From 9a2662c52394119fea93ef67ca65ad795047c3a3 Mon Sep 17 00:00:00 2001
From: Iris Mestres <iris.mestrespascual@unibas.ch>
Date: Sat, 4 Mar 2023 13:59:43 +0100
Subject: [PATCH] refactor: use local genome file
---
scripts/genome_process.sh | 47 +++++++++++----------------------------
1 file changed, 13 insertions(+), 34 deletions(-)
diff --git a/scripts/genome_process.sh b/scripts/genome_process.sh
index abc9d7f..9cf33d6 100755
--- a/scripts/genome_process.sh
+++ b/scripts/genome_process.sh
@@ -10,7 +10,7 @@
### DESCRIPTION ###
#####################
-# Download and process genome sequences fasta files.
+# Process genome sequences fasta file.
####################
### PARAMETERS ###
@@ -20,19 +20,14 @@
output_dir="$1"
log_dir="$2"
-# # Paths (DO NOT CHANGE!)
+# Paths (DO NOT CHANGE!)
root="$PWD"
-#root="$(cd "$(dirname "$0" )" && pwd)"
-
+fileDir="${root}/test_files"
resDir="${root}/${output_dir}"
-rawDir="${resDir}/raw"
logDir="${root}/${log_dir}"
-# URLs
-# ------
-# All URLs variables represent Bash arrays, so that multiple URLs can be provided; in that case,
-# files are concatenated after download
-genomeSeqURLs="$3" #Modified by Iborra P
+# Genome File
+genomeSeqFile="$3"
########################
### PRE-REQUISITES ###
@@ -45,7 +40,6 @@ set -o pipefail
# Create directories
mkdir --parents "$resDir"
-mkdir --parents "$rawDir"
mkdir --parents "$logDir"
# Create log file
@@ -57,37 +51,22 @@ rm -fr "$logFile"; touch "$logFile"
### MAIN ###
##############
-## GET & FILTER GENE ANNOTATIONS
-
-# Get genome sequences fasta files
-echo "Downloading genome sequences files..." >> "$logFile"
-# wget -i "${genomeSeqURLs}" --output-document "${rawDir}/${fileNamePrefix}.genome.fa.gz"
-# genomeSeq="${resDir}/${fileNamePrefix}.genome.fa.gz"
-
-for url in "${genomeSeqURLs[@]}"; do
- wget "$url" --output-document "${rawDir}/$(basename "$url")" &> /dev/null
-done
-
-# Concatenate genome sequences fasta files
-echo "Concatenating genome sequences files..." >> "$logFile"
-genomeSeq="${resDir}/genome.fa.gz"
-for url in "${genomeSeqURLs[@]}"; do
- cat "${rawDir}/$(basename "$url")" >> "$genomeSeq"
-done
-
-# Trim genome sequences IDs
+## TRIM GENOME SEQUENCES IDs
echo "Triming genome sequenes IDs..." >> "$logFile"
+
genomeSeqTrim="${resDir}/genome.processed.fa"
+cp "${genomeSeqFile}" "${output_dir}/genome.fa.gz"
+genomeSeq="${output_dir}/genome.fa.gz"
gunzip "$genomeSeq"
-genomeSeq="${resDir}/genome.fa"
+genomeSeq="${output_dir}/genome.fa"
awk '{if ($1 ~ /^>/) {print $1} else {print $0}}' "$genomeSeq" > "$genomeSeqTrim"
-rm "${resDir}/genome.fa"
+rm "${output_dir}/genome.fa"
#############
### END ###
#############
-echo "Original data in: $rawDir" >> "$logFile"
+echo "Original data in: $fileDir" >> "$logFile"
echo "Processed data in: $resDir" >> "$logFile"
echo "Done. No errors." >> "$logFile"
->&2 echo "Done. No errors."
+>&2 echo "Done. No errors."
\ No newline at end of file
--
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