Convert org mode README to markdown

README.md

@@ -1,68 +1,75 @@
 # locigenesis
 
-locigenesis is a tool that generates a human T-cell receptor (TCR), runs
+locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
-it through a sequence reader simulation tool and extracts CDR3.
 
-The goal of this project is to generate both HVR sequences with and
+The goal of this project is to generate both HVR sequences with and without sequencing errors, in order to create datasets for a Machine Learning algorithm.
-without sequencing errors, in order to create datasets for a Machine
+
-Learning algorithm.
+
+<a id="orgb4db211"></a>
 
 ## Technologies
 
--   [immuneSIM](https://github.com/GreiffLab/immuneSIM/): in silico
+-   [immuneSIM](https://github.com/GreiffLab/immuneSIM/): in silico generation of human and mouse BCR and TCR repertoires
-    generation of human and mouse BCR and TCR repertoires
+-   [CuReSim](http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/): read simulator that mimics Ion Torrent sequencing
--   [CuReSim](http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/):
+
-    read simulator that mimics Ion Torrent sequencing
+
+<a id="orgace1e30"></a>
 
 ## Installation
 
-This project uses [Nix](https://nixos.org/) to ensure reproducible
+This project uses [Nix](https://nixos.org/) to ensure reproducible builds.
-builds.
 
-1.  Install Nix (compatible with MacOS, Linux and
+1.  Install Nix (compatible with MacOS, Linux and [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
-    [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
 
-```bash
     curl -L https://nixos.org/nix/install | sh
-```
 
-2.  Clone the repository:
+1.  Clone the repository:
 
-```bash
     git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
-```
 
-3.  Change the working directory to the project:
+1.  Change the working directory to the project:
 
-```bash
     cd locigenesis
-```
 
-4.  Enter the nix-shell:
+1.  Enter the nix-shell:
 
-```bash
     nix-shell
-```
 
-After running these commands, you will find yourself in a shell that
+After running these commands, you will find yourself in a shell that contains all the needed dependencies.
-contains all the needed dependencies.
+
+
+<a id="org531bad5"></a>
 
 ## Usage
 
-An execution script that accepts 2 parameters is provided, the following
+An execution script that accepts 2 parameters is provided, the following command invokes it:
-command invokes it:
 
-```bash
     ./generation.sh <number of sequences> <number of reads>
-```
 
--   \<number of sequences\>: an integer that specifies the number of
+-   <number of sequences>: an integer that specifies the number of different sequences to generate
-    different sequences to generate
+-   <number of reads>: an integer that specifies the number of reads to perform on each sequence
--   \<number of reads\>: an integer that specifies the number of reads
-    to perform on each sequence
 
 The script will generate 2 files under the data directory:
 
-|HVR.fastq  | curesim-HVR.fastq |
+<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
-|:----:|:-----:|
+
-|Contains the original CDR3 sequence|Contains CDR3 after the read simulation, with sequencing errors |
+
+<colgroup>
+<col  class="org-left" />
+
+<col  class="org-left" />
+</colgroup>
+<tbody>
+<tr>
+<td class="org-left">HVR.fastq</td>
+<td class="org-left">Contains the original CDR3 sequence</td>
+</tr>
+
+
+<tr>
+<td class="org-left">CuReSim-HVR.fastq</td>
+<td class="org-left">Contains CDR3 after the read simulation, with sequencing errors</td>
+</tr>
+</tbody>
+</table>
+

src/alignment.r

@@ -34,11 +34,7 @@ parse_metadata <- function(metadata) {
 #' @return A \code{character} containing the gene sequence
 match_id_sequence <- function(names, vdj_segments, id) {
   matches <- grep(names, pattern = id)
-  if(id == "TRBJ2-2"){
-    row <- matches[2]
-  } else {
   row <- matches[1]
-  }
   return(as.character(vdj_segments[row]))
 }
 
@@ -110,9 +106,8 @@ get_cys_coordinates <- function(alignment) {
   insertion <- unlist(Biostrings::insertion(alignment))
   deletion <- unlist(Biostrings::deletion(alignment))
   delta_coordinates <- handle_indels(insertion, deletion, cys, alignment)
-  read_start <- unlist(start(Biostrings::Views(alignment)))
+  cys_start <- cys$start + delta_coordinates$start
-  cys_start <- cys$start + delta_coordinates$start + read_start - 1
+  cys_end <- cys$end + delta_coordinates$end
-  cys_end <- cys$end + delta_coordinates$end + read_start
   return(list("start" = cys_start, "end" = cys_end))
 }
 
@@ -131,7 +126,7 @@ get_hvr_sequences <- function(sequences, vdj_segments, cores = detectCores()) {
   )
   cys_coordinates <- parallel::mclapply(v_alignment, FUN = get_cys_coordinates)
   cys_df <- as.data.frame(do.call(rbind, cys_coordinates))
-  remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end) + 1)
+  remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end))
   j_alignment <- parallel::mcmapply(remaining,
     df$j_seq,
     FUN = align_sequence,
@@ -150,4 +145,4 @@ get_hvr_sequences <- function(sequences, vdj_segments, cores = detectCores()) {
 
 data <- parse_data(file = "data/curesim_sequence.fastq")
 hvr <- get_hvr_sequences(sequences = data[[1]], vdj_segments = data[[2]])
-Biostrings::writeXStringSet(hvr, "data/curesim-HVR.fastq", format = "fastq")
+Biostrings::writeXStringSet(hvr, "data/CuReSim-HVR.fastq", format = "fastq")