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Awk: conversion of matrix formats

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Top Forums Shell Programming and Scripting Awk: conversion of matrix formats
# 8  
Old 03-15-2013
dear don cragun,

i use the table for another program, therefore i don't need a pretty print. I need tab's.

and there i found another little problem,
after each line there seems to be a tab, but I don't need this tab for the last field in each line.

how can i easily replace the last tab with a newline.

Code:
fn=$1
fname=${fn%.*}
echo $fname

awk 'BEGIN {FS="\t"};
    NF >= 3 {HD[$1]++; HD[$3]++; PP[$1,$3] = PP[$3,$1] = 1 }
    END    {printf "\t"
        for (i in HD) { printf "%s\t" ,i } printf "\n" #<- here replace the tab with newline
        for (i in HD) {printf "%s\t", i ;
            for (j in HD) { printf "%s\t", PP[i,j]?PP[i,j]:"0" } printf "\n" #<- here replace the last tab with newline
            } }' $fn > $fname.adj

---------- Post updated at 07:55 AM ---------- Previous update was at 07:47 AM ----------

i should read more carefully:

here is the solution:

Code:
awk 'BEGIN {FS="\t"};
    NF >= 3 {HD[$1]++; HD[$3]++; PP[$1,$3] = PP[$3,$1] = 1 }
    END    {
        for (i in HD) { printf "\t%s" ,i } printf "\n"
        for (i in HD) {printf "%s", i ;
            for (j in HD) { printf "\t%s", PP[i,j]?PP[i,j]:"0" } printf "\n"
            } }' $fn > $fname.adj

# 9  
Old 03-15-2013
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

This User Gave Thanks to RudiC For This Post:
dietmar13
# 10  
Old 03-15-2013
Quote:
Originally Posted by dietmar13
dear don cragun,

i use the table for another program, therefore i don't need a pretty print. I need tab's.

and there i found another little problem,
after each line there seems to be a tab, but I don't need this tab for the last field in each line.

how can i easily replace the last tab with a newline.

Code:
fn=$1
fname=${fn%.*}
echo $fname

awk 'BEGIN {FS="\t"};
    NF >= 3 {HD[$1]++; HD[$3]++; PP[$1,$3] = PP[$3,$1] = 1 }
    END    {printf "\t"
        for (i in HD) { printf "%s\t" ,i } printf "\n" #<- here replace the tab with newline
        for (i in HD) {printf "%s\t", i ;
            for (j in HD) { printf "%s\t", PP[i,j]?PP[i,j]:"0" } printf "\n" #<- here replace the last tab with newline
            } }' $fn > $fname.adj

Please look again at the script I suggested in my last post in this thread. It got rid of the trailing tabs. The spots marked in red above are the areas that need to change to get rid of trailing tabs.

The BEGIN clause marked in green above does not match the sample input you provided, so I took it out. If you really have tab delimiters in your input AND have spaces in some of your field names, put that clause back in the script I provided. The ++'s marked in orange don't affect the output of your program, but will make it run a little slower. (It won't be noticeable with your sample data, but if you have millions of lines of input, it will make a difference. You will note that I removed them in the script I provided.)
This User Gave Thanks to Don Cragun For This Post:
dietmar13
# 11  
Old 03-16-2013
@Don Cragun and @RudiC

The task is solved, my downstream application works and I have learned a lot about programing awk...

thank you!

dietmar
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