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You know what? When I execute this, it does return the ".trim" part. So that's one mystery solved. That trimming is either done before or after perl.

$ perl -e 'print "gene_id\t", join("\t",...

Yes. Perl allows you to call things without the () if you really want to, and they did so here. How it would with them is:

map( {code block}, @ARGV)

So @ARGV is the input array, and {code...

map is confusing because it's actually a kind of loop. $1 is the bracketed part of /(.*)\// in this context.

The whole thing means, "For each item in @ARGV[N], do { /(.*)\//; output[N]=$1 }"
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