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cran / read.gb

:exclamation: This is a read-only mirror of the CRAN R package repository. read.gb — Open GenBank Files
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possible bug in reading a field within FEATURES #1

Open morfogeno opened 2 months ago

morfogeno commented 2 months ago

Dear Mr. Robin Mercier,

I am extracting some sequences with read.gb/extract.gb for a population genetics study and I found what it seems as a bug in "read.gb"

"read.gb" seems to skip (not write) one field in FEATURES$source.The field is named "geo_loc_name" (could be checked in ID="MW482079". I was able to exctract other fields with the code attached below. I tried to read it by downloading with "entrez_fetch" (both as character or writing in a file and re-reading it) or by direct download in entrez, so it seems is "read.gb".

I hope you could help me with a code or, better still, to implement it in "read.gb". More than 2000 sequences!

PS: It would be nice if "read.gb" could read deeper than FEATURES$source (e.g. FEATURES$source$Location$organism

Sincerely, Daniel Toffoli

gaborcsardi commented 2 months ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Look for Maintainer, BugReports and URL. Thanks!

morfogeno commented 2 months ago

Thanks! I wrote an email a week ago directly to the author but had no response. I thought here he would see it. Thank you for your solicitude!