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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READ(5) File Formats Manual READ(5)
NAME
read, write - transfer data from and to a file
SYNOPSIS
Tread tag[2] fid[2] offset[8] count[2]
Rread tag[2] fid[2] count[2] pad[1] data[count]
Twrite tag[2] fid[2] offset[8] count[2] pad[1] data[count]
Rwrite tag[2] fid[2] count[2]
DESCRIPTION
The read request asks for count bytes of data from the file identified by fid, which must be opened for reading, starting offset bytes
after the beginning of the file. Count must be less than or equal to MAXFDATA (8192, defined in <fcall.h>). The bytes are returned with
the read reply message.
The count field in the reply indicates the number of bytes returned. This may be less than the requested amount. If the offset field is
greater than the number of bytes in the file, a count of zero will be returned. For directories, read returns an integral number of direc-
tory entries exactly as in stat (see stat(5)), one for each member of the directory. The read request message must have offset and count
zero modulo DIRLEN.
The write request asks that count bytes of data be recorded in the file identified by fid, which must be opened for writing, starting off-
set bytes after the beginning of the file. If the file has been opened append only, the data will be placed at the end of the file regard-
less of offset. Directories may not be written.
The write reply records the number of bytes actually written. It is usually an error if this is not the same as requested.
ENTRY POINTS
Read and write messages are generated by the corresponding calls. Because of the MAXFDATA limit, more than one message may be produced by
a single call.
READ(5)