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And here you see the beauty of awk :)
awk '$1=$1' RS= infile
Note the space after RS= (same as RS="")

Or

awk 'NR>1{gsub("\n"," ",$0);print "Median "$0}' RS="Median" file

more for the smorgasbord:
awk '{printf ($0 ~ /^ *$/) ? "\n" : $0 " " } END {print ""}' input
or, look Ma! no awk!
while read line
do
printf "$line "
[ -z "$line" ] && echo ""
done < input...

It's an awk buffet:


awk '/Median/{if(NR!=1)print " ";}{printf("%s ", $0)}END{print " ";}' file

awk '/^$/ {print }
/^[M0-9]/ {printf ("%s ", $0) }
END {print ""} ' inputfile > newfile

try:
awk ' /^ *$/ {print} !/^ *$/ {printf $0 " "} END {print ""}' input

This works (on linux with bash and GNU tools!) for your four line 24 char example from post #1:$ cat sedfile
1 {s/\(.\)/\1\n/g;w1.tmp
}
2 {s/\(.\)/\1\n/g;w2.tmp
}
3 {s/\(.\)/\1\n/g;w3.tmp
...

22 lines of 3,278,824 chars to be compared char by char!? Wouldn't it be much easier if we could transpose that matrix (yet I don't know how, right now, from the top of my head) ?

For your second requirement..

assuming you have same number of characters per line..

try this..

sed -e 's/.\{1\}/& /g' file | awk '{ for(i=1;i<=NF;i++){a[NR,i]=$i;max=NF}maN=NR;}END{
for...

I think you can do it with awk ?
the 1)

awk '
/^.........patern/ {n+=1}
/^.....patern/ {m+=1}
end {print n ; print m}
' file 6 "." is for the patern in the 7th column.

You need to use an array. The following is a bash array example.
Arrays start counting at 0 (zero), so an array of three words has 3 elements: word1 word2 word3

word1 is 0, word2 is 1, word3 is...

awk -F"\t " '{printf("ID=%s,START=%s,END=%s\n",$11,$5,$6);}' input_file

Avoid the UUOC by using...cut -f1-6,8- filename