Changeset 9 for test


Ignore:
Timestamp:
Apr 22, 2010, 6:35:36 PM (10 years ago)
Author:
maarten
Message:

Fixed file names and parsing indels

File:
1 edited

Legend:

Unmodified
Added
Removed
  • test/test.pl

    r8 r9  
    1010use Omim2dbsnp;
    1111use Bio::Phenotype::OMIM::OMIMparser;
    12 use Test::More tests => 62;
     12use Test::More tests =>71;
    1313
    1414#lib "../lib";
     
    197197
    198198is(
     199        ProccesAllicVariants::extractnuclitdemutation( " bedu drg r g r syhrt eyh5tr r wefess AAG-to-AAC change bla", "75" ),
     200        "AAG-to-AAC",
     201        "nucleotide as tripple AAG-to-AAC"
     202);
     203
     204
     205is(
    199206        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");
    200207#acta .00010
     
    225232print("\ntesting format of deletions inserts and other awkward mutations\n");
    226233is(
    227         ProccesAllicVariants::formatInDelMutation("1-BP DEL, 1764G") ,
     234        ProccesAllicVariants::formatInDelMutation("1-BP DEL, 1764G","") ,
    228235        "1764delG",
    229236        "1-BP DEL, 1764G"
    230237);
    231 
    232 is(
    233         ProccesAllicVariants::formatInDelMutation( "2-BP DEL, 3283TC") ,
     238#600046.0004
     239is(
     240        ProccesAllicVariants::formatInDelMutation("3-BP DEL","In a French-Canadian family with familial high density lipoprotein deficiency (604091) previously reported by Marcil et al. (1995), Brooks-Wilson et al. (1999) found a 3-bp deletion that resulted in loss of nucleotides 2017-2019 and deletion of a leucine at position 633, which is conserved in mouse and C. elegans") ,
     241        "2017_2019del",
     242        "3-BP DEL"
     243);
     244
     245#tected a change in codon 747 in
     246#601199.0008
     247
     248is(
     249        ProccesAllicVariants::formatInDelMutation( "2-BP DEL/1-BP INS, CCC747TC","athyroidism (239200), Pearce et al. (1995) detected a change in codon 747 in ") ,
     250        "2239_2240delCCCinsTC",
     251        "2239_2240delCCCinsTC"
     252);
     253
     254is(
     255        ProccesAllicVariants::formatInDelMutation( "2-BP DEL/1-BP INS,747TC","athyroidism (239200), Pearce et al. (1995) detected a change in codon 747 in ") ,
     256        "2239_2240delinsTC",
     257        "2239_2240delinsTC"
     258);
     259
     260is(
     261        ProccesAllicVariants::formatInDelMutation( "2-BP DEL, 3283TC","") ,
    234262        "3283_3284delTC",
    235263        "3283_3284delTC"
     
    237265
    238266is(
    239         ProccesAllicVariants::formatInDelMutation( "40-BP DEL, NT1294") ,
     267        ProccesAllicVariants::formatInDelMutation( "40-BP DEL, NT1294","") ,
    240268        "1294_1333del",
    241269        "1294_1333del"
     
    243271
    244272is(
    245         ProccesAllicVariants::formatInDelMutation( "1675A DEL") ,
     273        ProccesAllicVariants::formatInDelMutation( "1675A DEL","") ,
    246274        "1675delA",
    247275        "1675delA"
    248276);
    249277is(
    250         ProccesAllicVariants::formatInDelMutation( "1-BP INS, 1135A") ,
     278        ProccesAllicVariants::formatInDelMutation( "1-BP INS, 1135A","") ,
    251279        "1135_1136insA",
    252280        "1135_1136insA"
     
    254282
    255283is(
    256         ProccesAllicVariants::formatInDelMutation( "110-BP INS/14-BP DEL") ,
     284        ProccesAllicVariants::formatInDelMutation( "110-BP INS/14-BP DEL","") ,
    257285        "110-BP INS/14-BP DEL",
    258286        "110-BP INS/14-BP DEL"
    259287);
    260288is(
    261         ProccesAllicVariants::formatInDelMutation( "INT12-14 DEL") ,
     289        ProccesAllicVariants::formatInDelMutation( "INT12-14 DEL","") ,
    262290        "IVS12+?_IVS14+?del",
    263291        "IVS12+?_IVS14+?del"
     
    265293
    266294is(
    267         ProccesAllicVariants::formatInDelMutation( "INT12-14 DEL, INT16-31 DEL") ,
     295        ProccesAllicVariants::formatInDelMutation( "INT12-14 DEL, INT16-31 DEL"," nothing") ,
    268296        "IVS12+?_IVS14+?del,IVS16+?_IVS31+?del",
    269297        "IVS12+?_IVS14+?del,IVS16+?_IVS31+?del"
     
