground} \{\{ar\}\}-t {\emph{INT}}\{\{nl\}\}-{}-threads {\emph{INT}} & specify number of threads / cpus to use {[}opt{]} \tn % Row Count 28 (+ 3) % Row 9 \SetRowColor{white} \{\{nobreak\}\}{\bf{sonar delete}} & {\emph{to delete sample(s)}} \tn % Row Count 30 (+ 2) \end{tabularx} \par\addvspace{1.3em} \vfill \columnbreak \begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Sample Management (cont)}} \tn % Row 10 \SetRowColor{LightBackground} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 2 (+ 2) % Row 11 \SetRowColor{white} \{\{ar\}\}\{\{nobreak\}\}-{}-sample {\emph{STR {[}STR, ...{]}}} & specify names of samples to delete {[}opt{]} \tn % Row Count 5 (+ 3) % Row 12 \SetRowColor{LightBackground} \{\{ar\}\}\{\{nobreak\}\}-{}-sample-file {\emph{FILE}} & specify file containing names of samples to delete {[}opt{]} \tn % Row Count 8 (+ 3) % Row 13 \SetRowColor{white} \{\{ar\}\}-{}-force {\emph{FILE}} & force deletion and skip user confirmation {[}opt{]} \tn % Row Count 11 (+ 3) % Row 14 \SetRowColor{LightBackground} \{\{nobreak\}\}{\bf{sonar optimize}} & \}{\emph{to clean database}} \tn % Row Count 13 (+ 2) % Row 15 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 15 (+ 2) % Row 16 \SetRowColor{LightBackground} \{\{nobreak\}\}{\bf{sonar db-upgrade}} & upgrade database to the latest version \tn % Row Count 17 (+ 2) % Row 17 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 19 (+ 2) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{x{2.18988 cm} x{2.78712 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Property Management}} \tn % Row 0 \SetRowColor{LightBackground} \{\{nobreak\}\}{\bf{sonar list-prop}} & {\emph{to list available properties}} \tn % Row Count 2 (+ 2) % Row 1 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 4 (+ 2) % Row 2 \SetRowColor{LightBackground} \{\{nobreak\}\}{\bf{sonar add-prop}} & add new property \tn % Row Count 6 (+ 2) % Row 3 \SetRowColor{white} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 8 (+ 2) % Row 4 \SetRowColor{LightBackground} \{\{ar\}\}-{}-name {\emph{STR}} & specify new property name matching to {[}A-Z{]}{[}A-Z0-9\_{]}+ \tn % Row Count 11 (+ 3) % Row 5 \SetRowColor{white} \{\{ar\}\}-{}-descr {\emph{STR}} & provide a short property description \tn % Row Count 13 (+ 2) % Row 6 \SetRowColor{LightBackground} \{\{ar\}\}-{}-dtype {\emph{STR}} & specify data type \tn % Row Count 15 (+ 2) % Row 7 \SetRowColor{white} \{\{ar\}\}-{}-qtype {\emph{STR}} & specify query type {[}opt{]} \tn % Row Count 17 (+ 2) % Row 8 \SetRowColor{LightBackground} \{\{ar\}\}-{}-default & specify default value {[}opt{]} \tn % Row Count 19 (+ 2) % Row 9 \SetRowColor{white} \{\{nobreak\}\}{\bf{sonar delete-prop}} & delete property \tn % Row Count 21 (+ 2) % Row 10 \SetRowColor{LightBackground} \{\{ar\}\}-{}-db {\emph{FILE}} & specify name of the database \tn % Row Count 23 (+ 2) % Row 11 \SetRowColor{white} \{\{ar\}\}-{}-name {\emph{STR}} & specify new property name \tn % Row Count 25 (+ 2) % Row 12 \SetRowColor{LightBackground} \{\{ar\}\}-{}-force & force deletion without user confirmation {[}opt{]} \tn % Row Count 28 (+ 3) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Query Genomes}} \tn % Row 0 \SetRowColor{LightBackground} \mymulticolumn{2}{x{5.377cm}}{\{\{nobreak\}\}{\bf{sonar match}}} \tn % Row Count 1 (+ 1) % Row 1 \SetRowColor{white} \{\{nobreak\}\}\{\{ar\}\}-{}-sample {\emph{STR {[}STR, ...