[Seqinr-forum] Error in oriloc for many sequences

[Jean Lobry]

Dear Matthew,

is there something after the ORIGIN qualifier in your
genbank file? Try:

 > tail(readLines("U00096.gb"))
[1] "                     /db_xref=\"ASAP:ABE-0014442\""
[2] "                     /db_xref=\"UniProtKB/Swiss-Prot:P37005\""
[3] "                     /db_xref=\"EcoGene:EG12309\""
[4] "ORIGIN      "
[5] "//"
[6] ""

If you have the same result it means that your genbank file
contains only the features and not the sequence itself.

Best,

JLO

Le 25/07/2017 à 03:07, Matthew Mark Parks a écrit :
> 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.
> 
> ------------------------------------------------------------------------
> *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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