<div dir="ltr">I believe the main problem is that this Variation feature, for some reason does not have a splice attached to it<font color="#000000" face="Courier New, Courier, monospace"><span style="font-size:12.222222328186035px;line-height:15.989583969116211px"> : </span></font><span style="font-family:arial,sans-serif;font-size:13.333333969116211px">'slice' => undef</span><div>
<span style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13.333333969116211px">so the method to extract the slice and expand </span></div>
<div><span style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></span></div><div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">471: my $slice = $self->feature_Slice->expand(</font></div>
<div><font face="arial, sans-serif">472: MAX_DISTANCE_FROM_TRANSCRIPT,</font></div><div><font face="arial, sans-serif">473: MAX_DISTANCE_FROM_TRANSCRIPT</font></div><div><font face="arial, sans-serif">474: );</font></div>
<div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></div></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Fails.</div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">
<br></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Anyone knows what might be causing this?</div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">
Best regards</div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br>Duarte</div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br></div><div><span style="font-family:arial,sans-serif;font-size:13.333333969116211px"><br>
</span></div></div><div class="gmail_extra"><br clear="all"><div><font style="background-color:rgb(255,255,255)" color="#999999">=========================<br> Duarte Miguel Paulo Molha <br></font><div><font style="background-color:rgb(255,255,255)" color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>
=========================</font></div></div>
<br><br><div class="gmail_quote">On Wed, Jul 31, 2013 at 5:05 PM, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">In an effort to understand better what might be causing this ... here is a dumb of one such object causing the error message:<div><br></div><div>the VCF line:</div><div>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample-01 sample-02 sample-03 sample-04 sample-05 sample-06<br>
</div><div>1<span style="white-space:pre-wrap"> </span>I777437<span style="white-space:pre-wrap"> </span>I.<span style="white-space:pre-wrap"> </span>IA<span style="white-space:pre-wrap"> </span>IC<span style="white-space:pre-wrap"> </span>I667.93<span style="white-space:pre-wrap"> </span>IPASS<span style="white-space:pre-wrap"> </span>IAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2<span style="white-space:pre-wrap"> </span>IGT:AD:DP:GQ:PL<span style="white-space:pre-wrap"> </span>I0/0:60,0:60:99:0,138,1819<span style="white-space:pre-wrap"> </span>I0/0:82,0:82:99:0,205,2614<span style="white-space:pre-wrap"> </span>I0/1:52,28:80:99:706,0,1290<span style="white-space:pre-wrap"> </span>I0/0:100,0:100:99:0,253,3074<span style="white-space:pre-wrap"> </span>I0/0:83,0:83:99:0,178,2360<span style="white-space:pre-wrap"> </span>I0/0:82,0:82:99:0,166,2135<br>
</div><div><br></div><div>at line 471 of /Bio/EnsEMBL/Variation/VariationFeature.pm</div><div><br></div><div>my object $self contains:</div><div><br><div><div>0 Bio::EnsEMBL::Variation::VariationFeature=HASH(0x57802b0)</div>
<div> '_line' => "1\cI777437\cI.\cIA\cIC\cI667.93\cIPASS\cIAC=1;AF=0.083;AN=12;BaseQRankSum=6.089;DP=487;Dels=0.00;FS=1.662;HRun=0;HaplotypeScore=0.9613;MQ=44.32;MQ0=49;MQRankSum=-1.435;QD=8.35;ReadPosRankSum=-1.520;SB=-247.14;set=variant2\cIGT:AD:DP:GQ:PL\cI0/0:60,0:60:99:0,138,1819\cI0/0:82,0:82:99:0,205,2614\cI0/1:52,28:80:99:706,0,1290\cI0/0:100,0:100:99:0,253,3074\cI0/0:83,0:83:99:0,178,2360\cI0/0:82,0:82:99:0,166,2135"</div>
