From 80aaf333dc1245b8bbec9aa7b628d85c5e413f4b Mon Sep 17 00:00:00 2001
From: Emma Rousseau <emmarou1@icloud.com>
Date: Fri, 13 Sep 2024 09:10:30 +0200
Subject: [PATCH] Add Kallisto index (#149)

---
 CHANGELOG.md                                  |   6 +-
 src/kallisto/kallisto_index/Kallisto          | Bin 0 -> 2439 bytes
 src/kallisto/kallisto_index/config.vsh.yaml   |  94 ++++++++++++++++++
 src/kallisto/kallisto_index/help.txt          |  21 ++++
 src/kallisto/kallisto_index/script.sh         |  34 +++++++
 src/kallisto/kallisto_index/test.sh           |  35 +++++++
 .../kallisto_index/test_data/d_list.fasta     |   5 +
 .../test_data/transcriptome.fasta             |  23 +++++
 8 files changed, 217 insertions(+), 1 deletion(-)
 create mode 100644 src/kallisto/kallisto_index/Kallisto
 create mode 100644 src/kallisto/kallisto_index/config.vsh.yaml
 create mode 100644 src/kallisto/kallisto_index/help.txt
 create mode 100644 src/kallisto/kallisto_index/script.sh
 create mode 100644 src/kallisto/kallisto_index/test.sh
 create mode 100644 src/kallisto/kallisto_index/test_data/d_list.fasta
 create mode 100644 src/kallisto/kallisto_index/test_data/transcriptome.fasta

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d88d0996..846007d8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -149,7 +149,11 @@
 * `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic 
                data. (PR #146)
 
-*  `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
+* `kallisto`:
+    - `kallisto_index`: Create a kallisto index (PR #149).
+
 
 ## MINOR CHANGES
 
diff --git a/src/kallisto/kallisto_index/Kallisto b/src/kallisto/kallisto_index/Kallisto
new file mode 100644
index 0000000000000000000000000000000000000000..3c7b5b2bff962965d99ca3f9a4a6b6af6da1f3f0
GIT binary patch
literal 2439
zcmeHJTTBx{6rFCj(iW7(R4PH@f{iwcTCEBOksY_VO)N&jMkQb@MkU0z5<nES+iDtq
ztcrfC@k>b%pZJItq>6y3i5QJ<W1@)>C02jb;7mKSNlWm{Po|xmnK|d)x%cj5cE^Hf
zo5Ms=gP>q-=Dx`Y&8Tam%b*(*sAYc)aw*sH`%Qmb#irI!wJd#g^%N{jJ942Y*B;7v
zR8myiWp1c$UHLL&=A`AC^o$*g(yPKxE9&k2TL(+#tPc&Aci!%O@N%%KUe}u^mgT!#
zi%Y`WO!oXjbAkQw#f0xZP+kZo&F8eXH{r?boldZcY~7r&DBNCpW#D;g<%>%V>88S*
zn(fP&_poKg&FeY4ul8ovgjcuEYhCLuEry9t<T_<r;)x-6Y*vFQbgQZF#X(b>sbgo;
zfcbNEMVB@;wf0@jF3-`vqIs3Vln>G5z~*-Q*|O7R4?+L_8<&^;{;|Iv=yw^0x?1Fq
zKKH{t-pk+KZ7B%++|bB;H`mVIyPQk@FmSG}@6usnuL2HvP5$1gzh1Rfd<xy4PRpnY
z$lwb>lA=oM8O*p9pU%UxMoXtZa4MiI;e6lN9)Zj9SsczoL4F-nxW<!$M?XHx=`41$
zNSX;JB>7gjS;lL#ITXLZTe7Tm{6y<^@7*BFcmyOu`fe-N>GMM_MNm8n3s15~-A-du
zs>S(M$mE>7gVQsBMnsW@M&}f>b(D#qkcNO}MG=t0Wgt?+7*11VW2Q|{Q<m5`y=8^|
z9+;~?zuCji5Og|U(_<Ox<qoL${owUfYj%<xv>bnyveDt-4O(8?_>}HQ+|nsHK}JD>
zEI}_&#snCR!wU`=ImWmY2!IuUp@YzBuGIbjA?Q;}NCbS6Ej{38{Q(Ed(9~7CHlh~@
z(zu?LfHTHk>o~Hk>ib8~11>`F@%qmr>8X$)4UE=ZAnP=qIJp|ns6M_j(fMdSqjeZP
zKmX@E#Gf*HzUVyzWeLinBtr;M7o$H(mPA>GqA1d9hM{`wuLpH{uWG16io*!3&Oq!~
zY>JwOK3Z%+$HT0KEnpYTsK*f41@5@T5O@KlCdndB3}+_eA<9%le@sX@NTS*o#e2qq
z{mZk6y~(I%5^AViqJ%~m(IWP&+TTT!n9y(~NA!$eA9;u!LWn;?@K-_t>bR9cmu<nq
hRn%Ezn!9QyjNx;|7(NH_$x(BVXNzpCjqI)ke*rf>5}*J8

