<bold>update</bold> I didn't read your code too well, so disregard the below.

Perl is nice, but you don't always need it: there is also the direct SQL possibility (syntax: create table new_table as myquery):

-- drop table if exists new_table;

create table new_table 
as 
        (
                select sequence_start,sequence_stop 
                from intergenic_and_experimental_results 
                where reading_direction = 'f'
        )
        union all 
        (
                select sequence_start,sequence_stop 
                from intergenic_and_experimental_results 
                where reading_direction = 'r' 
        )
        order by reading_direction, sequence_start
;
[download]

I always run a manual analyze on newly created table, just to make sure statistics (on which the planner relies) are up to date: 'analyze mytable;'

postgres manual: CREATE TABLE AS

(Or, in case you want to insert into an existing table: INSERT INTO (syntax: insert into mytable myquery)

(Or, in case you want to create a tab-separated file: COPY TO (syntax: copy ( myquery ) to 'file.txt' csv delimiter E'\t')

(and just btw: postgres is designated 'pgsql'; psql being the cli client)