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Top Forums Shell Programming and Scripting Help making simple perl or bash script to create a simple matrix Post 302630241 by neutronscott on Wednesday 25th of April 2012 02:41:21 PM
Old 04-25-2012
Ok. Three things I missed then.

1. I forgot to skip the header, which gave a non-numerical value and really messed up the column loop.
2. My output used spaces rather than tabs
3. Didn't expect quotes around field 2

new code:
Code:
#!/usr/bin/awk -f

BEGIN { FS="\t" }
NR==1 {next}    # skip header

# keep list of unique genes, in order
!($1 in genes_uniq) { genes_uniq[$1]; genes[gene_idx++]=$1; }

{
        # unquote
        gsub(/(^"|"$)/,"",$2)
        split($2, cols, /,/)
        for (col in cols) {
                if (cols[col] > max_col) max_col=cols[col]
                matrix[$1,cols[col]] = matrix[$1,cols[col]] "," $3
        }
}

END {
        # print header
        printf("gene\t")
        for (col = 1; col <= max_col; col++)
                printf("%d%c", col, (col==max_col)?"\n":"\t");

        for (i = 0; i < gene_idx; i++) {
                printf("%s\t", genes[i]);
                for (col = 1; col <= max_col; col++)
                        printf("%s%c", substr(matrix[genes[i],col],2),
                                (col==max_col)?"\n":"\t");
        }
}

also you can use awk -f script.awk input >output or chmod a+x script.awk and simply run ./script.awk input >output

Last edited by neutronscott; 04-25-2012 at 03:43 PM.. Reason: how to invoke
 

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COL(1)							    BSD General Commands Manual 						    COL(1)

NAME
col -- filter reverse line feeds from input SYNOPSIS
col [-bfhpx] [-l num] DESCRIPTION
The col utility filters out reverse (and half reverse) line feeds so that the output is in the correct order with only forward and half for- ward line feeds, and replaces white-space characters with tabs where possible. This can be useful in processing the output of nroff(1) and tbl(1). The col utility reads from the standard input and writes to the standard output. The options are as follows: -b Do not output any backspaces, printing only the last character written to each column position. -f Forward half line feeds are permitted (``fine'' mode). Normally characters printed on a half line boundary are printed on the fol- lowing line. -h Do not output multiple spaces instead of tabs (default). -l num Buffer at least num lines in memory. By default, 128 lines are buffered. -p Force unknown control sequences to be passed through unchanged. Normally, col will filter out any control sequences from the input other than those recognized and interpreted by itself, which are listed below. -x Output multiple spaces instead of tabs. The control sequences for carriage motion that col understands and their decimal values are listed in the following table: ESC-7 reverse line feed (escape then 7) ESC-8 half reverse line feed (escape then 8) ESC-9 half forward line feed (escape then 9) backspace moves back one column (8); ignored in the first column carriage return (13) newline forward line feed (10); also does carriage return shift in shift to normal character set (15) shift out shift to alternate character set (14) space moves forward one column (32) tab moves forward to next tab stop (9) vertical tab reverse line feed (11) All unrecognized control characters and escape sequences are discarded. The col utility keeps track of the character set as characters are read and makes sure the character set is correct when they are output. If the input attempts to back up to the last flushed line, col will display a warning message. ENVIRONMENT
The LANG, LC_ALL and LC_CTYPE environment variables affect the execution of col as described in environ(7). EXIT STATUS
The col utility exits 0 on success, and >0 if an error occurs. SEE ALSO
colcrt(1), expand(1), nroff(1), tbl(1) STANDARDS
The col utility conforms to Version 2 of the Single UNIX Specification (``SUSv2''). HISTORY
A col command appeared in Version 6 AT&T UNIX. BSD
August 4, 2004 BSD
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