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Synbiota / GENtle2

GENtle2 - Web-Based DNA Editor for Synthetic Biology
https://synbiota.com
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Loading some files from NCBI results in string of ??????????? #102

Open c0nn0r opened 11 years ago

c0nn0r commented 11 years ago

Hey @algrant ,

I'm trying to load whole genome of Actinomyces in GENtle via NCBI. I tried three from the list of hits after a search and they all loaded with script errors and producing a list of "???????????" question marks.

Same goes for search-term "Streptomyces"

I was able to load some of the smaller 10K's BPs from "Micromonospora", but not the larger ones.

These items are all important for the Antibiotics project - https://synbiota.com/projects/328/sequences

Mind you, these are large files in in the 100K's of BPs... But, they should still work. I've loaded bigger items in GENtle before without hitch.

What can we do to get these loading nicely?

c0nn0r commented 11 years ago

Same issue as listed in #90 from 5 months ago.

c0nn0r commented 11 years ago

Ok, so I did some experiments:

I made these files by hand for GENtle by cutting and pasting the text in an editor and saving the files.

http://files.synbiota.com/github/NZ_KI391970.fasta from http://www.ncbi.nlm.nih.gov/nuccore/551720208?report=fasta

and

http://files.synbiota.com/github/NZ_KI391970_genebank.txt from http://www.ncbi.nlm.nih.gov/nuccore/551720208?report=genbank

I was able to load the .fasta file manually in gentle via Drag-n-drop! remember that I could not load this from NCBI web, but if I went there and manually got and munged the file it worked.

This is bare bones though. No annotations or creator metadata!