33 lines
957 B
Bash
33 lines
957 B
Bash
#This is a 'master associated' sh script to operate from the /REMc source directory
|
|
#It is an altered Function.sh with a cd at start
|
|
|
|
cd GTF/Function
|
|
#Begin the Original Function.sh
|
|
#!/bin/bash
|
|
# this one code will load the terms2tsv_v4.pl to add two more columns: one is the gene names, the other one is the cluster name column
|
|
|
|
set $1 = ORF_List_Without_DAmPs.txt #ORF_List_Without_DAmPs.txt #ORFs_w_DAmP_list.txt
|
|
set $2 = REMcRdy_lm_only/*.txt
|
|
|
|
#if [ $argv -lt 2 ]; then
|
|
#echo "Usage: ./example_v4.sh backgroundFilePath geneListsFolder"
|
|
#else
|
|
|
|
|
|
for i in ${*:2}
|
|
do
|
|
#echo $1
|
|
#echo $i
|
|
./analyze_v2.pl -an gene_association.sgd -as F -o gene_ontology_edit.obo -b $1 $i
|
|
./terms2tsv_v4.pl $i.terms > $i.tsv
|
|
done
|
|
wait
|
|
echo "Function complete"
|
|
#fi
|
|
#Concatinatethe Process ontology outputs from the /REMcRdy_lm_only folder
|
|
python3 Concatenate_GTF_results.py REMcRdy_lm_only/ FuctionResults.txt
|
|
wait
|
|
echo "FunctionConcatenate complete"
|
|
pwd
|
|
#exit
|