1#!/bin/sh 2# test for fastatranslate utility 3 4FASTATRANSLATE="../../src/util/fastatranslate" 5FASTASUBSEQ="../../src/util/fastasubseq" 6FASTADIFF="../../src/util/fastadiff" 7 8CDNA="../data/cdna/calm.human.dna.fasta" 9PROTEIN="../data/protein/calm.human.protein.fasta" 10 11CDS="fastatranslate.test.cds.fasta" 12TRANSLATED="fastatranslate.test.translated.fasta" 13 14clean_exit(){ 15 rm -rf $CDS $TRANSLATED 16 exit $1 17 } 18 19$FASTASUBSEQ $CDNA --start 103 --length 447 > $CDS 20if [ $? -eq 0 ] 21then 22 echo Extraced CDS for translation 23else 24 echo Problem extracting CDS for tranlation 25 clean_exit 1 26fi 27 28$FASTATRANSLATE $CDS --frame 1 > $TRANSLATED 29if [ $? -eq 0 ] 30then 31 echo Tranlated sequence 32else 33 echo Failed to tranlate sequence 34 clean_exit 1 35fi 36 37$FASTADIFF --checkids no $TRANSLATED $PROTEIN 38if [ $? -eq 0 ] 39then 40 echo Tranlsated sequence correct 41else 42 echo Translated sequence is wrong 43 clean_exit 1 44fi 45 46clean_exit 0 47 48