For a reference I would start the awk man page on your system and the awk man pages on this site, and then look at the Wikipedia entry for awk; it provides a good overview of the language with examples, differences provided by various versions of awk, and a decent list of reference materials.

There are several regular expressions in this script, but none of them are in this statement. (And note that you missed a closing parenthesis at the end of this statement.)

Note that the variable s is intended to be a concatenation of the values of single alleles found in fields of the form allele=X with a / separating entries if more than one is found. Also note that awk sets all uninitialized variables to an empty string (or zero depending on context) and that the function pr() in this script resets s to an empty string whenever it is called to print the data that has been accumulated for an SNP. And, due to the if statement on the previous line, this line of code is executed only in the ith field on the current input line matches the regular expression /allele=/ and this will match if and only if the field contains the string "allele=".

The ? : operators behave the same way in awk as they do in C, C++, and several other languages (i.e., in this case if the expression before the ? is not an empty string, return the expression between the ? and the :; otherwise return the expression after the :); the substr() function returns a substring or the string named by its first operand starting at the offset specified by its second operand (and since there is no third argument, returns the rest of the string); the index() function finds the position in its first argument where the string specified by its second argument first appears. So stringing all of this together in a single statement:

Code:

s = (s ? s "/" : "") substr($i, index($i, "=") + 1)

Set the variable s to (if s is not an empty string, the concatenation of the current value of the variable s followed by a slash character, or if s is an empty string, an empty string) concatenated with the character(s) following the = sign in allele=X.

So assume you have an SNP listing in your input file contained the following fields (all on one line or on different lines):

Code:

allele=C | allele=A | allele=G

When the first one of these is found, s will be set to "C".
When the second one is found s will be set to the concatenation of "C", "/", and "A" (i.e., "C/A").
And, when the third one is found, s will be set to "C/A/G".