From 6a49c7d57dad3225d231389d8aab2124d6644eff Mon Sep 17 00:00:00 2001
From: Iris Mestres <iris.mestrespascual@unibas.ch>
Date: Sat, 4 Mar 2023 14:00:03 +0100
Subject: [PATCH] refactor: use local annotation file
---
scripts/filter_anno_gtf.sh | 31 +++++++++----------------------
1 file changed, 9 insertions(+), 22 deletions(-)
diff --git a/scripts/filter_anno_gtf.sh b/scripts/filter_anno_gtf.sh
index df121c9..6151a53 100755
--- a/scripts/filter_anno_gtf.sh
+++ b/scripts/filter_anno_gtf.sh
@@ -24,18 +24,16 @@ log_dir="$2"
# Paths (DO NOT CHANGE!) #Modified by Iborra P
root="$PWD"
resDir="${root}/${output_dir}"
-rawDir="${resDir}/raw"
+fileDir="${root}/test_files"
tmpDir="${root}/.tmp"
logDir="${root}/${log_dir}"
-# URLs
+# Annotation file
# ----
-# - All URLs variables represent Bash arrays, so that multiple URLs can be provided; in that case,
-# files are concatenated after download
# - It is assumed that the specified transcriptome files contain sequences for all transcripts in
# the (filtered) gene annotations
-geneAnnoURLs="$3" #Modified by Iborra P
+geneAnnoFile="$3"
# Filters
# -------
@@ -65,7 +63,6 @@ set -o pipefail
# Create directories
mkdir --parents "$resDir"
-mkdir --parents "$rawDir"
mkdir --parents "$tmpDir"
# Create log file
@@ -78,25 +75,14 @@ rm -fr "$logFile"; touch "$logFile"
### MAIN ###
##############
-## GET & FILTER GENE ANNOTATIONS
-
-# Get gene annotation files
-echo "Downloading gene annotations..." >> "$logFile"
-for url in "${geneAnnoURLs[@]}"; do
- wget "$url" --output-document "${rawDir}/$(basename "$url")" &> /dev/null
-done
-
-# Concatenate gene annotation files
-echo "Concatenating gene annotation files..." >> "$logFile"
-geneAnno="${resDir}/gene_annotations.gtf.gz"
-for url in "${geneAnnoURLs[@]}"; do
- cat "${rawDir}/$(basename "$url")" >> "$geneAnno"
-done
+## FILTER GENE ANNOTATIONS
# Filter gene annotations
geneAnnoFilt="${resDir}/gene_annotations.filtered.gtf.gz"
geneAnnoOut="${resDir}/gene_annotations.filtered.gtf"
geneAnnoFiltTmp="${tmpDir}/gene_annotations.filtered.gtf.gz.tmp"
+geneAnno="${resDir}/gene_annotations.gtf.gz"
+cp "$geneAnnoFile" "$geneAnno"
cp "$geneAnno" "$geneAnnoFiltTmp"
# Filter requested chromosomes
@@ -142,11 +128,12 @@ cp "$geneAnno" "$geneAnnoFiltTmp"
rm "${resDir}/gene_annotations.filtered.gtf.gz"
rm "${resDir}/gene_annotations.gtf.gz"
+
#############
### 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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