BioPython: How to set the order of qualifiers

Question

[mschmid]

I have the following code (just a snippet):

        ...
        my_feature.qualifiers["locus_tag"] = tmpStr
        my_feature.qualifiers["length"] = this_start - last_end
        my_feature.qualifiers["flanking_gene_1"] = last_gene_name
        my_feature.qualifiers["flanking_gene_2"] = this_gene
        seq_record.features.append(my_feature)
        ...

I want the qualifiers to be outputed to the genbank file in the order above.

But the result ist the folloing (flanking_gene_1 and flanking_gene_2 swapped):

 ...  
 IGR             263255..263440
                 /locus_tag="xyz_IGR_00165"
                 /length=186
                 /flanking_gene_2="xyz_01880"
                 /flanking_gene_1="xyz_01870"
 IGR             263801..263909
                 /locus_tag="xyz_IGR_00166"
                 /length=109
                 /flanking_gene_2="xyz_01890"
                 /flanking_gene_1="xyz_01880"
 ...

How do I set the order?

Thx Michael

Answer 1

[Peter]

The NCBI GenBank format doesn't explicitly document a preferred order for the key - does it actually matter in your use case?

Biopython just uses the dictionary order. You can deliberately control this by replacing my_feature.qualifiers with an ordered dictionary. e.g.

from collections import OrderedDict
...
my_feature.qualifiers = OrderedDict(my_feature.qualifiers)
my_feature.qualifiers["locus_tag"] = tmpStr
my_feature.qualifiers["length"] = this_start - last_end
my_feature.qualifiers["flanking_gene_1"] = last_gene_name
my_feature.qualifiers["flanking_gene_2"] = this_gene
seq_record.features.append(my_feature)
...

I'm assuming you are using Python 2.7 or later, this is slightly more complicated on Python 2.6