Comments (6)
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 scaturiginaBest 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.
Related Issues (20)
- Error encountered in mt_assembly using mitoz all command HOT 2
- How to introduce breakpoints? HOT 1
- overlap_information file empty and mitogenomes not circularised HOT 1
- How to make cirular map to linear? HOT 1
- I got an error when I install the taxdump.tar.gz into sqlite3, why ? HOT 2
- Open Reading Frame HOT 1
- Missing genes with Udocker HOT 4
- mitoz3.4 annotations draw circle diagrams all have a gap, but in other annotation platforms are circular HOT 13
- Annotation of Gene on Both Sides of Start and End Position Got Cut Off HOT 1
- Can not find assembly_file: HOT 13
- Incorrect stop codon HOT 8
- Mitoz is not working in different directory HOT 12
- samtools in draw_circos_for_mitogenome_auto_depth.pl line 138 HOT 4
- All sequences are low abundance (<10X) -- RNA Seq data HOT 3
- makeblastdb error with MitoZ3.5 using Singularity HOT 3
- Cnidaria HOT 1
- Hello. Platyhelminthes clade and taxa. HOT 4
- When using mitoz visualize --depth_file, there is no depth track in the resulting image HOT 4
- No QC.json file generated and run truncated HOT 1
- parameters_parser SyntaxError: invalid syntax HOT 4
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from mitoz.