    271299#BRCA1.0033: 5-BP INS, NT3171. Als de nucleotiden in de tekst gespecificeerd worden, zouden we die graag terug zien, bijv. 3171_3172insAGTCG.
    272300is(
    273         ProccesAllicVariants::formatInDelMutation( "5-BP INS, NT3171") ,
     301        ProccesAllicVariants::formatInDelMutation( "5-BP INS, NT3171","") ,
    274302        "",
    275303        ""
    276304);
    277305is(
    278         ProccesAllicVariants::formatInDelMutation( "") ,
     306        ProccesAllicVariants::formatInDelMutation( "","") ,
    279307        "",
    280308        ""
     
    282310
    283311is(
    284         ProccesAllicVariants::formatInDelMutation( "") ,
     312        ProccesAllicVariants::formatInDelMutation( "","") ,
    285313        "",
    286314        ""
     
    288316
    289317is(
    290         ProccesAllicVariants::formatInDelMutation( "") ,
     318        ProccesAllicVariants::formatInDelMutation( "","") ,
    291319        "",
    292320        ""
     
    303331
    304332is( ( $PAV->getPubmedID( \@refs, "Ilkovski", "2001", $numb ) ),
    305         "11333380", "get omim record " );
     333        "{PMID11333380:Ilkovski (2001)}", "get omim record " );
    306334        #               $self->createAuthorsOutput( $refsref,$authorsAndYears, $numb  );
    307335         $authandyear=["Ilkovski", "2001"];
     
    322350@avs = $omim_entry->each_AllelicVariant();
    323351
    324 print(Dumper(@refs));
    325 is( ( $PAV->getPubmedID( \@refs, "Pitteloud", "2004", $numb ) ),
    326         "Pitteloud(2004) J. Clin. Endocr. Metab. 89 1053-1058 (2004)", "get omim record without omim number " );
    327        
     352
    328353
    329354is( ( $PAV->getPubmedID( \@refs, "Brown", "1989", $numb ) ),
    330         "2563196", "get omim record Brown " );
     355        "{PMID2563196:Brown (1989)}", "get omim record Brown " );
    331356               
    332 is( ( $PAV->getPubmedID( \@refs, "Lumbroso", "1996", $numb ) ),
    333         "8626869", "get omim record Lumbroso 100" );
    334        
    335         is( ( $PAV->getPubmedID( \@refs, "McPhaul", "1991", $numb ) ),
    336         "2010552", "get omim record  McPhaul 112" );
    337        
    338                 is( ( $PAV->getPubmedID( \@refs, "Migeon", "1981", $numb ) ),
    339         "6947233", "get omim record Migeon 120" );
    340        
    341                 is( ( $PAV->getPubmedID( \@refs, "Mononen", "2000", $numb ) ),
    342         "11103816", "get omim record  Mononen 123" );
    343        
    344                         is( ( $PAV->getPubmedID( \@refs, "Montie", "2009", $numb ) ),
    345         "19279159", "get omim record  Montie 124" );
    346        
    347 #                               is( ( $PAV->getPubmedID( \@refs, "", "", $numb ) ),
    348 #       "", "get omim record  " );
     357
    349358       
    350359is( ( $PAV->getPubmedID( \@refs, "Mooney", "2003", $numb ) ),
    351         "12682377", "get omim record Mooney " );
     360        "{PMID12682377:Mooney (2003)}", "get omim record Mooney " );
    352361       
    353362is( ( $PAV->getPubmedID( \@refs, "Trifiro", "1989", $numb ) ),
    354         "Trifiro (1989) (Abstract) Am. J. Hum. Genet. 45 (suppl.): A225, 1989", "get omim record whitout PMID" );
     363        "Trifiro(1989) (Abstract) Am. J. Hum. Genet. 45 (suppl.) A225 (1989)", "get omim record whitout PMID" );
    355364                       
    356365       
     
    370379
    371380is( ( $PAV->getPubmedID( \@refs, "Allikmets", "1997", $numb ) ),
    372         "Pitteloud(2004) J. Clin. Endocr. Metab. 89 1053-1058 (2004)", "get omim record without omim number " );
     381        "{PMID9295268:Allikmets (1997)}{PMID9054934:Allikmets (1997)}", "get omim record with 2 entries " );
     382#THYMIDINE PHOSPHORYLASE: TYMP<_;;TP;;
     383is(ProccesAllicVariants::getfilename("THYMIDINE PHOSPHORYLASE: TYMP",";;TP;;"),"TYMP","get name");
     384        is(ProccesAllicVariants::getfilename("LMBR1 DOMAIN-CONTAINING PROTEIN 1: LMBRD1",";;LMBD1;;"),"LMBRD1","get name");
     385                        is(ProccesAllicVariants::getfilename("V-MYC AVIAN MYELOCYTOMATOSIS VIRAL-RELATED ONCOGENE, NEUROBLASTOMA-DERIVED;","MYCN\n;; afas sfsdas "),"MYCN","get name");
     386        is(ProccesAllicVariants::getfilename("LMBR1 DOMAIN-CONTAINING PROTEIN 1: LMBRD1",";;LMBD1;;"),"LMBRD1","get name");
     387        is(ProccesAllicVariants::getfilename("TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL, SUBFAMILY M, MEMBER 6;","TRPM6"),"TRPM6","get name");
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