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From: <boc...@su...> - 2006-02-17 01:57:17
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Update of /cvsroot/dev-boconnor/project_logic_analysis/scripts In directory sumo.genetics.ucla.edu:/tmp/cvs-serv7343/scripts Modified Files: extract_probesets.sh make_mas5.R Added Files: vgl_input_script.pl Log Message: Added quick script to make VGL sif file for Marc Index: make_mas5.R =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/scripts/make_mas5.R,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** make_mas5.R 11 Aug 2005 23:13:11 -0000 1.2 --- make_mas5.R 17 Feb 2006 01:57:10 -0000 1.3 *************** *** 3,7 **** library(affy); ! file_list = list.files(path="/raid5a/boconnor/cvsroot/dev-boconnor/project_logic_analysis/data/original_glioma_dataset/cel",pattern=".CEL",full.names=TRUE); for (file_name in file_list) --- 3,7 ---- library(affy); ! file_list = list.files(path="/raid5a/boconnor/cvsroot/dev-boconnor/project_logic_analysis/data/t-cell_leukemia_data_Soulier_et_al_2005/cel",pattern=".CEL",full.names=TRUE); for (file_name in file_list) Index: extract_probesets.sh =================================================================== RCS file: /cvsroot/dev-boconnor/project_logic_analysis/scripts/extract_probesets.sh,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** extract_probesets.sh 3 Feb 2006 04:39:30 -0000 1.1 --- extract_probesets.sh 17 Feb 2006 01:57:10 -0000 1.2 *************** *** 1,9 **** #!/bin/bash ! i=0 while [ $i -le $1 ] do ! echo "cat $2 | grep -P '^5' | grep HC_2B | awk '{ print $3 }' | sort | uniq > $3/$i.txt" ! cat $2 | grep -P '^5' | grep HC_2B | awk '{ print $3 }' | sort | uniq > $3/$i.txt i=$((i+1)) done --- 1,20 ---- #!/bin/bash ! # non-random list ! ! echo "Extracting Non-Random List" ! echo "cat $3 | grep -P '^5' | grep $2 | awk '{ print $3 }' | sort | uniq > $5/non_random.txt" ! cat $3 | grep -P '^5' | grep $2 | awk '{ print $3 }' | sort | uniq > $5/non_random.txt ! ! # random list ! echo "cat $4 | grep -P '^\d+' | awk '{ print $1 }' | sort | uniq > /tmp/all_probesets.txt" ! cat $4 | grep -P '^\d+' | awk '{ print $1 }' | sort | uniq > /tmp/all_probesets.txt ! ! i=1 while [ $i -le $1 ] do ! echo "Extracting Random List $i" ! echo "cat /tmp/all_probesets.txt | perl scripts/select_probesets_randomly.pl `wc $5/non_random.txt | awk '{ print $1 }'` > $5/random_$i.txt" ! cat /tmp/all_probesets.txt | perl scripts/select_probesets_randomly.pl `wc $5/non_random.txt | awk '{ print $1 }'` > $5/random_$i.txt i=$((i+1)) done --- NEW FILE: vgl_input_script.pl --- #!/usr/local/bin/perl # to make vgl hardcoded and ugly use Storable; my $data = retrieve("data/p53_breast_cancer_data_Miller_et_al_2005/sif_hash.storable"); foreach my $file (sort keys %{$data->{'files'}}) { my $dlda_mt = $data->{'files'}{$file}{'dlda_mt'}; my $dlda_txt = "DLDA_WT"; if ($dlda_mt) { $dlda_txt = "DLDA_MT"; } print "$file\t$file\t$dlda_txt\n"; } |