+ minor changes in the paths

[qpalma.git] / tools / run_specific_scripts / transcriptome_analysis / createGenefindingInfo.sh

diff --git a/tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh b/tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh
index 1d58abe..f7a6b3f 100755 (executable)
--- a/tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh
+++ b/tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 
-for((idx=1;idx<4;idx++))
+for((idx=1;idx<2;idx++))
 do
-   current_dir=/fml/ag-raetsch/home/fabio/tmp/vmatch_evaluation/spliced_${idx}
+   current_dir=/fml/ag-raetsch/share/projects/qpalma/thaliana_4_lanes/lane_${idx}/spliced
    input=$current_dir/alignment 
    result=$current_dir/alignment/alignmentInfo.genefinding
    result2=$current_dir/alignment/alignmentInfo.genefinding.chr1_only
@@ -11,7 +11,8 @@ do
    intron_starts=$current_dir/alignment/intron_starts
    intron_info=$current_dir/alignment/intron_info
 
-   #python createExonInfoForGenefinding.py $input $result
+   python createExonInfoForGenefinding.py $input $result
+
    #cat $result | grep '^1' > $result2
    #cat $result2 | sort > $result3