Replace niv with flakes

README.md

@@ -0,0 +1,68 @@
+# locigenesis
+
+locigenesis is a tool that generates a human T-cell receptor (TCR), runs
+it through a sequence reader simulation tool and extracts CDR3.
+
+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.
+
+## Technologies
+
+-   [immuneSIM](https://github.com/GreiffLab/immuneSIM/): in silico
+    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
+
+## Installation
+
+This project uses [Nix](https://nixos.org/) to ensure reproducible
+builds.
+
+1.  Install Nix (compatible with MacOS, Linux and
+    [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
+
+```bash
+curl -L https://nixos.org/nix/install | sh
+```
+
+2.  Clone the repository:
+
+```bash
+git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
+```
+
+3.  Change the working directory to the project:
+
+```bash
+cd locigenesis
+```
+
+4.  Enter the nix-shell:
+
+```bash
+nix-shell
+```
+
+After running these commands, you will find yourself in a shell that
+contains all the needed dependencies.
+
+## Usage
+
+An execution script that accepts 2 parameters is provided, the following
+command invokes it:
+
+```bash
+./generation.sh <number of sequences> <number of reads>
+```
+
+-   \<number of sequences\>: an integer that specifies the number of
+    different sequences to generate
+-   \<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 |
+|:----:|:-----:|
+|Contains the original CDR3 sequence|Contains CDR3 after the read simulation, with sequencing errors |

README.org

@@ -1,56 +0,0 @@
-* locigenesis
-
-locigenesis is a tool that generates a human T-cell receptor (TCR), runs it through a sequence reader simulation tool and extracts CDR3.
-
-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.
-
-** Technologies
-
-- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]: in silico generation of human and mouse BCR and TCR repertoires
-- [[http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/][CuReSim]]: read simulator that mimics Ion Torrent sequencing
-
-** Installation
-
-This project uses [[https://nixos.org/][Nix]] to ensure reproducible builds.
-
-1. Install Nix (compatible with MacOS, Linux and [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
-
-#+begin_src shell
-curl -L https://nixos.org/nix/install | sh
-#+end_src
-
-1. Clone the repository:
-
-#+begin_src shell
-git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
-#+end_src
-
-3. Change the working directory to the project:
-
-#+begin_src shell
-cd locigenesis
-#+end_src
-
-4. Enter the nix-shell:
-
-#+begin_src shell
-nix-shell
-#+end_src
-
-After running these commands, you will find yourself in a shell that contains all the needed dependencies.
-
-** Usage
-
-An execution script that accepts 2 parameters is provided, the following command invokes it:
-
-#+begin_src shell
-./generation.sh <number of sequences> <number of reads>
-#+end_src
-
-- <number of sequences>: an integer that specifies the number of different sequences to generate
-- <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         | Contains the original CDR3 sequence                             |
-| CuReSim-HVR.fastq | Contains CDR3 after the read simulation, with sequencing errors |

flake.lock

@@ -0,0 +1,41 @@
+{
+  "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

@@ -0,0 +1,13 @@
+{
+  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

@@ -1,26 +0,0 @@
-{
-    "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

@@ -1,174 +0,0 @@
-# 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 @@
-{ sources ? import ./nix/sources.nix, pkgs ? import sources.nixpkgs { } }:
+{ pkgs ? import <nixpkgs> { } }:
 
 with pkgs;
 
@@ -6,8 +6,7 @@ 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

@@ -34,7 +34,11 @@ 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)
-  row <- matches[1]
+  if(id == "TRBJ2-2"){
+    row <- matches[2]
+  } else {
+    row <- matches[1]
+  }
   return(as.character(vdj_segments[row]))
 }
 
@@ -106,8 +110,9 @@ get_cys_coordinates <- function(alignment) {
   insertion <- unlist(Biostrings::insertion(alignment))
   deletion <- unlist(Biostrings::deletion(alignment))
   delta_coordinates <- handle_indels(insertion, deletion, cys, alignment)
-  cys_start <- cys$start + delta_coordinates$start
-  cys_end <- cys$end + delta_coordinates$end
+  read_start <- unlist(start(Biostrings::Views(alignment)))
+  cys_start <- cys$start + delta_coordinates$start + read_start - 1
+  cys_end <- cys$end + delta_coordinates$end + read_start
   return(list("start" = cys_start, "end" = cys_end))
 }
 
@@ -126,7 +131,7 @@ 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$end))
+  remaining <- Biostrings::subseq(sequences, start = unlist(cys_df$end) + 1)
   j_alignment <- parallel::mcmapply(remaining,
     df$j_seq,
     FUN = align_sequence,
@@ -145,4 +150,4 @@ 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")