tools/run_specific_scripts/transcriptome_analysis/createGenefindingInfo.sh

   1 #!/bin/bash
   2
   3 for((idx=1;idx<2;idx++))
   4 do
   5    current_dir=/fml/ag-raetsch/share/projects/qpalma/thaliana_4_lanes/lane_${idx}/spliced
   6    input=$current_dir/alignment
   7    result=$current_dir/alignment/alignmentInfo.genefinding
   8    result2=$current_dir/alignment/alignmentInfo.genefinding.chr1_only
   9    result3=$current_dir/alignment/alignmentInfo.genefinding.chr1_only.sorted
  10    intron_stops=$current_dir/alignment/intron_stops
  11    intron_starts=$current_dir/alignment/intron_starts
  12    intron_info=$current_dir/alignment/intron_info
  13
  14    python createExonInfoForGenefinding.py $input $result
  15
  16    #cat $result | grep '^1' > $result2
  17    #cat $result2 | sort > $result3
  18
  19    for((chromo=1;chromo<6;chromo++))
  20    do
  21       for strand in "+" "-"
  22       do
  23          full_intron_stops=${intron_stops}_chr${chromo}_${strand}
  24          full_intron_starts=${intron_starts}_chr${chromo}_${strand}
  25          full_intron_info=${intron_info}_chr${chromo}_${strand}
  26          cat $result | grep "^$chromo" | grep " $strand " | cut -f3 | sed -e '/[,]\{1,1\}/!d' | cut -d ',' -f2 > $full_intron_stops
  27          cat $result | grep "^$chromo" | grep " $strand " | cut -f4 | sed -e '/[,]\{1,1\}/!d' | cut -d ',' -f1 > $full_intron_starts
  28          paste --delimiters=" " $full_intron_starts $full_intron_stops > $full_intron_info
  29          rm $full_intron_stops $full_intron_starts
  30       done
  31    done
  32 done