way: Unsuccessful floatlefttextright

report.md

@@ -13,14 +13,14 @@ Duplicate genes offers a pool of genetic material available for further experime
 
 ## Gene duplication mechanisms
 
-![img](./figures/lallemand2020-fig1_copy.svg)
+![img](./figures/lallemand2020-fig1_copy.svg "Different types of duplication. (A) Whole genome duplication. (B) An unequal crossing-over leads to a duplication of a fragment of a chromosome. (C) In tandem duplication, two (set of) genes are duplicated one after the other. (D) Retrotransposon enables retroduplication: a RNA transcript is reverse transcribed and inserted back without introns and with a polyA tail in the genome. (E) A DNA transposon can acquire a fragment of a gene. (F) Segmental duplication corresponds to long stretches of duplicated sequences with high identity. Adapted from (<a href="#citeproc_bib_item_14">Lallemand et al. 2020</a>) (fig. 1).")
 
 Multiple mechanisms may lead to gene duplication. The following sections review them.
 
 
 ### Polyploidisation and whole genome duplication
 
-In an event of WGD, the entire set of genes present on the chromosomes is duplicated (figure <ref:fig:gene-duplication-mechanisms> (A)).
+In an event of WGD, the entire set of genes present on the chromosomes is duplicated (<cref:fig:gene-duplication-mechanisms> (A)).
 WGD is more frequent in plants.
 A striking example is probably the *Triticum* genus (wheat) in which some species (such as *T. aestivum*) are hexaploid, due to hybridisation events (<a href="#citeproc_bib_item_11">Golovnina et al. 2007</a>).
 
@@ -34,7 +34,7 @@ WGD can occur thanks to polyspermy or in case of a non-reduced gamete.
 
 ### Unequal crossing-over
 
-A crossing-over may occur during cell division. Two chromatids may exchange a fragment of chromosome. If the cleavage of the two chromatids occurs at different positions, the shared fragments may have different lengths. Homologous recombination of such uneven crossover results in the incorporation of a duplicate region, as represented in figure <ref:fig:gene-duplication-mechanisms> (B, C).
+A crossing-over may occur during cell division. Two chromatids may exchange a fragment of chromosome. If the cleavage of the two chromatids occurs at different positions, the shared fragments may have different lengths. Homologous recombination of such uneven crossover results in the incorporation of a duplicate region, as represented in <cref:fig:gene-duplication-mechanisms> (B, C).
 This mechanism leads to the duplication of the whole set of genes present in the inserted fragment. These duplicate genes locate one set after the other, and are thus called TAG.
 
 
@@ -43,19 +43,19 @@ This mechanism leads to the duplication of the whole set of genes present in the
 Retrotransposons, or RNA transposons are one type of transposable elements. Retrotransposons share similar structure and mechanism with retroviruses.
 They may replicate in the genome through a mechanism known as &ldquo;copy-and-paste&rdquo;.
 These transposons typically contain a reverse transcriptase gene. This enzyme may proceed in the reverse transcription of an mRNA transcript into DNA sequence which can then be inserted elsewhere in the genome.
-More generally, retroduplication refers to the duplication of a region of a chromosome through reverse transcription of a RNA transcript. In this case the duplicate gene lost its intronic sequences and brings a polyA tail with it (figure <ref:fig:gene-duplication-mechanisms> (D)).
+More generally, retroduplication refers to the duplication of a region of a chromosome through reverse transcription of a RNA transcript. In this case the duplicate gene lost its intronic sequences and brings a polyA tail with it ( <cref:fig:gene-duplication-mechanisms> (D)).
 
 
 ### Transduplication
 
 DNA transposons are another type of transposable elements whose transposition mechanism can also lead to gene duplication.
 This type of transposable element moves in the genome through a mechanisms known as &ldquo;cut-and-paste&rdquo;.
-A typical DNA transposon contains a transposase gene. This enzyme recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage and excision of the transposon. The transposase can then insert the transposon in a new genome locus. A transposon can bring a fragment of a gene during its transposition in the other locus (figure <ref:fig:gene-duplication-mechanisms> (E)).
+A typical DNA transposon contains a transposase gene. This enzyme recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage and excision of the transposon. The transposase can then insert the transposon in a new genome locus. A transposon can bring a fragment of a gene during its transposition in the other locus (<cref:fig:gene-duplication-mechanisms> (E)).
 
