38 regels
1.2 KiB
Bash
38 regels
1.2 KiB
Bash
#This is a 'master associated' sh script to operate from the REMc source directory
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#It is an altered Process.sh with a cd at start
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cd GTF/Process
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#Begin the Original Process.sh
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#!/bin/bash
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# 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
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set $1 = ORF_List_Without_DAmPs.txt #ORFs_w_DAmP_list.txt #ORF_List_Without_DAmPs.txt
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set $2 = REMcRdy_lm_only/*.txt
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#paths= ORF_List_Without_DAmPs.txt:REMcRdy_lm_only/*.txt
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#if [ $argv -lt 2 ]; then
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#echo "Usage: ./example_v4.sh backgroundFilePath geneListsFolder"
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#else
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for i in ${*:2}
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do
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#echo $1
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#echo $i
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./analyze_v2.pl -an gene_association.sgd -as P -o gene_ontology_edit.obo -b $1 $i
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./terms2tsv_v4.pl $i.terms > $i.tsv
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done
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#fi
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wait
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echo "Process complete"
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#Concatinatethe Process ontology outputs from the /REMcReady_lm_only folder
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#python2 Concatenate_GTF_results.py ./REMcReady_lm_only/ ProcessResultsTest.txt
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pwd
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python3 Concatenate_GTF_results.py REMcRdy_lm_only/ ProcessResults.txt
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#python2 ConcatGTFdebug.py REMcRdy_lm_only/ ProcessResults.txt
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#python2 ConcatGTFdebug.py REMcRdy_lm_only/ PresDebug4.txt
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wait
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echo "Process Concatenate complete"
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pwd
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#exit
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