Adding Feature To Genbank In Biopython

Question

[Gorysko]

Dear all now I'm writing small script for adding feature to genbank file

"

from Bio import SeqIO

from Bio.SeqFeature import SeqFeature, FeatureLocation

record = SeqIO.read("mirum.gbk", "genbank")

for sub_feature in record.features:

    for  seq_record in SeqIO.parse("mirum_ort.fasta", "fasta"):

      dbxref = sub_feature.qualifiers.get("db_xref")

          if dbxref == seq.record:

              dbxref.append("ortholog")

"

But in general it's working without appending new feature in bioperl I've written such script which is looking like

"

use Bio::SeqIO;

$| = 1;

my $seqio_object = Bio::SeqIO->new(-file => "mirum.gbk" );

my $seq_object = $seqio_object->next_seq;

for my $feat_object ($seq_object->get_SeqFeatures)

    {

    for my $tag ($feat_object->get_all_tags)

            {

            if ($tag eq "db_xref")

                    {

                    for my $value ($feat_object->get_tag_values($tag))

                            {

                            if ($value =~ m/^([0-9]+)/)

                                    {

                                    my $gi_gbk = "$1";

                                    my $seqio_object_fasta = Bio::SeqIO->new(-file =>"mirum_ort.fasta" );

                                    while (my $seq_object_fasta = $seqio_object_fasta->next_seq)

                                            {

                                            my $gi_fasta = $seq_object_fasta->id();

                                            $gi_fasta =~ s/^gi\|([0-9]+)\|ref.*$/$1/;

                                            if ($gi_gbk eq $gi_fasta)

                                                    {

                                                    my $misc_feat = new Bio::SeqFeature::Generic(-start => $feat_object->location->start(), -end => $feat_object->location->end(), -strand => $feat_object->location->strand(), -primary$

                                                    $seq_object->add_SeqFeature($misc_feat);



                                                    }

                                            }



                                    }

                            }

                    }

            }

    }

my $seqio_object_out = Bio::SeqIO->new(-file => ">mirum_ort.gbk" );

$seqio_object_out->write_seq($seq_object);

"

But my interest is to write it in Biopython

What could You advice me to change in this script

Thank You

[Peter]

If you want to add a new feature, make a SeqFeature object. instead it looks like you are trying to add a database cross reference.

[Manu Prestat]

I really cannot answer, but I'm curious: why are you doing this? Thx

[Gorysko]

thnx you Peter ,you comment auiqte good in this situation