Split a file using 2-D indexing system Post: 302775461

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Top Forums Shell Programming and Scripting Split a file using 2-D indexing system Post 302775461 by Don Cragun on Tuesday 5th of March 2013 12:38:40 AM

03-05-2013

Registered User

If the awk on your system only supports single character settings for RS, or if you'd like to base the output filenames on the input filenames, be able to specify more than one input file, and be able to specify the number of files to be produced before updating the value of the 1st numeric value in the output filename, you could try the following script:

Code:

#!/bin/ksh
cnt=3
Usage="Usage: $(basename $0) [-n cnt] file..."
# Split input file(s) into files named file.X.Y where X and Y reset to 1
# and 1, respectively, for each file operand.  A new file is created
# when a line in an input file starts with a <greater-than> character
# (">").  Lines starting with a <greater-than> character are not
# included in any of the output files, but all other lines are copied 
# unchanged into the corresponding output file.  When a new file is
# created, Y is incremented until it exceeds cnt (which defaults to 3 if
# the -n option is not given on the command line.  When Y exceeds cnt, X
# is incremented and Y is reset to 1.
while getopts n: opt
do      case $opt in
        (n)     cnt="$OPTARG";;
        (?)     echo "$Usage" >&2
                exit 1
        esac
done
shift $(($OPTIND - 1))
if [ $# -lt 1 ]
then    echo "$(basename $0): At least one file operand is required." >&2
        echo "$Usage" >&2
        exit 2
fi
awk -v cnt=$cnt '
FNR == 1 {
        # This is the first record of a new input file.
        # If this is not the first input file, close the last output file for
        # the previous input file.
        if(NR != FNR) close(fn)
        # Create output filename based on input filename.
        x = y = 1
        fn = FILENAME "." x "." y
}
/^>/ {  # Close current output file
        close(fn)
        if(y == cnt) {
                y = 1
                x++
        } else  y++
        fn = FILENAME "." x "." y
        next
}
{       print > fn
}' "$@"

It uses the Korn shell, but will also work with any other shell that accepts parameter expansions specified by the POSIX Standards (including bash).

Note that if the first line in an input file or two or more adjacent lines in an input file start with a >, empty files will not be created; the corresponding filename will just be skipped.

Don Cragun

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LEARN ABOUT HPUX

unknown

UNKNOWN(1)						      General Commands Manual							UNKNOWN(1)

NAME

       unknown - identify possible genotypes for unknowns

SYNOPSIS

       A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree.

       unknown [ -cl ]

DESCRIPTION

       unknown infers possible genotypes and mating combinations for parents with unknown genotypes for ilink(1), mlink(1) and linkmap(1).

OPTIONS

       -c     Use conditional allele frequencies.

       -l     Choose a good set of loop breakers automatically.

RETURN VALUE

       0     Successful completion

ERRORS

       10    File not found
       255   Failure

EXAMPLES

       Normally, unknown(1) is run immediately prior to its sister programs, ilink(1), mlink(1) and linkmap(1), like this:

       unknown
       mlink

FILES

       unknown(1) reads the two files pedfile.dat and datafile.dat as its own input and produces various temporary files that are used as input to
       the next program. These temporary files are ipedfile.dat, upedfile.dat, speedfile.dat and newspeedfile.dat.

NOTES

       unknown(1) is part of the FASTLINK package, which is a re-implementation of the LINKAGE suite  of  computer  tools  that  help  investigate
       genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott.

AUTHORS

       Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al.

       This manual page was written by Elizabeth Barham <lizzy@soggytrousers.net> for the Debian GNU/Linux system (but may be used by others).

WORD-WIDE-WEB
       http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

SEE ALSO

       ilink(1), linkmap(1), lodscore(1), mlink(1).

								  April 15, 2003							UNKNOWN(1)