 
 ### Segment duplication
 
-Segment duplications, also called low copy repeats are long stretches of DNA with high identity score (figure <ref:fig:gene-duplication-mechanisms> (E)). Their exact duplication mechanisms remains unclear (<a href="#citeproc_bib_item_14">Lallemand et al. 2020</a>), they may results from an accidental replication, distinct from an uneven cross-over or a double stranded breakage.
+Segment duplications, also called low copy repeats are long stretches of DNA with high identity score (<cref:fig:gene-duplication-mechanisms> (E)). Their exact duplication mechanisms remains unclear (<a href="#citeproc_bib_item_14">Lallemand et al. 2020</a>), they may results from an accidental replication, distinct from an uneven cross-over or a double stranded breakage.
 Nevertheless, transposable elements may well be involved as a high enrichment of transposable elements has been found at segment extremities, in *Drosophila* (<a href="#citeproc_bib_item_14">Lallemand et al. 2020</a>).
 
 

report.org

@@ -2,6 +2,7 @@
 #+author: Samuel Ortion
 #+date: 2023-2024
 #+LATEX_CLASS: scientific-project
+#+LATEX_CLASS_OPTIONS: [twoside=false]
 #+LATEX_HEADER: \usepackage{sty/lamme2024}
 
 #+bibliography: references.bib
@@ -22,6 +23,7 @@
 \makeatletter
 \hypersetup{
 	pdfkeywords={duplicate genes, tandemly arrayed genes, pipeline},
+        pdfauthor={Samuel Ortion},
 }
 \makeatother
 #+end_export
@@ -39,7 +41,7 @@
 [[printglossaries:]]
 
 #+begin_export latex
-%\afterpage{\flblankpage}
+%\flstart
 #+end_export
 
 * Scientific context
@@ -48,6 +50,9 @@ Duplicate genes offers a pool of genetic material available for further experime
 
 ** Gene duplication mechanisms
 
+#+begin_export latex
+%\begin{addfigure}
+#+end_export
 #+name: fig:gene-duplication-mechanisms
 #+begin_src emacs-lisp :exports results :results value raw
 (setq caption "#+caption[Different types of duplication]: Different types of duplication. (A) Whole genome duplication. (B) An unequal crossing-over leads to a duplication of a fragment of a chromosome. (C) In tandem duplication, two (set of) genes are duplicated one after the other. (D) Retrotransposon enables retroduplication: a RNA transcript is reverse transcribed and inserted back without introns and with a polyA tail in the genome. (E) A DNA transposon can acquire a fragment of a gene. (F) Segmental duplication corresponds to long stretches of duplicated sequences with high identity. Adapted from [cite:@lallemandOverviewDuplicatedGene2020] (fig. 1).
@@ -60,6 +65,10 @@ Duplicate genes offers a pool of genetic material available for further experime
  (t "[[file:./figures/lallemand2020-fig1_copy.svg]]")))
 (concat caption file)
 #+end_src
+#+begin_export latex
+%\end{addfigure}
+#+end_export
+
 
