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Top Forums Shell Programming and Scripting Tricky task with DNA sequences. Post 302551983 by radoulov on Thursday 1st of September 2011 09:39:36 AM
Old 09-01-2011
I think they are included in the output:


Code:
zsh-4.3.12[t]% cat infile 
>Influenza
TGGATATGAT
>Dengue
AGTTACTCCGAAA
>Varicella
CTTTGGATA
zsh-4.3.12[t]% perl -nle'BEGIN {
quote>   @map{ A, C, G, T } = ( T, G, C, A )
quote>   }
quote>   print /^>/ ?
quote>     $_ :
quote>       join //, map $map{ $_ }, split //, scalar reverse
quote>   ' infile
>Influenza
ATCATATCCA
>Dengue
TTTCGGAGTAACT
>Varicella
TATCCAAAG


Am I missing something?
This User Gave Thanks to radoulov For This Post:
 

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SEQ(1)							    BSD General Commands Manual 						    SEQ(1)

NAME
seq -- print sequences of numbers SYNOPSIS
seq [-w] [-f format] [-s string] [-t string] [first [incr]] last DESCRIPTION
The seq utility prints a sequence of numbers, one per line (default), from first (default 1), to near last as possible, in increments of incr (default 1). When first is larger than last the default incr is -1. All numbers are interpreted as floating point. Normally integer values are printed as decimal integers. The seq utility accepts the following options: -f format Use a printf(3) style format to print each number. Only the A, a, E, e, F, f, G, g, and % conversion characters are valid, along with any optional flags and an optional numeric mimimum field width or precision. The format can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). The default is %g. -s string Use string to separate numbers. The string can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). The default is . -t string Use string to terminate sequence of numbers. The string can contain character escape sequences in backslash notation as defined in ANSI X3.159-1989 (``ANSI C89''). This option is useful when the default separator does not contain a . -w Equalize the widths of all numbers by padding with zeros as necessary. This option has no effect with the -f option. If any sequence numbers will be printed in exponential notation, the default conversion is changed to %e. The seq utility exits 0 on success and non-zero if an error occurs. EXAMPLES
# seq 1 3 1 2 3 # seq 3 1 3 2 1 # seq -w 0 .05 .1 0.00 0.05 0.10 SEE ALSO
jot(1), printf(1), printf(3) HISTORY
The seq command first appeared in Plan 9 from Bell Labs. A seq command appeared in NetBSD 3.0. This command was based on the command of the same name in Plan 9 from Bell Labs and the GNU core utilities. The GNU seq command first appeared in the 1.13 shell utilities release. BUGS
The -w option does not handle the transition from pure floating point to exponent representation very well. The seq command is not bug for bug compatible with the Plan 9 from Bell Labs or GNU versions of seq. BSD
May 27, 2010 BSD
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