01-20-2009
How to use the programming in UNIX to count the total G+C and the GC%?What command li
Seems like can use awk and perl command. But I don't have the idea to write the command line. Thanks for all of your advise.
For example, if I have the file whose content are:
Sample 1. ATAGCAGAGGGAGTGAAGAGGTGGTGGGAGGGAGCT
Sample 2. ACTTTTATTTGAATGTAATATTTGGGACAATTATTC
Sample 3. AAATCATGGTGGGTTTATTGATGGTTAGAAAGTTCC
All the sample above, got 36 nucleotide.
I want my output to count the G + C and GC %. So my output should look like this:
Sample 1: G+C = 21 GC%= 58.33%
Sample 2: G+C = 8 GC%=22.22%
Sample 3: G+C = 13 GC%=36.11%
Thanks and appreciate of your answer.
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LEARN ABOUT OPENDARWIN
sleep
SLEEP(1) BSD General Commands Manual SLEEP(1)
NAME
sleep -- suspend execution for an interval of time
SYNOPSIS
sleep seconds
DESCRIPTION
The sleep command suspends execution for a minimum of seconds.
If the sleep command receives a signal, it takes the standard action.
IMPLEMENTATION NOTES
The SIGALRM signal is not handled specially by this implementation.
The sleep command will accept and honor a non-integer number of specified seconds (with a '.' character as a decimal point). This is a non-
portable extension, and its use will nearly guarantee that a shell script will not execute properly on another system.
EXAMPLES
To schedule the execution of a command for x number seconds later (with csh(1)):
(sleep 1800; sh command_file >& errors)&
This incantation would wait a half hour before running the script command_file. (See the at(1) utility.)
To reiteratively run a command (with the csh(1)):
while (1)
if (! -r zzz.rawdata) then
sleep 300
else
foreach i (`ls *.rawdata`)
sleep 70
awk -f collapse_data $i >> results
end
break
endif
end
The scenario for a script such as this might be: a program currently running is taking longer than expected to process a series of files, and
it would be nice to have another program start processing the files created by the first program as soon as it is finished (when zzz.rawdata
is created). The script checks every five minutes for the file zzz.rawdata, when the file is found, then another portion processing is done
courteously by sleeping for 70 seconds in between each awk job.
DIAGNOSTICS
The sleep utility exits 0 on success, and >0 if an error occurs.
SEE ALSO
nanosleep(2), sleep(3)
STANDARDS
The sleep command is expected to be IEEE Std 1003.2 (``POSIX.2'') compatible.
HISTORY
A sleep command appeared in Version 4 AT&T UNIX.
BSD
April 18, 1994 BSD