<div> 'adaptor' => Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor=HASH(0x4b06030)</div><div> '_is_multispecies' => ''</div><div> 'db' => Bio::EnsEMBL::Variation::DBSQL::DBAdaptor=HASH(0x52b4f08)</div>
<div> '_dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)</div><div> '_dbname' => 'homo_sapiens_variation_72_37'</div><div> '_driver' => 'mysql'</div>
<div> '_host' => '<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a>'</div><div> '_port' => 5306</div><div> '_query_count' => 4</div>
<div> '_timeout' => 0</div><div> '_username' => 'anonymous'</div><div> 'connected32406' => 1</div><div> 'db_handle32406' => DBI::db=HASH(0x51e5ee8)</div>
<div> empty hash</div><div> 'reconnect_when_lost' => 1</div><div> '_group' => 'variation'</div><div> '_is_multispecies' => ''</div>
<div> '_no_cache' => 1</div><div> '_species' => 'homo_sapiens'</div><div> '_species_id' => 1</div><div> 'dbc' => Bio::EnsEMBL::DBSQL::DBConnection=HASH(0x52b50d0)</div>
<div> -> REUSED_ADDRESS</div><div> 'species_id' => 1</div><div> 'allele_string' => 'A'</div><div> 'chr' => 1</div><div> 'end' => 777437</div><div>
'existing' => ARRAY(0x10861900)</div>
<div> empty array</div><div> 'genotype' => ARRAY(0x577ff80)</div><div> 0 'A'</div><div> 1 'A'</div><div> 'individual' => 'sample-01'</div><div> 'map_weight' => 1</div>
<div> 'non_variant' => 1</div><div> 'phased' => 1</div><div> 'slice' => undef</div><div> 'start' => 777437</div><div> 'strand' => 1</div><div> 'variation_name' => '1_777437_A'</div>
</div><div><br></div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br clear="all"><div><font style color="#999999">=========================<br> Duarte Miguel Paulo Molha <br>
</font><div><font style color="#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</font></div></div><div><div class="h5">
<br><br><div class="gmail_quote">On 31 July 2013 13:52, Duarte Molha <span dir="ltr"><<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><p>Hi Devs</p>
<p> I have been trying to run a VCF file by the variant
annotation script and I've been getting a warning message that I have never
before encountered..</p><p></p>
<p> I was wondering if someone could let me know if it is
something I am doing wrong…</p><p></p>
<p> The message is :</p><p></p>
<p> <b>Can't call method "expand" on an undefined value
at <sic>/Bio/EnsEMBL/Variation/VariationFeature.pm line 471</b></p><p><b></b></p>
<p><b> </b></p>
<p>Here are the configuration options I am using:</p>
<p> </p>
<p>Configuration options:</p>
<p> ###</p><p></p>
<p>allow_non_variant 1</p>
<p>cache 1</p>
<p>canonical 1</p>
<p>ccds 1</p>
<p>check_alleles 1</p>
<p>check_existing 1</p>
<p>config
vep_human.ini</p>
<p>core_type
core</p>
<p>custom
./vep_additional_annotations/Somatic_variation_phenotypes.bed.gz,Somatic,bed,exact
./vep_additional_annotations/dbsnp135_ensembl_variation_phenotype.bed.gz,dbsnp135,bed,exact</p>
<p>db_version
72</p>
<p>dir
/ReferenceData/vep_cache</p>
<p>dir_cache
/ReferenceData/vep_cache</p>
<p>dir_plugins
./Plugins</p>
<p>domains 1</p>
<p>force_overwrite 1</p>
<p>fork 5</p>
<p>gmaf 1</p>
<p>hgnc 1</p>
<p>host
<a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a></p>
<p>individual all</p>
<p>input_file All_BOTH_SNPINDELfilter_PASSED.vcf</p>
<p>maf_1kg 1</p>
<p>numbers 1</p>
<p>output_file All_BOTH_SNPINDELfilter_PASSED.ann</p>
<p>plugin
OGT_NHBLI_MAF,/ReferenceData/NHLBI_EVS/NHLBI_OGT.gz OGT_selected_VCF_fields_output Blosum62 Carol
OGT_Condel,b OGT_Grantham TSSDistance Downstream</p>
<p>polyphen b</p>
<p>port
5306</p>
<p>protein 1</p>
<p>regulatory 1</p>
<p>sift b</p>
<p>species
homo_sapiens</p>
<p>stats
HASH(0x4370ad8)</p>
<p>terms
SO</p>
<p>verbose 1</p>
<p> </p>
<p>I would be very grateful for your help.</p><span><font color="#888888">
<p> Duarte Molha</p>
</font></span></div>
</blockquote></div><br></div></div></div>
</blockquote></div><br></div>