 # https://stackoverflow.com/questions/13611837/how-can-i-use-different-image-formats-for-different-exports-in-org-mode
 
@@ -85,9 +94,9 @@ More generally, retroduplication refers to the duplication of a region of a chro
 *** Transduplication
 DNA transposons are another type of transposable elements whose transposition mechanism can also lead to gene duplication.
 This type of transposable element moves in the genome through a mechanisms known as "cut-and-paste".
-A typical DNA transposon contains a transposase gene. This enzyme recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage and excision of the transposon. The transposase can then insert the transposon in a new genome locus. A transposon can bring a fragment of a gene during its transposition in the other locus ( cref:fig:gene-duplication-mechanisms (E)).
+A typical DNA transposon contains a transposase gene. This enzyme recognize two sites surrounding the donnor transposon sequence in the chromosome resulting in a DNA cleavage and excision of the transposon. The transposase can then insert the transposon in a new genome locus. A transposon can bring a fragment of a gene during its transposition in the other locus (cref:fig:gene-duplication-mechanisms (E)).
 *** Segment duplication
-Segment duplications, also called low copy repeats are long stretches of DNA with high identity score ( [[cref:fig:gene-duplication-mechanisms]] (E)). Their exact duplication mechanisms remains unclear [cite:@lallemandOverviewDuplicatedGene2020], they may results from an accidental replication, distinct from an uneven cross-over or a double stranded breakage.
+Segment duplications, also called low copy repeats are long stretches of DNA with high identity score ([[cref:fig:gene-duplication-mechanisms]] (E)). Their exact duplication mechanisms remains unclear [cite:@lallemandOverviewDuplicatedGene2020], they may results from an accidental replication, distinct from an uneven cross-over or a double stranded breakage.
 Nevertheless, transposable elements may well be involved as a high enrichment of transposable elements has been found at segment extremities, in /Drosophila/ [cite:@lallemandOverviewDuplicatedGene2020].
 ** Fate of duplicate genes in genome evolution
 In his book /Evolution by Gene Duplication/, Susumu [[latex:textsc][Ohno]] proposed that gene duplication plays a major role in species evolution [cite:@ohnoEvolutionGeneDuplication1970], as it provides a new genetic material to build on new phenotypes while keeping a backup gene for the previous function.
@@ -141,6 +150,10 @@ Another objective of my internship will be to port FTAG Finder on a workflow man
 We will have to make a choice for the tool we will use.
 The two main options are Snakemake and Nextflow. Snakemake is a python powered workflow manager based on rules /à la/ GNU Make [cite:@kosterSnakemakeScalableBioinformatics2012]. Nextflow, is a groovy powered workflow manager, which rely on data flows [cite:@ditommasoNextflowEnablesReproducible2017]. Both are widely used in the bioinformatics community, and their use have been on the rise since they came out in 2012 and 2013 respectively [cite:@djaffardjyDevelopingReusingBioinformatics2023].
 
+#+begin_export latex
+%\flstop
+#+end_export
+
 #+begin_export html
 <h3>Bibliography</h3>
 #+end_export

sty/floatlefttextright.sty

@@ -1,26 +1,34 @@
 % https://www.developpez.net/forums/d910711/autres-langages/autres-langages/latex/mise-forme/texte-recto-figures-verso/
-% Solution by Martigan on Developpez.net
+% Solution by Martigan on Developpez.net, adapted
 
-\iffalse
 \RequirePackage{afterpage}
 \RequirePackage{caption}
-\newcommand\@addfig{\relax}
+\RequirePackage{etoolbox}
-\newcommand\addfig[1]{\global\long\def\@addfig{#1}}
+\RequirePackage{environ}
-\newcommand\@putfig{\@addfig\addfig{\relax}}
+\newbool{flcontinue}
+\newcommand{\flstart}{
+  \booltrue{flcontinue}
+  \afterpage{\flblankpage}
+}
+
+\newcommand{\flstop}{
+  \boolfalse{flcontinue}
+}
+\newcommand\@fladdfig{\relax}
+\newcommand\fladdfig[1]{\global\long\def\@fladdfig{#1}}
+\newcommand\@flputfig{\@fladdfig\fladdfig{\relax}}
 \newcommand\flblankpage{%
 	\null
 	\vfill
-	\begin{figure}[H]
+	  \@flputfig%
-	\captionsetup{type=figure} % Warning: this could be faulty if tables are required
-	\@putfig%
-	\end{figure}
 	\vfill
-	\thispagestyle{empty}%
+	%\thispagestyle{empty}%
 	\clearpage%
-	%\addtocounter{page}{-1}
+	% \addtocounter{page}{-1}
-	\afterpage{\flblankpage}
+	\ifbool{flcontinue}{
-  }
+		\afterpage{\flblankpage}
-  \fi
+	 }
+ }
 
