Hi, I am parsing many of genbank files. I have to trim sequence by coordinates (START,END). If situation look like:
3447..3578 or
complement(3102..3323) or
join(3447..3578,3447..3578) or
complement(join(3102..3323,3500..3722)),
everything is fine. The problem begins when a gene copy is placed in both strands marked in file like:
CDS join(61784..61897,complement(99364..99595),
complement(98797..98822))
/gene="rps12"
/locus_tag="AZ333_gp051"
/trans_splicing
/note="trans splicing of 5'rps12 exon and 3'rps 12 exon"
The + strand is lost (61784..61897), first complement is right and second complement ( which is placed in new line) is without start coordinate and R returns warnig :
Warning message:
In FUN(X[[i]], ...) : NAs introduced by coercion
How deal with it? Maybe, is it a way to edit a genbank file to get coordinates properly?
Hi, I am parsing many of genbank files. I have to trim sequence by coordinates (START,END). If situation look like: 3447..3578 or complement(3102..3323) or join(3447..3578,3447..3578) or complement(join(3102..3323,3500..3722)), everything is fine. The problem begins when a gene copy is placed in both strands marked in file like:
CDS join(61784..61897,complement(99364..99595), complement(98797..98822)) /gene="rps12" /locus_tag="AZ333_gp051" /trans_splicing /note="trans splicing of 5'rps12 exon and 3'rps 12 exon"
The + strand is lost (61784..61897), first complement is right and second complement ( which is placed in new line) is without start coordinate and R returns warnig : Warning message: In FUN(X[[i]], ...) : NAs introduced by coercion
How deal with it? Maybe, is it a way to edit a genbank file to get coordinates properly?