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
-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
-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
-cd locigenesis
-```
 
-4.  Enter the nix-shell:
+1.  Enter the nix-shell:
 
-```bash
+    nix-shell
-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>
-./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>
+

flake.lock

@@ -1,41 +0,0 @@
-{
-  "nodes": {
-    "flake-utils": {
-      "locked": {
-        "lastModified": 1634851050,
-        "narHash": "sha256-N83GlSGPJJdcqhUxSCS/WwW5pksYf3VP1M13cDRTSVA=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "c91f3de5adaf1de973b797ef7485e441a65b8935",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "nixpkgs": {
-      "locked": {
-        "lastModified": 1635865339,
-        "narHash": "sha256-fmI8PxMmL7WXV/O8m6vT9/yW42buxvAYeRNpcABvnKs=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "26a56abd090ec5c8f4c6c9e1189fbfa4bcb8db3f",
-        "type": "github"
-      },
-      "original": {
-        "id": "nixpkgs",
-        "type": "indirect"
-      }
-    },
-    "root": {
-      "inputs": {
-        "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs"
-      }
-    }
-  },
-  "root": "root",
-  "version": 7
-}

flake.nix

@@ -1,13 +0,0 @@
-{
-  description = ''
-    locigenesis is a tool that generates a human T-cell receptor (TCR), runs
-    it through a sequence reader simulation tool and extracts CDR3.
-  '';
-
-  inputs.flake-utils.url = "github:numtide/flake-utils";
-
-  outputs = { self, nixpkgs, flake-utils }:
-    flake-utils.lib.eachDefaultSystem (system:
-      let pkgs = nixpkgs.legacyPackages.${system};
-      in { devShell = import ./shell.nix { inherit pkgs; }; });
-}

nix/sources.json

@@ -0,0 +1,26 @@
+{
+    "niv": {
+        "branch": "master",
+        "description": "Easy dependency management for Nix projects",
+        "homepage": "https://github.com/nmattia/niv",
+        "owner": "nmattia",
+        "repo": "niv",
+        "rev": "af958e8057f345ee1aca714c1247ef3ba1c15f5e",
+        "sha256": "1qjavxabbrsh73yck5dcq8jggvh3r2jkbr6b5nlz5d9yrqm9255n",
+        "type": "tarball",
+        "url": "https://github.com/nmattia/niv/archive/af958e8057f345ee1aca714c1247ef3ba1c15f5e.tar.gz",
+        "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
+    },
+    "nixpkgs": {
+        "branch": "release-20.09",
+        "description": "Nix Packages collection",
+        "homepage": "",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "a565a2165ab6e195d7c105a8416b8f4b4d0349a4",
+        "sha256": "1x90qm533lh8xh172rqfcj3pwg8imyx650xgr41rqppmm6fli4w1",
+        "type": "tarball",
+        "url": "https://github.com/NixOS/nixpkgs/archive/a565a2165ab6e195d7c105a8416b8f4b4d0349a4.tar.gz",
+        "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
+    }
+}