literal 0
HcmV?d00001

diff --git a/src/kallisto/kallisto_index/config.vsh.yaml b/src/kallisto/kallisto_index/config.vsh.yaml
new file mode 100644
index 00000000..2c4f65c7
--- /dev/null
+++ b/src/kallisto/kallisto_index/config.vsh.yaml
@@ -0,0 +1,94 @@
+name: kallisto_index
+namespace: kallisto
+description: |
+  Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.
+keywords: [kallisto, index]
+links:
+  homepage: https://pachterlab.github.io/kallisto/about
+  documentation: https://pachterlab.github.io/kallisto/manual
+  repository: https://github.com/pachterlab/kallisto
+  issue_tracker: https://github.com/pachterlab/kallisto/issues
+references: 
+  doi: https://doi.org/10.1038/nbt.3519
+license: BSD 2-Clause License
+
+argument_groups:
+- name: "Input"
+  arguments: 
+  - name: "--input"
+    type: file
+    description: |
+      Path to a FASTA-file containing the transcriptome sequences, either in plain text or 
+      compressed (.gz) format.
+    required: true
+  - name: "--d_list"
+    type: file
+    description: |
+      Path to a FASTA-file containing sequences to mask from quantification.
+
+- name: "Output"
+  arguments:
+  - name: "--index"
+    type: file
+    direction: output
+    example: Kallisto_index
+
+- name: "Options"
+  arguments:
+  - name: "--kmer_size"
+    type: integer
+    description: |
+      Kmer length passed to indexing step of pseudoaligners (default: '31').
+    example: 31
+  - name: "--make_unique"
+    type: boolean_true
+    description: |
+      Replace repeated target names with unique names.
+  - name: "--aa"
+    type: boolean_true
+    description: |
+      Generate index from a FASTA-file containing amino acid sequences.
+  - name: "--distiguish"
+    type: boolean_true
+    description: |
+       Generate index where sequences are distinguished by the sequence names.
+  - name: "--min_size"
+    alternatives: ["-m"]
+    type: integer
+    description: |
+      Length of minimizers (default: automatically chosen).
+  - name: "--ec_max_size"
+    alternatives: ["-e"]
+    type: integer
+    description: |
+      Maximum number of targets in an equivalence class (default: no maximum).
+  - name: "--tmp"
+    alternatives: ["-T"]
+    type: string
+    description: |
+      Path to a directory for temporary files.
+    example: "tmp"
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data
+
+engines:
+  - type: docker
+    image: ubuntu:22.04
+    setup:
+      - type: docker
+        run: |
+          apt-get update && \
+          apt-get install -y --no-install-recommends wget && \
+          wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
+          tar -xzf kallisto_linux-v0.50.1.tar.gz && \
+          mv kallisto/kallisto /usr/local/bin/
+runners:
+  - type: executable
+  - type: nextflow  
diff --git a/src/kallisto/kallisto_index/help.txt b/src/kallisto/kallisto_index/help.txt
new file mode 100644
index 00000000..28778ac0
--- /dev/null
+++ b/src/kallisto/kallisto_index/help.txt
@@ -0,0 +1,21 @@
+```
+kallisto index
+```
+kallisto 0.50.1
+Builds a kallisto index
+
+Usage: kallisto index [arguments] FASTA-files
+
+Required argument:
+-i, --index=STRING          Filename for the kallisto index to be constructed 
+
+Optional argument:
+-k, --kmer-size=INT         k-mer (odd) length (default: 31, max value: 31)
+-t, --threads=INT           Number of threads to use (default: 1)
+-d, --d-list=STRING         Path to a FASTA-file containing sequences to mask from quantification
+    --make-unique           Replace repeated target names with unique names
+    --aa                    Generate index from a FASTA-file containing amino acid sequences
+    --distinguish           Generate index where sequences are distinguished by the sequence name
+-T, --tmp=STRING            Temporary directory (default: tmp)
+-m, --min-size=INT          Length of minimizers (default: automatically chosen)
+-e, --ec-max-size=INT       Maximum number of targets in an equivalence class (default: no maximum)
diff --git a/src/kallisto/kallisto_index/script.sh b/src/kallisto/kallisto_index/script.sh
new file mode 100644
index 00000000..59a5d3de
--- /dev/null
+++ b/src/kallisto/kallisto_index/script.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+unset_if_false=( par_make_unique par_aa par_distinguish )
+
