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