3 for((idx
=1;idx
<2;idx
++))
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
14 python createExonInfoForGenefinding.py
$input $result
16 #cat $result | grep '^1' > $result2
17 #cat $result2 | sort > $result3
19 for((chromo
=1;chromo
<6;chromo
++))
23 full_intron_stops
=${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