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1 #!/usr/bin/env perl
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2 use strict;
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3 use warnings;
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4 use Data::Dumper;
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5 use File::Basename;
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6
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7 BEGIN { unshift( @INC, './lib' ) }
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8 $ENV{PATH} .= ":./bin";
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9
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10 BEGIN {
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11 use Test::Most;
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12 use_ok('Bio::Roary::PrepareInputFiles');
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13 }
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14
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15 my $obj;
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16
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17 ok(
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18 $obj = Bio::Roary::PrepareInputFiles->new(
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19 input_files => [
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20 't/data/example_annotation.gff', 't/data/example_1.faa',
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21 't/data/example_annotation_2.gff', 't/data/example_2.faa','t/data/sequences_with_unknowns.faa'
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22 ],
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23 ),
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24 'initalise'
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25 );
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26
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27 my @sorted_fasta_files = sort map { basename($_) } sort @{$obj->fasta_files};
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28 my @expected_fasta_files = sort((
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29 'example_1.faa.tmp.filtered.fa',
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30 'example_2.faa.tmp.filtered.fa',
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31 'example_annotation.gff.proteome.faa',
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32 'example_annotation_2.gff.proteome.faa',
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33 'sequences_with_unknowns.faa.tmp.filtered.fa'
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34 ));
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35
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36 is_deeply(
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37 \@sorted_fasta_files,
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38 \@expected_fasta_files,
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39 'proteome extracted from gff files, input fasta files filtered'
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40 );
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41
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42 my @input_files_lookup = sort map { basename($_) } @{$obj->lookup_fasta_files_from_unknown_input_files( [ 't/data/example_annotation_2.gff', 't/data/example_1.faa' ] )};
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43 is_deeply(
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44 \@input_files_lookup,
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45 ['example_1.faa.tmp.filtered.fa','example_annotation_2.gff.proteome.faa'],
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46 'previously created faa file looked up from gff filename'
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47 );
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48
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49 unlink('example_annotation.gff.proteome.faa');
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50 unlink('example_annotation_2.gff.proteome.faa');
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51 unlink('sequences_with_unknowns.faa.tmp.filtered.fa');
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52 unlink('example_1.faa.tmp.filtered.fa');
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53 unlink('example_2.faa.tmp.filtered.fa');
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54
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55 done_testing();
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56
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