t/SeqIO/kegg.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 16);
  10
  11         use_ok('Bio::SeqIO::kegg');
  12 }
  13
  14 my $verbose = test_debug();
  15
  16 my $io = Bio::SeqIO->new(-format => 'kegg',
  17                                                                  -verbose => $verbose,
  18                                                                  -file => test_input_file('AHCYL1.kegg'));
  19 isa_ok($io, 'Bio::SeqIO');
  20 my $kegg = $io->next_seq();
  21 ok($kegg);
  22 isa_ok($kegg, 'Bio::Seq::RichSeq');
  23 is($kegg->accession, '10768');
  24 is($kegg->display_id, 'AHCYL1');
  25 is($kegg->alphabet, 'dna');
  26 is($kegg->seq,'atgtcgatgcctgacgcgatgccgctgcccggggtcggggaggagctgaagcaggccaaggagatcgaggacgccgagaagtactccttcatggccaccgtcaccaaggcgcccaagaagcaaatccagtttgctgatgacatgcaggagttcaccaaattccccaccaaaactggccgaagatctttgtctcgctcgatctcacagtcctccactgacagctacagttcagctgcatcctacacagatagctctgatgatgaggtttctccccgagagaagcagcaaaccaactccaagggcagcagcaatttctgtgtgaagaacatcaagcaggcagaatttggacgccgggagattgagattgcagagcaagacatgtctgctctgatttcactcaggaaacgtgctcagggggagaagcccttggctggtgctaaaatagtgggctgtacacacatcacagcccagacagcggtgttgattgagacactctgtgccctgggggctcagtgccgctggtctgcttgtaacatctactcaactcagaatgaagtagctgcagcactggctgaggctggagttgcagtgttcgcttggaagggcgagtcagaagatgacttctggtggtgtattgaccgctgtgtgaacatggatgggtggcaggccaacatgatcctggatgatgggggagacttaacccactgggtttataagaagtatccaaacgtgtttaagaagatccgaggcattgtggaagagagcgtgactggtgttcacaggctgtatcagctctccaaagctgggaagctctgtgttccggccatgaacgtcaatgattctgttaccaaacagaagtttgataacttgtactgctgccgagaatccattttggatggcctgaagaggaccacagatgtgatgtttggtgggaaacaagtggtggtgtgtggctatggtgaggtaggcaagggctgctgtgctgctctcaaagctcttggagcaattgtctacattaccgaaatcgaccccatctgtgctctgcaggcctgcatggatgggttcagggtggtaaagctaaatgaagtcatccggcaagtcgatgtcgtaataacttgcacaggaaataagaatgtagtgacacgggagcacttggatcgcatgaaaaacagttgtatcgtatgcaatatgggccactccaacacagaaatcgatgtgaccagcctccgcactccggagctgacgtgggagcgagtacgttctcaggtggaccatgtcatctggccagatggcaaacgagttgtcctcctggcagagggtcgtctactcaatttgagctgctccacagttcccacctttgttctgtccatcacagccacaacacaggctttggcactgatagaactctataatgcacccgaggggcgatacaagcaggatgtgtacttgcttcctaagaaaatggatgaatacgttgccagcttgcatctgccatcatttgatgcccaccttacagagctgacagatgaccaagcaaaatatctgggactcaacaaaaatgggccattcaaacctaattattacagatactaa');
  27 ok($kegg->translate->seq);
  28
  29 is(($kegg->annotation->get_Annotations('description'))[0]->text,
  30    'S-adenosylhomocysteine hydrolase-like 1 [EC:3.3.1.1]');
  31
  32 is(($kegg->annotation->get_Annotations('pathway'))[0]->text,
  33    'Metabolism; Amino Acid Metabolism; Methionine metabolism');
  34
  35 is( (grep {$_->database eq 'KO'}
  36      $kegg->annotation->get_Annotations('dblink'))[0]->comment,
  37     'adenosylhomocysteinase' );
  38
  39 is( (grep {$_->database eq 'PATH'}
  40      $kegg->annotation->get_Annotations('dblink'))[0]->primary_id,
  41     'hsa00271' );
  42
  43 is( ($kegg->annotation->get_Annotations('aa_seq'))[0]->text,
  44 'MSMPDAMPLPGVGEELKQAKEIEDAEKYSFMATVTKAPKKQIQFADDMQEFTKFPTKTGRRSLSRSISQSSTDSYSSAASYTDSSDDEVSPREKQQTNSKGSSNFCVKNIKQAEFGRREIEIAEQDMSALISLRKRAQGEKPLAGAKIVGCTHITAQTAVLIETLCALGAQCRWSACNIYSTQNEVAAALAEAGVAVFAWKGESEDDFWWCIDRCVNMDGWQANMILDDGGDLTHWVYKKYPNVFKKIRGIVEESVTGVHRLYQLSKAGKLCVPAMNVNDSVTKQKFDNLYCCRESILDGLKRTTDVMFGGKQVVVCGYGEVGKGCCAALKALGAIVYITEIDPICALQACMDGFRVVKLNEVIRQVDVVITCTGNKNVVTREHLDRMKNSCIVCNMGHSNTEIDVTSLRTPELTWERVRSQVDHVIWPDGKRVVLLAEGRLLNLSCSTVPTFVLSITATTQALALIELYNAPEGRYKQDVYLLPKKMDEYVASLHLPSFDAHLTELTDDQAKYLGLNKNGPFKPNYYRY');
  45
  46 is( ($kegg->annotation->get_Annotations('position'))[0]->text, '1:join(26813..26932,50794..50905,52974..53117,54122..54222,54657..
  47             54759,56523..56617,57185..57291,58104..58220,58427..58490,59255..
  48             59343,59706..59776,60133..60227,60312..60410,60811..60879,61308..
  49             61386,62491..62611,63434..63440)');
  50
  51 is($kegg->species->common_name , 'H.sapiens');