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#!/bin/bash
set -e
pkg="alter-sequence-alignment"
CUR_DIR=`pwd`
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cp -a ${CUR_DIR}/alter-lib/src/main/java/* $AUTOPKGTEST_TMP
cp -a ${CUR_DIR}/alter-web/src/main/resources/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
gunzip -r *
echo "Test 1"
alter-sequence-alignment -i muscle.aln -ia -of FASTA -oo Linux -op MUSCLE -o test1
[ -s test1 ] || exit 1
rm -f ./test1
echo "PASS"
echo "Test 2"
alter-sequence-alignment -i tcoffee.aln -ia -of MSF -oo Linux -op TCoffee -o test2
[ -s test2 ] || exit 1
rm -f ./test2
echo "PASS"
echo "Test converter"
cat >TestAlter.java <<HERE
import es.uvigo.ei.sing.alter.converter.Converter;
import es.uvigo.ei.sing.alter.converter.DefaultFactory;
import es.uvigo.ei.sing.alter.parser.ParseException;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
public class TestAlter {
public static void main(String[] args) throws IOException {
Converter converter = new DefaultFactory().getConverter(
"Linux", // Input operating system (Linux, MacOS or Windows)
"clustal", // Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)
"NEXUS", // Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
false, // Autodetect format (other input options are omitted)
false, // Collapse sequences to haplotypes
true, // Treat gaps as missing data when collapsing
false, // Count missing data as differences when collapsing
0, // Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0)
"windows", // Output operating system (Linux, MacOS or Windows)
"general", // Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,
// ProtTest, RAxML, TCS, CodABC,
// BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,
// MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)
"aln", // Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)
false, // Low case output
false, // Output residue numbers (only ALN format)
false, // Sequential output (only NEXUS and PHYLIP formats)
false, // Output match characters
"MyConverterApp" // identifier for log messages
);
try {
String inputSequence = new String(Files.readAllBytes(Paths.get("clustal.nex")));
String converted = converter.convert(inputSequence);
System.out.println("converted file:");
System.out.println(converted);
} catch (ParseException e) {
System.err.println("the input file seems to contain errors");
e.printStackTrace();
}
}
}
HERE
CLASSPATH=".:/usr/share/java/alter-lib.jar:/usr/share/java/alter.jar"
javac TestAlter.java
java TestAlter
rm -f ./TestAlter*
echo "PASS"
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