set genome = hg19 set gffDir = /hive/groups/wet/illumina/geneModels/${genome}/miso_gff/${genome} set eventList = (AFE ALE A3SS A5SS MXE SE TandemUTR RI) set eventList = (AFE ALE A3SS SE) cd $gffDir foreach ae ($eventList) set gffName = ${ae}.${genome}.gff3 echo "" echo "--------------------------------------------" echo "${ae} stats for lengths (in Mb) of gene items in event gff" echo "gffDir: $gffDir" echo "gffName: $gffName" cat $gffDir/$gffName | \ gawk '($3 == "gene")' | \ cut -f 4,5 | \ gawk '{print ($2 - $1)/1000000}' \ > temp.${ae}.lengths echo "" cat temp.${ae}.lengths | ave stdin echo "" cat temp.${ae}.lengths | textHistogram -binSize=10 stdin rm -f temp.${ae}.lengths end -------------------------------------------- AFE stats for lengths (in Mb) of gene items in event gff gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19 gffName: AFE.hg19.gff3 Q1 0.011718 median 0.036585 Q3 0.118308 average 2.235597 min 0.000061 max 242.543000 count 19720 total 44085.963859 standard deviation 11.335027 0 ************************************************************ 18616 10 0 20 *** 897 30 23 40 10 50 5 60 113 70 28 80 0 90 4 100 0 110 2 120 1 130 0 140 1 150 0 160 0 170 0 180 5 190 0 200 0 210 0 220 0 230 0 240 15 -------------------------------------------- ALE stats for lengths (in Mb) of gene items in event gff gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19 gffName: ALE.hg19.gff3 Q1 0.007085 median 0.019504 Q3 0.060781 average 2.011639 min 0.000229 max 242.515000 count 10269 total 20657.518733 standard deviation 9.984358 0 ************************************************************ 9742 10 0 20 *** 414 30 12 40 3 50 5 60 68 70 14 80 0 90 2 100 1 110 0 120 2 130 0 140 1 150 0 160 1 170 0 180 2 190 0 200 0 210 0 220 0 230 0 240 2 -------------------------------------------- A3SS stats for lengths (in Mb) of gene items in event gff gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19 gffName: A3SS.hg19.gff3 Q1 0.000873 median 0.001723 Q3 0.003937 average 0.013791 min -0.002440 max 90.101800 count 14960 total 206.309608 standard deviation 0.737491 0 ************************************************************ 14959 10 0 20 0 30 0 40 0 50 0 60 0 70 0 80 0 90 1 -------------------------------------------- SE stats for lengths (in Mb) of gene items in event gff gffDir: /hive/groups/wet/illumina/geneModels/hg19/miso_gff/hg19 gffName: SE.hg19.gff3 Q1 0.003207 median 0.006770 Q3 0.015347 average 0.020211 min -0.022779 max 90.101500 count 39232 total 792.911753 standard deviation 0.643884 0 ************************************************************ 39230 10 0 20 0 30 0 40 0 50 0 60 0 70 0 80 0 90 2