1#!/bin/sh -e 2 3########################################################################## 4# Function description: 5# Pause until user presses return 6########################################################################## 7 8pause() 9{ 10 local junk 11 12 printf "Press return to continue..." 13 read junk 14} 15 16if [ $0 != ./small-test.sh ]; then 17 printf "Must be run as ./small-test.sh" 18 exit 19fi 20 21rm -f small-test-augmented*.bed small-test-overlaps.tsv 22cd .. 23make clean all 24cd Small-test 25 26printf "Viewing pruned GFF input...\n" 27pause 28awk '{ if ( $0 ~ "^#" ) print $0; else printf("%s\t%u\t%u\t%u\t%s(%s)\n", 29 $1, $4, $5, $5 - $4, $3, $7); }' small-test.gff3 | more 30 31printf "Running peak-classifier...\n" 32pause 33../peak-classifier small-test.bed small-test.gff3 small-test-overlaps.tsv 34 35printf "Viewing augmented GFF data...\n" 36pause 37more small-test-augmented.bed 38 39printf "Viewing sorted GFF data...\n" 40pause 41more small-test-augmented+sorted.bed 42 43printf "Viewing overlaps...\n" 44pause 45more small-test-overlaps.tsv 46 47printf "Filtering overlaps...\n" 48pause 49../filter-overlaps small-test-overlaps.tsv small-test-filtered.tsv intron exon 50more small-test-filtered.tsv 51