Shell Programming and Scripting

#!/bin/sh
#
# usage:
#     nawk -F$'\t' -v JF=3,5 -f concatene.awk ~/tmp/tmp15
#     nawk -F$'\t' -v JF=15,16,17,18 -f concatene.awk split/snp_j > concat
#
# JF stands for "join fields"
BEGIN { FS="\t";OFS="\t" }
{ 
    if (NR==1) {    # to do it only once (NR starts at 1)
        N=split(JF,JFS,",");
        for (i=1;i<=N;i++) {    # reverse it
            RJFS[JFS[i]] = i;
        }
    }

    LINE="";
    for (FIELD_INDEX=1 ; FIELD_INDEX<=N ; FIELD_INDEX++ ) {
        LINE=(FIELD_INDEX==1 ? "" : LINE"|")$JFS[FIELD_INDEX];
    }
    for (FIELD_INDEX=1 ; FIELD_INDEX<=NF ; FIELD_INDEX++ ) {
        if (!RJFS[FIELD_INDEX]) {
            LINE=LINE"\t"$FIELD_INDEX;
        }
    }
    print LINE;
}

#!/bin/sh
# nawk -F$'\t' -v JF=3,5 -f unconcatene.awk test
BEGIN { FS="\t";OFS="\t" }
{ 
    if (NR==1) {    # to do it only once (NR starts at 1)
        N=split(JF,JFS,",");
        for (i=1;i<=N;i++) {    # reverse it
            RJFS[JFS[i]] = i;
        }
    }

    N2=split($1,JFS2,"|");    # N=N2
    for (i=1;i<=N;i++) {    # reverse it
        RJFS[JFS[i]] = JFS2[i];
    }

    SIZE=NF-1+N;
    FIELD_INDEX=2;
    LINE="";
    for (NEW_FIELD_INDEX=1 ; NEW_FIELD_INDEX<=SIZE ; NEW_FIELD_INDEX++ ) {
        LINE=LINE(NEW_FIELD_INDEX==1 ? "" : "\t");
        if (RJFS[NEW_FIELD_INDEX]) {
            LINE=(LINE)RJFS[NEW_FIELD_INDEX];
        } else {
            LINE=(LINE)$FIELD_INDEX;        
            FIELD_INDEX++;
        }
    }
    print LINE;
}

input: a b c d e f
output: c|e a b d f

a    b    c    d    e    f
g    h    i    j    k    l
m    n    o    p    q    r

b|c|f    a    d    e
h|i|l    g    j    k
n|o|r    m    p    q

nawk -f anthony.awk myFile
OR
nawk -v jf='2,3,6' -f anthony.awk myFile

BEGIN {
  FS=OFS="\t"

  SEP_jf="|"
  if (!jf) jf="3,5"

  n=split(jf, jfA, ",")
  for(i=1;i<=n;i++)
    jfO[jfA[i]]
}
{
  line=jfS=""
  for(i=1;i<=NF;i++)
    if (i in jfO)
       jfS=(jfS)?jfS SEP_jf $i: $i
    else
      line=(line)?line OFS $i:$i
  print jfS, line
}