Overview

dnaapler_wrapper.py is a Python script that respects the [topology=...] tags of contig headers:

• [topology=circular]: contigs are rotated (default Dnaapler behavior)
• [topology=linear]: contigs are reverse-complemented
• No topology tag: behavior depends on --default-topology; by default it raises an error

It is inspired by this issue: gbouras13/dnaapler#82

Installation

Simply run dnaapler_wrapper.py in the same environment where dnaapler is installed. It requires no additional dependencies.

Usage

Try python dnaapler_wrapper.py --help to see the available options.

Reasoning

I use NCBI PGAP FASTA headers after assembly and this may look as follows:

>contig_1 [topology=circular]
...
>contig_2 [topology=linear]
...
>contig_3
...

Dnaapler does not respect the [topology=...] tags and will simply rotate all of these contigs.

I only want it to rotate the contigs that are tagged as circular. This is what dnaapler_wrapper.py does.

The output for contigs 1 and 2 will be:

>contig_1 [topology=circular] [dnaapler=rotated] [dnaapler-gene=repA]
...
>contig_2 [topology=linear] [dnaapler=reverse-complement] [dnaapler-gene=repA]
...

For the ambiguous contig_3, the output depends on --default-topology:

1. raise: dnaapler_wrapper.py crashes: ValueError: Unknown topology in contig_3
2. linear: >contig_3 [dnaapler=reverse-complement] [dnaapler-gene=repA]
3. circular: >contig_3 [dnaapler=rotated] [dnaapler-gene=repA]