[Nelsonlab-cmts] dev-boconnor/project_logic_analysis/scripts vgl_input_script.pl,NONE,1.1 extract_probesets.sh,1.1,1.2 make_mas5.R,1.2,1.3

[<boc...@su...>]

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";
}