[Seqinr-forum] Error in oriloc for many sequences

[Matthew Mark Parks]

Indeed, this stems from incorrect reading of the fasta file of the Genbank record (GBK).  "lseq" has value e.g. 2 somehow, when it should be ~ 4.5 Million.

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From: seqinr-forum-bounces at lists.r-forge.r-project.org <seqinr-forum-bounces at lists.r-forge.r-project.org> on behalf of Matthew Mark Parks <map2085 at med.cornell.edu>
Sent: Monday, July 24, 2017 8:01:40 PM
To: seqinr-forum at lists.r-forge.r-project.org
Subject: [Seqinr-forum] Error in oriloc for many sequences


Dear SeqinR developers,


The function "oriloc" returns the following error:


ERROR : wrong sign in 'by' argument


For many records from Genbank, even for very common, well documented organisms.


For example:

library(seqinr)

oriloc(gbk = "U00096.gb" )

ERROR : wrong sign in 'by' argument

This occurs for many other Genbank records as well, including:  CP007592.1, AMKD01000101.1, JXMX01000001.1


Thank you,

Matthew


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