 \iffalse
 	% Example
@@ -28,16 +36,17 @@
 	% Add this at the beggining of the document:
 	\afterpage{\flblankpage}
 
-	\addfig{%
+	\fladdfig{%
 		\centering
 		\includegraphics[scale=1]{Image1}
 		\caption{Test}
 		\label{Ima1}
 	}
 \fi
-\def\@floatplacement{\global\@topnum\c@topnumber
+
-   \global\@toproom \topfraction\@colht
+% Wrap figure environment
-   \global\@botnum  \c@bottomnumber
+\NewEnviron{addfigure}{%
-   \global\@botroom \bottomfraction\@colht
+ % \fladdfig{%
-   \global\@colnum  \ifodd\c@page\c@totalnumber\else\z@\fi%<<<<<<<
+    \BODY%
-   \@fpmin   \floatpagefraction\@colht}
+  %}%
+}

sty/lamme2024.sty

@@ -1,13 +1,11 @@
 
-\usepackage{scrhack}
 
 % Font
 \usepackage{fontspec}
 \setmainfont{TeX Gyre Termes} % Times New Roman alternative
-\usepackage{setspace}
+\usepackage[onehalfspacing]{setspace} % 1.5 interline spacing
-\onehalfspacing % 1.5 interline spacing
 \defaultfontfeatures[\rmfamily,\sffamily]{Ligatures=TeX}
-
+\setkomafont{disposition}{\bfseries}
 
 % Float
 \RequirePackage{graphicx}
@@ -33,24 +31,24 @@
 	backend=biber,
 	citestyle=authoryear-comp,
 	natbib=true
-	]{biblatex}
+]{biblatex}
 
 \RequirePackage{doi}
 \RequirePackage{xurl}
 % \AtEveryBibitem{\clearfield{number}}
 \DeclareSortingNamekeyScheme{
-  \keypart{
+	\keypart{
-    \namepart{given}
+		\namepart{given}
-  }
+	}
-  \keypart{
+	\keypart{
-    \namepart{prefix}
+		\namepart{prefix}
-  }
+	}
-  \keypart{
+	\keypart{
-    \namepart{family}
+		\namepart{family}
-  }
+	}
-  \keypart{
+	\keypart{
-    \namepart{suffix}
+		\namepart{suffix}
-  }
+	}
 }
 
 \RequirePackage{orcidlink}
@@ -72,44 +70,31 @@
 	nomain,                % don't create "main" glossary
 	stylemods=longbooktabs, % do the adjustments for the longbooktabs styles,
 	automake
-  ]{glossaries-extra}
+]{glossaries-extra}
 \setabbreviationstyle[acronym]{long-short}
 
 \usepackage{hyperref}
 
-% Force text on right side, float on left side
+% Force text on right side, float on left side (does not work well)
-\usepackage{sty/floatlefttextright}
+%\usepackage{sty/floatlefttextright}
 
 \renewcommand\maketitle{\include{titlepage}}
 
-% Abstract
-\providecommand{\myabstractname}{Abstract} % not in scrbook class
-\newenvironment{myabstract}[1]{%
-  \hrule
-  \vspace{0.25cm}
-\small\textbf{\myabstractname: }
-%\small\emph #1     %  emph takes an argument
-\small\emph{#1} % or \small\textit{#1}
-\itshape % use this if you want the text to be in italics
-}{%
-\newline\hrule
-\vspace{0.6cm}
-}
-
 \hypersetup{
-  hidelinks
+	hidelinks
 }
 
 \renewcommand*{\mkbibnamefamily}[1]{\textsc{#1}}
 \renewcommand*{\mkbibnameprefix}[1]{\textsc{#1}}
 
 % Ensure summary is on even page
-
 \newcommand*\cleartoleftpage{
-\clearpage\ifodd\c@page
+	\clearpage\ifodd\c@page
-\hbox{}
+		\hbox{}
-\vspace*{\fill}
+		\vspace*{\fill}
-\thispagestyle{empty}
+		\thispagestyle{empty}
-\newpage
+		\newpage
-\fi
+	\fi
-}
+  }
+
+\usepackage{scrhack}