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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::Path qw(remove_tree);
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6 use Test::Files;
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7
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8 BEGIN { unshift( @INC, './lib' ) }
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9 $ENV{PATH} .= ":./bin";
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10
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11 BEGIN {
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12 use Test::Most;
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13 use_ok('Bio::Roary::ReformatInputGFFs');
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14 }
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15
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16
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17 my $obj;
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18 remove_tree('fixed_input_files');
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19 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff']), 'initialise with one input gff');
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20 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with one input gff');
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21 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff'] ,'list of gff files with one input gff, nothing should change');
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22 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist because there arent any fixed input files');
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23
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24
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25 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff',]), 'initialise with 2 input gffs');
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26 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
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27 is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_1.gff'),[
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28 '1_1',
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29 'abc_00002',
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30 'abc_00003',
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31 'abc_00004',
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32 '1_2'
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33 ],'extract ids');
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34 is_deeply($obj->_get_ids_for_gff_file('t/data/reformat_input_gffs/query_2.gff'),[
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35 '1_1',
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36 'abc_00002',
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37 'abc_00003',
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38 'abc_00004',
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39 '1_2'
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40 ],'extract ids');
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41 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 2 input gffs');
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42 ok(( -d 'fixed_input_files'), 'Directory should exist because there is one gff thats fixed');
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43 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files one in the fixed directory');
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44 ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
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45 compare_ok('fixed_input_files/query_2.gff', 't/data/reformat_input_gffs/expected_fixed_query_2.gff', 'fixed file should have expected changes');
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46 remove_tree('fixed_input_files');
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47
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48 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/query_1.gff', 't/data/reformat_input_gffs/query_2.gff', 't/data/reformat_input_gffs/query_3.gff']), 'initialise with 3 input gffs, 2 identical duplicates');
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49 ok(!( -d 'fixed_input_files'), 'Directory shouldnt exist before running');
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50 ok($obj->fix_duplicate_gene_ids, 'fix duplicates with 3 input gffs');
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51 ok(( -d 'fixed_input_files'), 'Directory should exist because there are 2 gffs thats fixed');
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52 is_deeply($obj->fixed_gff_files, ['t/data/reformat_input_gffs/query_1.gff','fixed_input_files/query_2.gff' ] ,'list of gff files 2 in the fixed directory');
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53 ok(( -e 'fixed_input_files/query_2.gff'), 'fixed file should exist');
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54 ok(!( -e 'fixed_input_files/query_3.gff'), 'fixed file should exist');
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55 compare_ok('fixed_input_files/query_2.gff','t/data/reformat_input_gffs/expected_fixed_query_2.gff', 'fixed file should have expected changes');
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56 remove_tree('fixed_input_files');
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57
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58
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59 ok($obj = Bio::Roary::ReformatInputGFFs->new(gff_files => ['t/data/reformat_input_gffs/real_1.gff']), 'initialise with 1 gff that has shown to have a bug');
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60 ok(my $fixed_file = $obj->_add_suffix_to_gene_ids_and_return_new_file('t/data/reformat_input_gffs/real_1.gff', 'id__'), 'fix duplicates');
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61 ok(( -e 'fixed_input_files/real_1.gff'), 'fixed file should exist');
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62 compare_ok('fixed_input_files/real_1.gff', 't/data/reformat_input_gffs/expected_real_1.gff', 'fixed file should have expected changes');
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63 remove_tree('fixed_input_files');
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64
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65
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66 done_testing();
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67
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