Join multiple SeqRecord with subfeatures in BioPython

Question

[Manuel Mendoza]

Hi folks,

I've created a function that generates a gene sequence and now I wanna concatenate n genes together. I've tried reiterative adding using a for loop but at the ned, al subfeatures of genes n > 1were lost...

>>> gene_a = sim_gene(n_exons = 3)
>>> gene_b = sim_gene(n_exons = 2)
>>> genes = gene_a + gene_b
>>> with open('genes.gff', "w") as out_handle:
...     GFF.write([genes], out_handle)

The output if the followign:

##gff-version 3
##sequence-region SimSeq 1 38054
SimSeq  sim gene    1   21056   .   +   .   ID=Gene_0
SimSeq  sim exon    1125    3249    .   +   .   Parent=Gene_0
SimSeq  sim exon    5514    11139   .   +   .   Parent=Gene_0
SimSeq  sim exon    13618   16410   .   +   .   Parent=Gene_0
SimSeq  sim gene    42113   59110   .   +   .   ID=Gene_1

And it should be this:

##gff-version 3
##sequence-region SimSeq 1 36058
SimSeq  sim gene    1   21056   .   +   .   ID=Gene_0
SimSeq  sim exon    1125    3249    .   +   .   Parent=Gene_0
SimSeq  sim exon    5514    11139   .   +   .   Parent=Gene_0
SimSeq  sim exon    13618   16410   .   +   .   Parent=Gene_0
SimSeq  sim gene    21057   38054   .   +   .   ID=Gene_1
SimSeq  sim exon    23948   25492   .   +   .   Parent=Gene_1
SimSeq  sim exon    29648   36058   .   +   .   Parent=Gene_1

If I export each gene generate independently, and then join the different gff it works but it's not smart at all...