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Biopython's GenomeDiagram input files

Hi all

I am currently trying to draw up a synteny map using Biopython's GenomeDiagram package. I have been able to complete some examples with .gb files and now I want to try it on my own data.

Problem: my data is in fasta format. Any one with experience on this?

  1. Can GenomeDiagram use fasta files?
  2. Has anyone tried to convert fasta to genbank files?

Help will be much appreciated!

Regards

synteny genomediagram biopython
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updated by Ram Ram • written by ab.tsubaki • ab.tsubaki

can you post the code you've used with your genbank file?

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written by mgalactus mgalactus

GenomeDiagram doesn't draw sequences - they are just the horizontal scale/axis, what you draw is usually annotation/features along the sequence (as boxes, arrows, etc). You're probably using the annotation from a GenBank file (e.g. genes as SeqFeature objects), but do you have similar annotation for your FASTA sequences?

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updated by Ram Ram • written by Peter Peter

1 answer

Hi,

Sure, you can use fasta files to draw genome diagrams; you could provide the features you want to draw on top of the sequence from other files (say a gff file or a simple table you might have). You can convert a fasta file to a Genbank file with the following python script:

from Bio import SeqIO
SeqIO.write(SeqIO.parse('input.fasta', 'fasta'), 'output.gbk', 'genbank')

Marco

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updated by Ram Ram • written by mgalactus mgalactus

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