protein coding

jiang548 · May 1, 2022 · 0ea5df5 · 0ea5df5
1 parent 3a6358c
commit 0ea5df5
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/script/adj/adj_adjust_gtex.sh b/script/adj/adj_adjust_gtex.sh
@@ -17,7 +17,7 @@ empty.txt \
 all_covs_withoutigtpc_${tissue}_no_peer &&
 
 echo -e 'Begin Preprocessing ...\n'
-cd $SIGNET_ROOT
+cd $SIGNET_TMP_ROOT/tmpa
 ## adjust expression by the covariates: top  pcs, without PEER factors, Sex, Platform, Protocol
 $SIGNET_SCRIPT_ROOT/adj/gexp_cov_adjust.py --expr ${rest}_expression_normalized_igt2log_GTEx_${tissue}.expression.bed.gz \
 --covf $SIGNET_TMP_ROOT/tmpa/all_covs_withoutigt_${tissue}_no_peer.combined_covariates.txt \
@@ -27,4 +27,4 @@ $SIGNET_SCRIPT_ROOT/adj/gexp_cov_adjust.py --expr ${rest}_expression_normalized_
 --covf $SIGNET_TMP_ROOT/tmpa/all_covs_withoutigtpc_${tissue}_no_peer.combined_covariates.txt \
 --prefix tmp > log_lung_withoutigt_no_peer
 
-Rscript protein_coding_gtex.R
+Rscript $SIGNET_SCRIPT_ROOT/adj/protein_coding_gtex.R
diff --git a/script/adj/protein_coding_gtex.R b/script/adj/protein_coding_gtex.R
@@ -2,7 +2,8 @@
 ##Filter and order genes 
 library(data.table)
 library(rtracklayer)
-gtf <- rtracklayer::import(Sys.getenv(gtf))
+print(Sys.getenv("gtf"))
+gtf <- rtracklayer::import(Sys.getenv("gtf"))
 gtf <- as.data.frame(gtf)
 gtf[, 1] <- substring(gtf[, 1], 4)
 

diff --git a/script/adj_portal_gtex.sh b/script/adj_portal_gtex.sh
@@ -10,7 +10,7 @@ usage() {
 }
 
 pheno=$($SIGNET_ROOT/signet -s --pheno | sed -r '/^\s*$/d' | xargs readlink -f)
-gtf=$($SIGNET_ROOT/signet -s --gtf | sed -r '/^\s*$/d' | xargs readlink -f)
+gtf=$($SIGNET_ROOT/signet -s --gtf.file | sed -r '/^\s*$/d' | xargs readlink -f)
 tissue=$($SIGNET_ROOT/signet -s --tissue | sed -r '/^\s*$/d')
 anno=$($SIGNET_ROOT/signet -s --anno | sed -r '/^\s*$/d' | xargs readlink -f)
 resa=$($SIGNET_ROOT/signet -s --resa.gtex | sed -r '/^\s*$/d' | xargs readlink -f)
@@ -59,6 +59,7 @@ do
 export "${i}"
 done
 
+
 # check file existence
 input_file="pheno anno"
 for i in $input_file