+for var in "${unset_if_false[@]}"; do
+    temp_var="${!var}"
+    [[ "$temp_var" == "false" ]] && unset $var
+done
+
+if [ -n "$par_kmer_size" ]; then
+    if [[ "$par_kmer_size" -lt 1 || "$par_kmer_size" -gt 31 || $(( par_kmer_size % 2 )) -eq 0 ]]; then
+        echo "Error: Kmer size must be an odd number between 1 and 31."
+        exit 1
+    fi
+fi
+
+kallisto index \
+    -i "${par_index}" \
+    ${par_kmer_size:+--kmer-size "${par_kmer_size}"} \
+    ${par_make_unique:+--make-unique} \
+    ${par_aa:+--aa} \
+    ${par_distinguish:+--distinguish} \
+    ${par_min_size:+--min-size "${par_min_size}"} \
+    ${par_ec_max_size:+--ec-max-size "${par_ec_max_size}"} \
+    ${par_d_list:+--d-list "${par_d_list}"} \
+    ${meta_cpus:+--cpu "${meta_cpus}"} \
+    ${par_tmp:+--tmp "${par_tmp}"} \
+    "${par_input}"
+
diff --git a/src/kallisto/kallisto_index/test.sh b/src/kallisto/kallisto_index/test.sh
new file mode 100644
index 00000000..2646dcd8
--- /dev/null
+++ b/src/kallisto/kallisto_index/test.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+echo ">>>Test 1: Testing $meta_functionality_name with non-default k-mer size"
+
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/transcriptome.fasta" \
+  --index Kallisto \
+  --kmer_size 21
+
+
+echo ">>> Checking whether output exists and is correct"
+[ ! -f "Kallisto" ] && echo "Kallisto index does not exist!" && exit 1
+[ ! -s "Kallisto" ] && echo "Kallisto index is empty!" && exit 1
+
+kallisto inspect Kallisto 2> test.txt
+grep "number of k-mers: 989" test.txt || { echo "The content of the index seems to be incorrect." && exit 1; }
+
+################################################################################
+
+echo ">>>Test 2: Testing $meta_functionality_name with d_list argument"
+
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/transcriptome.fasta" \
+  --index Kallisto \
+  --d_list "$meta_resources_dir/test_data/d_list.fasta"
+
+echo ">>> Checking whether output exists and is correct"
+[ ! -f "Kallisto" ] && echo "Kallisto index does not exist!" && exit 1
+[ ! -s "Kallisto" ] && echo "Kallisto index is empty!" && exit 1
+
+kallisto inspect Kallisto 2> test.txt
+grep "number of k-mers: 959" test.txt || { echo "The content of the index seems to be incorrect." && exit 1; }
+
+echo "All tests succeeded!"
+exit 0
diff --git a/src/kallisto/kallisto_index/test_data/d_list.fasta b/src/kallisto/kallisto_index/test_data/d_list.fasta
new file mode 100644
index 00000000..ad5e05bf
--- /dev/null
+++ b/src/kallisto/kallisto_index/test_data/d_list.fasta
@@ -0,0 +1,5 @@
+>YAL067W-A CDS=1-228
+ATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGG
+TCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGT
+CTGCTTTAAACGGCTTCCGCGGAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTG
+GGAGTCGTATACTGTTAG
diff --git a/src/kallisto/kallisto_index/test_data/transcriptome.fasta b/src/kallisto/kallisto_index/test_data/transcriptome.fasta
new file mode 100644
index 00000000..94c06163
--- /dev/null
+++ b/src/kallisto/kallisto_index/test_data/transcriptome.fasta
@@ -0,0 +1,23 @@
+>YAL069W CDS=1-315
+ATGATCGTAAATAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTC
+ACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTC
+AGATTCCACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACG
+GCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATTTTGATAT
+CTATATCTCATTCGGCGGTCCCAAATATTGTATAA
+>YAL068W-A CDS=1-255
+ATGCACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTATCCACATT
+TTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAATACATACGTTATACCACT
+TTTGCACCATATACTTACCACTCCATTTATATACACTTATGTCAATATTACAGAAAAATCCCCACAAAAA
+TCACCTAAACATAAAAATATTCTACTTTTCAACAATAATACATAA
+>YAL068C CDS=1-363
+ATGGTCAAATTAACTTCAATCGCCGCTGGTGTCGCTGCCATCGCTGCTACTGCTTCTGCAACCACCACTC
+TAGCTCAATCTGACGAAAGAGTCAACTTGGTGGAATTGGGTGTCTACGTCTCTGATATCAGAGCTCACTT
+AGCCCAATACTACATGTTCCAAGCCGCCCACCCAACTGAAACCTACCCAGTCGAAGTTGCTGAAGCCGTT
+TTCAACTACGGTGACTTCACCACCATGTTGACCGGTATTGCTCCAGACCAAGTGACCAGAATGATCACCG
+GTGTTCCATGGTACTCCAGCAGATTAAAGCCAGCCATCTCCAGTGCTCTATCCAAGGACGGTATCTACAC
+TATCGCAAACTAG
+>YAL067W-A CDS=1-228
+ATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGG
+TCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGT
+CTGCTTTAAACGGCTTCCGCGGAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTG
+GGAGTCGTATACTGTTAG
\ No newline at end of file