Mitogenome_reorder Error about mitoz HOT 6 CLOSED

Dear Vahap,

I checked my code and found there is a little bug in that script. I am sorry for that make your time.

Now you can use the attached script to reorder your mitogenome as the way you did. I will let Guanliang update this script later.

Best wishes,
Chentao
Mitogenome_reorder.py.zip

from mitoz.

Dear Guanliang,

There is another issue about useful script called "circle_check.py" when running this script, the output considers the mtDNA assembly as "linear", but however, the summary file of MitoZ output indicates the mtDNA assembly is circular. Could we clarify this issue?

cat jjj.mitogenome.fa

C108631;len=16571;topology=circular topology=linear

#Seq_id Length(bp) Circularity Closely_related_species
C108631 16571 yes Schistura scaturigina

Best wishes

from mitoz.

Dear Guanliang,

There is another issue about useful script called "circle_check.py" when running this script, the output considers the mtDNA assembly as "linear", but however, the summary file of MitoZ output indicates the mtDNA assembly is circular. Could we clarify this issue?

cat jjj.mitogenome.fa

C108631;len=16571;topology=circular topology=linear

#Seq_id Length(bp) Circularity Closely_related_species
C108631 16571 yes Schistura scaturigina

Best wishes

Dear Vahap,

The basic idea of circle_check.py script is to check if the two ends of a sequence are overlapping, regardless of the sequence title information. The overlapping region will be removed in the output.

So I think the MitoZ summary output saying "Circular" looks good.

If you run circle_check.py again with the "circularized" sequence, in which its two ends have no overlapping regions anymore, then circle_check.py will add topology=linear comment on the output title.

Best wishes,
Guanliang

from mitoz.

Dear Vahap,

I think this problem is raised by your sequence ID. I remember the assembly result generated by MitoZ looks like "C720972 topology=circular", there is " " after sequence id "C720972", not linked by ";".

In this case, the script Mitogenome_reorder.py will find topology information from string "topology=circular" which is defined as the description for a fasta sequence.
So, try to change the format of your sequence, it will work!

Best wishes,
Chentao

from mitoz.

Dear Guanliang & Chentao,

Thank you for the quick response but despite my numerous effort, I could not reorder our mtDNA like the reference. Here I am sharing the mtDNA assembly and reference genome with you and code, it will be perfect if you overcome this problem! Many thanks in advance for all your help.

Code:
python3 Mitogenome_reorder.py -f Ase1.fasta -r Schistura_longa.fasta

Schistura_longa.zip
Ase1.fasta.zip

from mitoz.

Dear Chentao,

Thank you for all your help, now, the script is working seamlessly with your help!

Best wishes!

from mitoz.