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#!/usr/bin/perl -w
##
# args.pl
#
# Basic tests to ensure that bad combinations of arguments are rejected
# and good ones are accepted.
#
my $bowtie = "./bowtie";
my $bowtie_build = "./bowtie-build";
my $bowtie_l = $bowtie . " --large-index";
if(system("$bowtie --version") != 0) {
print STDERR "Could not execute ./bowtie; looking in PATH...\n";
$bowtie = `which bowtie`;
chomp($bowtie);
if(system("$bowtie --version") != 0) {
die "Could not find bowtie in current directory or in PATH\n";
}
}
if(! -f "e_coli_c.1.ebwt") {
print STDERR "Making colorspace e_coli index\n";
if(system("$bowtie_build --version") != 0) {
print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
$bowtie_build = `which $bowtie_build`;
chomp($bowtie_build);
if(system("$bowtie_build --version") != 0) {
die "Could not find bowtie-build in current directory or in PATH\n";
}
}
system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
} else {
print STDERR "Colorspace e_coli index already present...\n";
}
if(! -f "e_coli_c.1.ebwtl") {
print STDERR "Making large colorspace e_coli index\n";
my $bowtie_build = "./bowtie-build --large-index";
if(system("$bowtie_build --version") != 0) {
print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
$bowtie_build = `which $bowtie_build`;
chomp($bowtie_build);
if(system("$bowtie_build --version") != 0) {
die "Could not find bowtie-build in current directory or in PATH\n";
}
}
system("$bowtie_build -C genomes/NC_008253.fna e_coli_c") && die;
} else {
print STDERR "Colorspace e_coli index already present...\n";
}
if(! -f "e_coli.1.ebwt") {
system("$bowtie_build genomes/NC_008253.fna e_coli") && die;
} else {
print STDERR "e_coli index already present...\n";
}
if(! -f "e_coli.1.ebwtl") {
system("$bowtie_build --large-index genomes/NC_008253.fna e_coli") && die;
} else {
print STDERR "e_coli index already present...\n";
}
open TMP, ">.args.pl.1.fa" || die;
print TMP ">\nT0120012002012030303023\n";
close(TMP);
open TMP, ">.args.pl.1.qv" || die;
print TMP ">\n10 11 12 10 10 11 12 10 10 12 10 22 33 23 13 10 12 23 24 25 26 27\n";
close(TMP);
open TMP, ">.args.pl.2.qv" || die;
print TMP ">\n9 10 11 12 10 10 11 12 10 10 12 10 22 33 23 13 10 12 23 24 25 26 27\n";
close(TMP);
my @bad = (
"-n 6".
"-v 6",
"-n 4",
"-v 4",
"-v 2 -n 4",
"-v -1",
"-n -10",
"-3 -3",
"-5 -1",
"-e -1",
"-l 4",
"-l 0"
);
my @badEx = (
"e_coli -f .args.pl.1.fa -Q .args.pl.1.qv",
"e_coli_c -f .args.pl.1.fa -Q .args.pl.1.qv"
);
my @good = (
"-n 0",
"-n 1",
"-n 2",
"-n 3",
"-v 0",
"-v 1",
"-v 2",
"-v 3",
"-v 3 -n 3"
);
my @goodEx = (
"-C e_coli_c -f .args.pl.1.fa -Q .args.pl.1.qv",
"-C e_coli_c -f .args.pl.1.fa -Q .args.pl.2.qv"
);
sub run($) {
my $cmd = shift;
print "$cmd\n";
return system($cmd);
}
print "Bad:\n";
for my $a (@bad) {
run("$bowtie $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie should have rejected: \"$a\"\n";
run("$bowtie --debug $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
run("$bowtie_l --debug $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
print "PASSED: bad args \"$a\"\n";
}
print "\nBadEx:\n";
for my $a (@badEx) {
run("$bowtie $a /dev/null") != 0 || die "bowtie should have rejected: \"$a\"\n";
run("$bowtie --debug $a /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
run("$bowtie_l --debug $a /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
print "PASSED: bad args \"$a\"\n";
}
print "\nGood:\n";
for my $a (@good) {
run("$bowtie $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie should have accepted: \"$a\"\n";
run("$bowtie --debug $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
run("$bowtie_l --debug $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
print "PASSED: good args \"$a\"\n";
}
print "\nGoodEx:\n";
for my $a (@goodEx) {
run("$bowtie $a /dev/null") == 0 || die "bowtie should have accepted: \"$a\"\n";
run("$bowtie --debug $a /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
run("$bowtie_l --debug $a /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
print "PASSED: good args \"$a\"\n";
}
|