{]}}} & consider given samples only {[}opt{]} \tn % Row Count 4 (+ 3) % Row 2 \SetRowColor{LightBackground} \{\{ar\}\}-{}-sample-file *FILE & consider samples listed in the given file only {[}opt{]} \tn % Row Count 7 (+ 3) % Row 3 \SetRowColor{white} \{\{ar\}\}-{}-profile {\emph{STR {[}STR, ...{]}}} & match given mutation profile (use argument multiple times to define alternate profiles) {[}opt{]} \tn % Row Count 12 (+ 5) % Row 4 \SetRowColor{LightBackground} \{\{nobreak\}\}\{\{ar\}\}-{}-{\emph{PROP}} {\emph{VALUE {[}VALUE, ...{]}}} & filter based on sample property ({\emph{PROP}} has to be replaced by the actual property name) {[}opt{]} \tn % Row Count 17 (+ 5) % Row 5 \SetRowColor{white} \{\{ar\}\}-{}-with-sublineage {\emph{PROP}} & include pangolin sub-lineages for the given property {[}opt{]} \{\{nl\}\}\textasciicircum{}\{\{fa-info-circle\}\} Use {\emph{sonar update-lineage-info}} to update lineage info before\textasciicircum{} \tn % Row Count 25 (+ 8) % Row 6 \SetRowColor{LightBackground} \{\{ar\}\}-{}-showNX & show uninformative variant allels for genome profiles {[}opt{]} \tn % Row Count 28 (+ 3) % Row 7 \SetRowColor{white} \{\{ar\}\}-{}-out-cols {\emph{STR {[}STR, ...{]}}} & specify columns to show (for tsv and csv only) {[}opt{]} \tn % Row Count 31 (+ 3) \end{tabularx} \par\addvspace{1.3em} \vfill \columnbreak \begin{tabularx}{5.377cm}{x{2.4885 cm} x{2.4885 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Query Genomes (cont)}} \tn % Row 8 \SetRowColor{LightBackground} \{\{ar\}\}-{}-count & show number of matching genomes only {[}opt{]} \tn % Row Count 3 (+ 3) % Row 9 \SetRowColor{white} \{\{ar\}\}-{}-format {\emph{\{csv, tsv, vcf\}}} & specify the output format {[}opt{]} \tn % Row Count 5 (+ 2) % Row 10 \SetRowColor{LightBackground} \{\{ar\}\}-o {\emph{FILE}}\{\{nl\}\}-{}-out {\emph{FILE}} & write output to the given file {[}opt{]} \tn % Row Count 7 (+ 2) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{x{1.28156 cm} x{1.64772 cm} x{1.64772 cm} } \SetRowColor{DarkBackground} \mymulticolumn{3}{x{5.377cm}}{\bf\textcolor{white}{Mutation Notations}} \tn % Row 0 \SetRowColor{LightBackground} & {\bf{Genome level}} & {\bf{Protein level}} \tn % Row Count 2 (+ 2) % Row 1 \SetRowColor{white} \seqsplit{Substitution} & {\emph{REFposALT}}\{\{nl\}\}\textasciicircum{}e.g. A3451T\textasciicircum{} & {\emph{PROT}}:{\emph{REFposALT}}\{\{nl\}\}\textasciicircum{}e.g. A3451T\textasciicircum{} \tn % Row Count 5 (+ 3) % Row 2 \SetRowColor{LightBackground} Insertion & {\emph{REFposALT}}\{\{nl\}\}\textasciicircum{}e.g. A4057TGAT\textasciicircum{} & {\emph{PROT}}:{\emph{REFposALT}}\{\{nl\}\}\textasciicircum{}e.g. N:A34AK\textasciicircum{} \tn % Row Count 8 (+ 3) % Row 3 \SetRowColor{white} 1-bp Deletion & del:{\emph{pos}}\{\{nl\}\}\textasciicircum{}e.g. del:11288\textasciicircum{} & {\emph{PROT}}:del:{\emph{pos}}\{\{nl\}\}\textasciicircum{}e.g. ORF1ab:del:300\textasciicircum{} \tn % Row Count 12 (+ 4) % Row 4 \SetRowColor{LightBackground} multi-bp Deletion & del:{\emph{start}}-{\emph{end}}\{\{nl\}\}\textasciicircum{}e.g. del:112-115\textasciicircum{} & {\emph{PROT}}:del:{\emph{start}}-{\emph{end}}\{\{nl\}\}\textasciicircum{}e.g. S:del:68-69\textasciicircum{} \tn % Row Count 16 (+ 4) % Row 5 \SetRowColor{white} Deletion with fixed \seqsplit{coordinates} & del:={\emph{start}}-={\emph{end}}\{\{nl\}\}\textasciicircum{}e.g. del:=8-=11\textasciicircum{} & {\emph{PROT}}:del:={\emph{start}}-={\emph{end}}\{\{nl\}\}\textasciicircum{}e.g. S:del:=68-=69\textasciicircum{} \tn % Row Count 20 (+ 4) \hhline{>{\arrayrulecolor{DarkBackground}}---} \SetRowColor{LightBackground} \mymulticolumn{3}{x{5.377cm}}{\{\{fa-info-circle\}\} Any notation can be negated by a preceding caret (\textasciicircum{}), e.g. \textasciicircum{}A1345G only matches target genomes not carrying this SNP. \newline \{\{fa-exclamation-circle\}\} {\emph{REF}}: reference allele; {\emph{ALT}}: variant allele; {\emph{pos}}: reference position (1-based); {\emph{start}} and {\emph{end}}: start and end reference coordinates (1-based); {\emph{PROT}}: protein symbol} \tn \hhline{>{\arrayrulecolor{DarkBackground}}---} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{p{0.74655 cm} x{4.23045 cm} } \SetRowColor{DarkBackground} \mymulticolumn{2}{x{5.377cm}}{\bf\textcolor{white}{Data Types for Properties}} \tn % Row 0 \SetRowColor{LightBackground} \seqsplit{integer} & for storing integers \tn % Row Count 2 (+ 2) % Row 1 \SetRowColor{white} float & for storing decimal numbers \tn % Row Count 3 (+ 1) % Row 2 \SetRowColor{LightBackground} text & for storing strings \tn % Row Count 4 (+ 1) % Row 3 \SetRowColor{white} dates & for storing dates in the form YYYY-MM-DD \tn % Row Count 6 (+ 2) % Row 4 \SetRowColor{LightBackground} zip & for storing zip codes \tn % Row Count 7 (+ 1) \hhline{>{\arrayrulecolor{DarkBackground}}--} \end{tabularx} \par\addvspace{1.3em} \begin{tabularx}{5.377cm}{p{0.77809 cm} x{2.51735 cm} x{1.28156 cm} } \SetRowColor{DarkBackground} \mymulticolumn{3}{x{5.377cm}}{\bf\textcolor{white}{Operators for Data Types}} \tn % Row 0 \SetRowColor{LightBackground} {\bf{Operator}} & {\bf{Description}} & {\bf{Valid data type}} \tn % Row Count 2 (+ 2) % Row 1 \SetRowColor{white} \textgreater{} & larger than (e.g. \textgreater{}1) & integer, float, date \tn % Row Count 4 (+ 2) % Row 2 \SetRowColor{LightBackground} \textless{} & smaller than (e.g. \textless{}1) & integer, float, date \tn % Row Count 6 (+ 2) % Row 3 \SetRowColor{white} \textgreater{}= & larger than or equal to (e.g. \textgreater{}=1) & integer, float, date \tn % Row Count 8 (+ 2) % Row 4 \SetRowColor{LightBackground} \textless{}= & smaller than or equal to (e.g. \textless{}=1) & integer, float, date \tn % Row Count 10 (+ 2) % Row 5 \SetRowColor{white} != & different than (e.g. !=1) & integer, float, date \tn % Row Count 12 (+ 2) % Row 6 \SetRowColor{LightBackground} : & {\emph{from}}:{\emph{to}} range (e.g. \{\{nl\}\}2021-01-01:2021-12-31) & integer, float, date \tn % Row Count 15 (+ 3) % Row 7 \SetRowColor{white} \textasciicircum{} & not the same as (e.g. \textasciicircum{}B.1.1.7) & text \tn % Row Count 17 (+ 2) % Row 8 \SetRowColor{LightBackground} \% & wildcard standing for any character(s) (e.g. \%human\%) & text \tn % Row Count 20 (+ 3) \hhline{>{\arrayrulecolor{DarkBackground}}---} \SetRowColor{LightBackground} \mymulticolumn{3}{x{5.377cm}}{\{\{fa-warning\}\} Make sure that expressions with \textgreater{} or \textless{} are quoted to prevent misinterpretation by the shell} \tn \hhline{>{\arrayrulecolor{DarkBackground}}---} \end{tabularx} \par\addvspace{1.3em} % That's all folks \end{multicols*} \end{document}