From 1e543b39890a708b3342f2845991fc550ae49aec Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Thu, 9 Jan 2025 12:06:10 -0500
Subject: [PATCH] Adding TPM calculating script (Salmon)

---
 Utilities/for_fastas/Salmon.sh | 65 ++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)
 create mode 100644 Utilities/for_fastas/Salmon.sh

diff --git a/Utilities/for_fastas/Salmon.sh b/Utilities/for_fastas/Salmon.sh
new file mode 100644
index 0000000..d48ccad
--- /dev/null
+++ b/Utilities/for_fastas/Salmon.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+## Last updated on Jan 9th 2024 by Auden Cote-L'Heureux
+
+#Intent: Calculate TPM for assembled transcripts
+#Dependencies: None
+#Inputs: Must be in a folder along with a folder called 'Transcriptomes', containing assembled transcripts as output by rnaSpades (transcripts.fasta), 
+## and a folder called 'RawReads' containing the fwd and rev reads prior to assembly, with the same file prefixes as the corresponding assembled transcript files
+#Outputs: A folder, containing a 'quant' file which has TPM data.
+
+## If running on an HPC, include parameters here! For example, on a Slurm system you might use
+
+
+#SBATCH --job-name=tpm
+#SBATCH --output=Salmon.%j.out # Stdout (%j expands to jobId)
+#SBATCH --nodes=1
+#SBATCH --ntasks=60
+#SBATCH --mem=60G
+
+mkdir Indices
+
+## First, build transcript indices
+
+cd Transcriptomes
+
+IFS='/'
+for TRANS in *; do
+        #read -a trapsplit <<<"$TRANS"
+        #traf=${trapsplit[1]}
+        tax=${TRANS:0:10}
+
+	./../salmon-1.9.0_linux_x86_64/bin/salmon index -t $TRANS -i ../Indices/$tax
+done
+
+## Now calculate TPM
+
+cd Indices
+
+IFS='/'
+for TRANS in *; do
+        read -a trapsplit <<<"$TRANS"
+        tax=${TRANS:0:10}
+        fpe='NA'; rpe='NA'; fpesub="FPE"; rpesub="RPE"
+        for TRIM in ../RawReads/*; do
+                read -a tripsplit <<<"$TRIM"
+                trif=${tripsplit[2]}
+                if [ "${trif:0:10}" == "$tax" ]; then
+                        if [[ "$trif" == *"$fpesub"* ]]; then
+                                fpe=$trif
+                        fi
+                        if [[ "$trif" == *"$rpesub"* ]]; then
+                                rpe=$trif
+                        fi
+                fi
+        done
+        
+        if [ "$rpe" != 'NA' ]; then
+                ./../salmon-1.9.0_linux_x86_64/bin/salmon quant -i $TRANS -l A -1 ../RawReads/$fpe -2 ../RawReads/$rpe --validateMappings -o ../quants/$tax
+        fi
+
+        if [ "$rpe" == 'NA' ]; then
+                ./../salmon-1.9.0_linux_x86_64/bin/salmon quant -i $TRANS -l A -r ../RawReads/$fpe --validateMappings -o ../quants/$tax
+        fi
+
+done
\ No newline at end of file