[ensembl-dev] issue with my script to fetch genes from a file using API

[Hans-Rudolf Hotz]

Hi Nathalie


What do you mean you only get "1 gene name"?


Well, I copy/paste'd your script and run it with a short version of your 
file (ie the first five lines) and I got back the following two lines:
1	gain	38934531	38934531	38934531	38934531	Chst10 
PPAB_21_9f_PT_251469518757.txt,PPAB_21_9g_PT_251469518753.txt,PPAB_27_9c_PT_251469518755.txt
1	gain	74668174	74678672	74668174	74678672	Stk36 
PPAA_3_4g_PT_251469518838.txt,PPAB_3_6b_PT_251469518594.txt

without any errors/problems.


If I run the complete file, I get your error as soon as I ask for 
chromosome 20

maybe you should change

my $slice_adaptor = $registry->get_adaptor('Mouse', 'Core', 'Slice');

to

my $slice_adaptor = $registry->get_adaptor('Human', 'Core', 'Slice');


and then your script runs through the whole file.



Regards, Hans



On 11/02/2011 04:18 PM, Nathalie Conte wrote:
> HI, I have a file see format attached
> basically the coordinates of the regions I want to retrieve genes from
> are column 1( chromosome) 5(start) and 6(end)
> I used this script to parse through the file and give my external gene
> names , in the output I get only 1 gene name and a message:
> Can't call method "get_all_Genes" on an undefined value at
> ./fetch_gene_API.pl line 34.
> I don't understand where this comes from , I wanted to check whether you
> could help/advise
> thanks
> Nathalie
>
> #!/software/bin/perl
> use warnings;
> use strict;
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
> #use lib "/nfs/team82/nac/amy/may2011/lib";
>
> my $registry = "Bio::EnsEMBL::Registry";
> $registry->load_registry_from_db(-host => 'ensembldb.ensembl.org', -user
> => 'anonymous');
> my $file =
> "/nfs/team82/nac/Roland/November_2011/PT_mcrs0.25T_50_2_20M_sdundo.bind_API.txt";
>
>
> unless (open(REGIONS, $file)){
> print "Cannot open file \"$file\"\n\n";
> }
>
> my @regions = <REGIONS>;
>
> close REGIONS;
> open(OUT,">PT_mcrs0.25T_50_2_20M_sdundo.bind_API_fetchGene.txt");
> my $slice_adaptor = $registry->get_adaptor('Mouse', 'Core', 'Slice');
>
> foreach my $region(@regions){
> chomp $region;
>
> my @coordinates = split(/\t/, $region);
>
> my $chromosome = $coordinates[0];
> my $start = $coordinates[4];
> my $end = $coordinates[5];
>
> my $slice = $slice_adaptor->fetch_by_region('chromosome',$chromosome,
> $start, $end);
>
>
> my $genes = $slice->get_all_Genes;
> foreach my $gene( @{$genes} ){
> print OUT
> $coordinates[0],"\t",$coordinates[1],"\t",$coordinates[2],"\t",$coordinates[3],"\t",$coordinates[4],"\t",$coordinates[5],"\t",$gene->external_name,"\t",$coordinates[6],
> "\n";
>
> }
> }
>
>
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