nix/sources.nix

@@ -0,0 +1,174 @@
+# This file has been generated by Niv.
+
+let
+
+  #
+  # The fetchers. fetch_<type> fetches specs of type <type>.
+  #
+
+  fetch_file = pkgs: name: spec:
+    let
+      name' = sanitizeName name + "-src";
+    in
+      if spec.builtin or true then
+        builtins_fetchurl { inherit (spec) url sha256; name = name'; }
+      else
+        pkgs.fetchurl { inherit (spec) url sha256; name = name'; };
+
+  fetch_tarball = pkgs: name: spec:
+    let
+      name' = sanitizeName name + "-src";
+    in
+      if spec.builtin or true then
+        builtins_fetchTarball { name = name'; inherit (spec) url sha256; }
+      else
+        pkgs.fetchzip { name = name'; inherit (spec) url sha256; };
+
+  fetch_git = name: spec:
+    let
+      ref =
+        if spec ? ref then spec.ref else
+          if spec ? branch then "refs/heads/${spec.branch}" else
+            if spec ? tag then "refs/tags/${spec.tag}" else
+              abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!";
+    in
+      builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; };
+
+  fetch_local = spec: spec.path;
+
+  fetch_builtin-tarball = name: throw
+    ''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`.
+        $ niv modify ${name} -a type=tarball -a builtin=true'';
+
+  fetch_builtin-url = name: throw
+    ''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`.
+        $ niv modify ${name} -a type=file -a builtin=true'';
+
+  #
+  # Various helpers
+  #
+
+  # https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695
+  sanitizeName = name:
+    (
+      concatMapStrings (s: if builtins.isList s then "-" else s)
+        (
+          builtins.split "[^[:alnum:]+._?=-]+"
+            ((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name)
+        )
+    );
+
+  # The set of packages used when specs are fetched using non-builtins.
+  mkPkgs = sources: system:
+    let
+      sourcesNixpkgs =
+        import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; };
+      hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath;
+      hasThisAsNixpkgsPath = <nixpkgs> == ./.;
+    in
+      if builtins.hasAttr "nixpkgs" sources
+      then sourcesNixpkgs
+      else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then
+        import <nixpkgs> {}
+      else
+        abort
+          ''
+            Please specify either <nixpkgs> (through -I or NIX_PATH=nixpkgs=...) or
+            add a package called "nixpkgs" to your sources.json.
+          '';
+
+  # The actual fetching function.
+  fetch = pkgs: name: spec:
+
+    if ! builtins.hasAttr "type" spec then
+      abort "ERROR: niv spec ${name} does not have a 'type' attribute"
+    else if spec.type == "file" then fetch_file pkgs name spec
+    else if spec.type == "tarball" then fetch_tarball pkgs name spec
+    else if spec.type == "git" then fetch_git name spec
+    else if spec.type == "local" then fetch_local spec
+    else if spec.type == "builtin-tarball" then fetch_builtin-tarball name
+    else if spec.type == "builtin-url" then fetch_builtin-url name
+    else
+      abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}";
+
+  # If the environment variable NIV_OVERRIDE_${name} is set, then use
+  # the path directly as opposed to the fetched source.
+  replace = name: drv:
+    let
+      saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name;
+      ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}";
+    in
+      if ersatz == "" then drv else
+        # this turns the string into an actual Nix path (for both absolute and
+        # relative paths)
+        if builtins.substring 0 1 ersatz == "/" then /. + ersatz else /. + builtins.getEnv "PWD" + "/${ersatz}";
+
+  # Ports of functions for older nix versions
+
+  # a Nix version of mapAttrs if the built-in doesn't exist
+  mapAttrs = builtins.mapAttrs or (
+    f: set: with builtins;
+    listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set))
+  );
+
+  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295
+  range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1);
+
+  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257
+  stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1));
+
+  # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269
+  stringAsChars = f: s: concatStrings (map f (stringToCharacters s));
+  concatMapStrings = f: list: concatStrings (map f list);
+  concatStrings = builtins.concatStringsSep "";
+
+  # https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331
+  optionalAttrs = cond: as: if cond then as else {};
+
+  # fetchTarball version that is compatible between all the versions of Nix
+  builtins_fetchTarball = { url, name ? null, sha256 }@attrs:
+    let
+      inherit (builtins) lessThan nixVersion fetchTarball;
+    in
+      if lessThan nixVersion "1.12" then
+        fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
+      else
+        fetchTarball attrs;
+
+  # fetchurl version that is compatible between all the versions of Nix
+  builtins_fetchurl = { url, name ? null, sha256 }@attrs:
+    let
+      inherit (builtins) lessThan nixVersion fetchurl;
+    in
+      if lessThan nixVersion "1.12" then
+        fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
+      else
+        fetchurl attrs;
+
+  # Create the final "sources" from the config
+  mkSources = config:
+    mapAttrs (
+      name: spec:
+        if builtins.hasAttr "outPath" spec
+        then abort
+          "The values in sources.json should not have an 'outPath' attribute"
+        else
+          spec // { outPath = replace name (fetch config.pkgs name spec); }
+    ) config.sources;
+
+  # The "config" used by the fetchers
+  mkConfig =
+    { sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null
+    , sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile)
+    , system ? builtins.currentSystem
+    , pkgs ? mkPkgs sources system
+    }: rec {
+      # The sources, i.e. the attribute set of spec name to spec
+      inherit sources;
+
+      # The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers
+      inherit pkgs;
+    };
+
+in
+mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); }

shell.nix

@@ -1,4 +1,4 @@
-{ pkgs ? import <nixpkgs> { } }:
+{ sources ? import ./nix/sources.nix, pkgs ? import sources.nixpkgs { } }:
 
 with pkgs;
 
@@ -6,7 +6,8 @@ let
   CuReSim = stdenv.mkDerivation rec {
     name = "CuReSim";
     version = "1.3";
-    src = fetchzip { url =
+    src = fetchzip {
+      url =
         "http://www.pegase-biosciences.com/wp-content/uploads/2015/08/${name}${version}.zip";
       sha256 = "1hvlpgy4haqgqq52mkxhcl9i1fx67kgwi6f1mijvqzk0xff77hkp";
       stripRoot = true;

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[1]
-    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")