Awk: conversion of matrix formats Post: 302780883

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Top Forums Shell Programming and Scripting Awk: conversion of matrix formats Post 302780883 by RudiC on Friday 15th of March 2013 08:57:20 AM

03-15-2013

Registered User

This proposal makes use of the fact that we're dealing with a symmetrical matrix, needing to retain only the upper triangular matrix. A sorting step would be much easier to implement, and only half of the "interaction" array elements would be needed:

Code:

awk     '               {B1 = B3 = 0                                    # boolean variable for finding headers
                         for (i=1; i<=n; i++)                           # check all headers found up to now
                                {B1 = B1 || (HD[i] == $1)               # if $1 or $3 found in headers array,
                                 B3 = B3 || (HD[i] == $3)               # record in respective boolean var
                                }
                           if (!B1) HD[++n] = $1                        # if new header, record in new
                           if (!B3) HD[++n] = $3                        # header array element
                         PP[$1,$3] = 1                                  # record protein interaction
                        }
         END            {printf "\t"                                    # a header sort step may slip in here!
                         for (i=1; i<=n; i++)   printf "%s\t", HD[i]    # print column headers
                                                printf "\n"
                         for (i=1; i<=n; i++)
                                {printf "%s\t",HD[i]
                                 for (j=1; j<i; j++)
                                        printf "%d\t", PP[HD[j],HD[i]]  # print lower triangular matrix
                                 printf "%d\t", 0                       # diagonal elements are always zero!
                                 for (j=i+1; j<=n; j++)
                                        printf "%d\t", PP[HD[i],HD[j]]  # print upper triangular matrix
                                 printf "\n"
                                }
                        }
        ' file

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