I've tried for ages and I haven't even gotten close. Using awk, how do I: replace every '*' with '-' on every line > 1 in every column, but only if the corresponding column in line 1 is not an '*'?
Example input:
a|s|d|f|g|*|A|*|*|g|c|a|*|A|*
a|*|*|f|g|*|*|*|*|g|c|a|*|A|*
*|s|*|f|g|*|a|t|*|g|c|a|*|A|*
a|s|d|*|g|*|T|*|C|g|c|a|a|A|T
Example output
a|s|d|f|g|*|A|*|*|g|c|a|*|A|*
a|-|-|f|g|*|-|*|*|g|c|a|*|A|*
-|s|-|f|g|*|a|t|*|g|c|a|*|A|*
a|s|d|-|g|*|T|*|C|g|c|a|a|A|T
The line of headers needs to be scanned to find all "not *".
That a column "has not" an * could be stored in an array a[].
For all next lines, only the columns that exist in a[] may need change.
That could be implemented as:
awk -F'|' 'BEGIN{OFS=FS}
NR==1 {
for(i=1;i<=NF;i++) if( $i != "*" ) a[i]
}
NR>1 {
for(i in a) if( $i == "*" ) $i="-"
}
1
' file
a|s|d|f|g|*|A|*|*|g|c|a|*|A|*
a|-|-|f|g|*|-|*|*|g|c|a|*|A|*
-|s|-|f|g|*|a|t|*|g|c|a|*|A|*
a|s|d|-|g|*|T|*|C|g|c|a|a|A|T
This implements the least amount of changes needed. It should be the fastest.
One possible way (may not be the best)
awk -F'|' '
BEGIN{OFS=FS}
NR==1 {
for(i=1;i<=NF;i++) if($i=="*") a[i]
}
{
for(i=1;i<=NF;i++) if($i=="*" && !(i in a)) $i="-"
}
1
' file
a|s|d|f|g|*|A|*|*|g|c|a|*|A|*
a|-|-|f|g|*|-|*|*|g|c|a|*|A|*
-|s|-|f|g|*|a|t|*|g|c|a|*|A|*
a|s|d|-|g|*|T|*|C|g|c|a|a|A|T
