genbank_seqblock {asciiruler}

Generate a GenBank sequence block

Description

'

'     1    6     11   16    21   26    31   36    41   46    51   56   
'     |    |     |    |     |    |     |    |     |    |     |    |    
'     |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
'   1 GATCACAGGT CTATCACCCT ATTAACCACT CACGGGAGCT CTCCATGCAT TTGGTATTTT
'  61 CGTCTGGGGG GTGTGCACGC GATAGCATTG CGAGACGCTG GAGCCGGAGC ACCCTATGTC
' 121 GCAGTATCTG TCTTTGATTC CTGCCCCATC CTATTATTTA TCGCACCTAC GTTCAATATT
' 181 ACAGGCGAAC ATACTTACTA AAGTGTGTTA ATTAATTAAT GCTTGTAGGA CATAATAATA
' 241 ACAATTGAAT GTCTGCACAG CCGCTTTCCA CACAGACATC ATAACAAAAA ATTTCCACCA
' 301 AACCCCCCCT CCCCCGCTTC TGGCCACAGC ACTTAAACAC ATCTCTGC
' 

Usage

genbank_seqblock(string, start = 1L, end = 0L, blocksize = 10L,
  width = 60L, sep = " ", line_break = "\n", ruler = TRUE, ...)

Arguments

string

the sequence string to display

start

the substring start, should be 1 or greater

end

substring end, should be >start, negative to trim

blocksize

number of characters in each block

width

width of the sequence block

sep

space character between blocks

line_break

the line break character(s)

ruler

display an ascii ruler

...

additional arguments passed to asciiruler

Value

delimited GenBank block string ready to cat

Examples

my_sequence<-'GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG
GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC
CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA
ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC'
my_seqblock<-genbank_seqblock(my_sequence)
cat(my_seqblock)