Hi everybody,
It is not the first time I meet the issue. GFF3 format allows to have lines that are not features like ###. But using Bio::Tools::GFF I don't find any method allowing to print that kind of non-feature lines.
Does someone know a way to perform that task ? I'm only interested in Perl solution.
Thank you !
2 answers
Here is the code that actually works after I did some digging. It's a little bit of a hack but I don't believe it will cause any problems. Also I changed it to Bio::FeatureIO which I think is a little more mainstream. In this one-liner, ### is printed to the output file after each input feature, but you can change it to however you want.
perl -MBio::FeatureIO -e '
$in=Bio::FeatureIO->new(-file=>"in.gff");
$out=Bio::FeatureIO->new(-file=>">tmp.gff");
$fh=$out->{"_filehandle"};
while($feat=$in->next_feature){
$out->write_feature($feat);
print $fh "###\n";
}
'
The method fh() actually performs some tie and Symbol::gensym magic which I found in the source code. This magic forces you to use a feature object when you write to the file.
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
To get around that, I found that the filehandle is actually embedded in the object's variables, under _filehandle. Therefore you can exploit $out->{"_filehandle"} by printing to it directly.
Jean-Karim is correct that the GFF module will probably only output features. However, you probably can manually write to the file in your perl script! There is a method called $obj->fh which returns the filehandle of your GFF object. Therefore you could write to the file as desired. For example:
$gffObj->write_feature($something);
# Get the filehandle
my $fh=$gffObj->fh;
# Print comments to the file
print $fh "###\n";
$gffObj->write_feature($something2);
$gffObj->close
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Could you write an example of what you'd like to see in the GFF3 file?
Something like:
It seems Bio::Tools::GFF can only output features. The solution is to output the non-feature lines yourself. If you want to use forward reference closing (###), you could output relevant features with Bio::Tools::GFF then output ### then output the next batch of features and so on. If that's not convenient, you could output all features then insert the non-feature lines. You would need to keep track of where they should go in the file. Also you could do this in memory before actually printing everything to file.
I wanted to print directly in a file, but to put everything in memory before to print it seems to be the only convenient solution. I'm a bit worry because my files are over 2gb ... so I hope my computer can digest it easily.