From aa9e0db45b8c5e7e1d96c435d60d3b70948137b0 Mon Sep 17 00:00:00 2001 From: mcmero Date: Tue, 28 Sep 2021 11:10:16 +1000 Subject: [PATCH] Fixed order of setting up trans_fasta annotation --- setup_references_hg38.sh | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/setup_references_hg38.sh b/setup_references_hg38.sh index bc2b8fd..29edd06 100755 --- a/setup_references_hg38.sh +++ b/setup_references_hg38.sh @@ -6,7 +6,7 @@ mkdir -p ref cd ref gmap_refdir=$PWD -commands="genome_fasta trans_fasta tx_annotation ann_info tx2gene gmap_refdir gmap_genome" +commands="genome_fasta tx_annotation trans_fasta ann_info tx2gene gmap_refdir gmap_genome" function genome_fasta_setup { file=hg38.fa @@ -26,16 +26,6 @@ function genome_fasta_setup { fi } -function trans_fasta_setup { - file=chess2.2.fa - wget --no-check-certificate http://ccb.jhu.edu/software/stringtie/dl/gffread-0.11.6.Linux_x86_64.tar.gz - tar -xvzf gffread-0.11.6.Linux_x86_64.tar.gz && rm gffread-0.11.6.Linux_x86_64.tar.gz - gffread-0.11.6.Linux_x86_64/gffread chess2.2.gtf -g hg38.fa -w $file - if [ -s $file ]; then - echo -e "$PWD/$file" > trans_fasta.success - fi -} - function tx_annotation_setup { file=chess2.2.gtf wget http://ccb.jhu.edu/chess/data/${file}.gz @@ -47,6 +37,16 @@ function tx_annotation_setup { fi } +function trans_fasta_setup { + file=chess2.2.fa + wget --no-check-certificate http://ccb.jhu.edu/software/stringtie/dl/gffread-0.11.6.Linux_x86_64.tar.gz + tar -xvzf gffread-0.11.6.Linux_x86_64.tar.gz && rm gffread-0.11.6.Linux_x86_64.tar.gz + gffread-0.11.6.Linux_x86_64/gffread chess2.2.gtf -g hg38.fa -w $file + if [ -s $file ]; then + echo -e "$PWD/$file" > trans_fasta.success + fi +} + function ann_info_setup { file=chess2.2.info python ../util/make_exon_reference.py chess2.2.gtf