1#!/bin/sh 2# test for fastadiff utility 3 4FASTAREVCOMP="../../src/util/fastarevcomp" 5FASTADIFF="../../src/util/fastadiff" 6FASTALENGTH="../../src/util/fastalength" 7CALM="../data/cdna/calm.human.dna.fasta" 8CALM_RC="fastarevcomp.rc.test.fasta" 9CALM_RCRC="fastarevcomp.rc.rc.test.fasta" 10 11clean_exit(){ 12 rm -f $CALM_RC $CALM_RCRC 13 exit $1 14 } 15 16run_revcomp(){ 17 $FASTAREVCOMP $1 > $2 18 if [ $? -eq 0 ] 19 then 20 echo Reverse complement created : $1 21 else 22 echo Problem generating reverse complement : $1 23 clean_exit 1 24 fi 25 } 26 27run_revcomp $CALM $CALM_RC 28run_revcomp $CALM_RC $CALM_RCRC 29 30check_length(){ 31 $FASTALENGTH $1 | (read LENGTH IDENTIFIER 32 if [ $LENGTH -eq 2175 ] 33 then 34 echo RC length is the same 35 else 36 echo RC length changed 37 clean_exit 1 38 fi 39 ) 40 return 41 } 42 43check_length $CALM_RC 44check_length $CALM_RCRC 45 46$FASTADIFF -c no $CALM $CALM_RCRC 47if [ $? -eq 0 ] 48then 49 echo 2nd reverse complement same as original 50else 51 echo 2nd reverse complement not same as original 52 clean_exit 1 53fi 54 55clean_exit 0 56 57