Changeset 10 for test


Ignore:
Timestamp:
Apr 27, 2010, 4:30:24 PM (9 years ago)
Author:
maarten
Message:

reference

File:
1 edited

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Added
Removed
  • test/test.pl

    r9 r10  
    1010use Omim2dbsnp;
    1111use Bio::Phenotype::OMIM::OMIMparser;
    12 use Test::More tests =>71;
     12use Test::More tests =>77;
    1313
    1414#lib "../lib";
     
    1818my $omim2pubmed = Omim2Pubmed->new();
    1919$omim2pubmed->loadpubmed_cited($pubmedcited);
     20
    2021my $omim_parser =
    2122  Bio::Phenotype::OMIM::OMIMparser->new( -omimtext => $filename );
     
    2526my $dbsnpref="../data/dbsnp-to-OMIM.cvs";
    2627my $dbsnp=Omim2dbsnp->new();
    27 $dbsnp->loadCrossReference($dbsnpref);
     28print($dbsnp->loadCrossReference($dbsnpref));
    2829$PAV->addOmim2dbsnp($dbsnp);
     30
     31
    2932is($PAV->{Omim2DBsnp}->getdbsnp("600046","0025"),"3890182","testing getdbsnp only with numbers");
    3033is($PAV->{Omim2DBsnp}->getdbsnp("600046","0025a"),"3890182","testing getdbsnp  with numbers and junk");
    3134
    3235
    33 
     36is($PAV->{Omim2DBsnp}->getdbsnp("600046","0014"),"28937313","dbsnp");
    3437
    3538my $string =
     
    146149is( ProccesAllicVariants::getDeceaseID($string), "161800", "get decease id" );
    147150is(
    148         ProccesAllicVariants::extractnuclitdemutation( $string, "999" ),
     151        ProccesAllicVariants::extractnuclitdemutation( $string, "999",0 ),
    149152        "heterozygous G-to-C transversion in exon 2",
    150153        "extract exon info"
     
    169172
    170173is(
    171         ProccesAllicVariants::extractnuclitdemutation( $string, "74" ),
     174        ProccesAllicVariants::extractnuclitdemutation( $string, "74" ,0),
    172175        "222G-T transversion",
    173176        "get mutation 222G-T transversion"
     
    176179is(
    177180        ProccesAllicVariants::extractnuclitdemutation(
    178                 "RGF 222G-T transversion ASD", "74"
     181                "RGF 222G-T transversion ASD", "74",0
    179182        ),
    180183        "222G-T transversion",
     
    183186
    184187is(
    185         ProccesAllicVariants::extractnuclitdemutation( $string, "75" ),
     188        ProccesAllicVariants::extractnuclitdemutation( $string, "75",0 ),
    186189        "223C-T transition",
    187190        "get mutation 223C-T transition"
     
    191194
    192195is(
    193         ProccesAllicVariants::extractnuclitdemutation( " A-to-G transition at nucleotide 1730 in exon 13, resulting in the substitu exon 34", "75" ),
     196        ProccesAllicVariants::extractnuclitdemutation( " A-to-G transition at nucleotide 1730 in exon 13, resulting in the substitu exon 34", "75",0 ),
    194197        "A-to-G transition at nucleotide 1730 in exon 13",
    195198        "nucleotide with exon"
     
    197200
    198201is(
    199         ProccesAllicVariants::extractnuclitdemutation( " bedu drg r g r syhrt eyh5tr r wefess AAG-to-AAC change bla", "75" ),
     202        ProccesAllicVariants::extractnuclitdemutation( " bedu drg r g r syhrt eyh5tr r wefess AAG-to-AAC change bla", "75" ,0),
    200203        "AAG-to-AAC",
    201204        "nucleotide as tripple AAG-to-AAC"
     
    204207
    205208is(
    206         ProccesAllicVariants::extractnuclitdemutation("on on 1 chromosome in the proband was a T-to-C transition predicted to result in a cys1417-to-arg substitution.The mutation was located in exon 30","10"),"T-to-C transition in exon 30","T-to-C transition BLABLA in exon 30");
     209        ProccesAllicVariants::extractnuclitdemutation("on on 1 chromosome in the proband was a T-to-C transition predicted to result in a cys1417-to-arg substitution.The mutation was located in exon 30","10",0),"T-to-C transition in exon 30","T-to-C transition BLABLA in exon 30");
    207210#acta .00010
    208211$string = "In 5 affected members spanning 3 generations of a Chinese family with
     
    217220
    218221is(
    219         ProccesAllicVariants::extractnuclitdemutation( $string, "334" ),
     222        ProccesAllicVariants::extractnuclitdemutation( $string, "334",0 ),
    220223        "1110A-C transversion",
    221224        "get 1110A-C transversion"
     
    300303is(
    301304        ProccesAllicVariants::formatInDelMutation( "5-BP INS, NT3171","") ,
    302         "",
    303         ""
    304 );
    305 is(
    306         ProccesAllicVariants::formatInDelMutation( "","") ,
    307         "",
    308         ""
    309 );
    310 
    311 is(
    312         ProccesAllicVariants::formatInDelMutation( "","") ,
    313         "",
    314         ""
    315 );
    316 
    317 is(
    318         ProccesAllicVariants::formatInDelMutation( "","") ,
    319         "",
    320         ""
    321 );
     305        "3171_3172ins",
     306        "3171_3172ins"
     307);
     308is(
     309        ProccesAllicVariants::formatInDelMutation( "IVS9, G-T,-1","") ,
     310        "IVS9-1G>T",
     311        "IVS9-1G>T"
     312);
     313
     314is(
     315        ProccesAllicVariants::formatInDelMutation( "IVS9, G-T,+1","") ,
     316        "IVS9+1G>T",
     317        "IVS9+1G>T"
     318);
     319#col7a1.0030
     320is(
     321        ProccesAllicVariants::formatInDelMutation( "IVS2AS, G-C, -1","mal recessive pretibial epidermolysis bullosa (131850), Gardella et al. (2002) reported a splicing mutation in the COL7A1 gene, 267-1G-C, which abolis") ,
     322        "267-1G>C",
     323        "267-1G>C"
     324);
     325#601691.0019
     326is(
     327        ProccesAllicVariants::formatInDelMutation( "IVS5AS, A-G, -2","d a homozygous acceptor splice site mutation in the ABCA4 gene, an A-to-G change in intron 5 at position -2.") ,
     328        "IVS5-2A>G",
     329        "IVS5-2A>G"
     330);
     331
    322332
    323333
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