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marbl / MetagenomeScope

Visualization tool for (meta)genome assembly graphs
https://marbl.github.io/MetagenomeScope/
GNU General Public License v3.0
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Write python script to convert node ID list / AGP file to FASTA file #43

Open fedarko opened 7 years ago

fedarko commented 7 years ago

From @fedarko on April 16, 2017 9:29

I guess the input to the script would be:

  1. the list of node IDs, created by the viewer application
  2. some source of DNA for nodes in the assembly graph in question. for GFA/LastGraph files I guess this would just be the original GFA/LastGraph file in question; for Bambus 3 GML files I guess this information would be contained in some .fa files or something.

The output would be a FASTA file containing all the DNA information in order, I guess? Ask to see what the ideal such format would be.

Copied from original issue: fedarko/MetagenomeScope#181

fedarko commented 6 years ago

This should work with AGP files, also.

(Apparently solutions exist for AGP -> FASTA -- see https://www.biostars.org/p/69964/.)