01-03-2017
Thanks Don Cragun and RudiC,
I apologies for not clarifying properly, its exactly how RuiC described.
RudiC your code worked as expected, is there a way to ignore certain columns e.g #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT (from 1-9) thanks again for your code and explanation.
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LEARN ABOUT DEBIAN
stag-filter
STAG-FILTER(1p) User Contributed Perl Documentation STAG-FILTER(1p)
NAME
stag-filter - filters a stag file (xml, itext, sxpr) for nodes of interest
SYNOPSIS
stag-filter person -q name=fred file1.xml
stag-filter person 'sub {shift->get_name =~ /^A*/}' file1.xml
stag-filter -p My::Foo -w sxpr record 'sub{..}' file2
USAGE
stag-filter [-p|parser PARSER] [-w|writer WRITER] NODE -q tag=val FILE
stag-filter [-p|parser PARSER] [-w|writer WRITER] NODE SUB FILE
stag-filter [-p|parser PARSER] [-w|writer WRITER] NODE -f PERLFILE FILE
DESCRIPTION
parsers an input file using the specified parser (which may be a built in stag parser, such as xml) and filters the resulting stag tree
according to a user-supplied subroutine, writing out only the nodes/elements that pass the test.
the parser is event based, so it should be able to handle large files (although if the node you parse is large, it will take up more
memory)
ARGUMENTS
-p|parser FORMAT
FORMAT is one of xml, sxpr or itext, or the name of a perl module
xml assumed as default
-w|writer FORMAT
FORMAT is one of xml, sxpr or itext, or the name of a perl module
-c|count
prints the number of nodes that pass the test
-filterfile|f
a file containing a perl subroutine (in place of the SUB argument)
-q|query TAG1=VAL1 -q|query TAG2=VAL2 ... -q|query TAGN=VALN
filters based on the field TAG
other operators can be used too - eg <, <=, etc
multiple q arguments can be passed in
for more complex operations, pass in your own subroutine, see below
SUB a perl subroutine. this subroutine is evaluated evry time NODE is encountered - the stag object for NODE is passed into the subroutine.
if the subroutine passes, the node will be passed to the writer for display
NODE
the name of the node/element we are filtering on
FILE
the file to be parser. If no parser option is supplied, this is assumed to a be a stag compatible syntax (xml, sxpr or itext);
otherwise you should parse in a parser name or a parser module that throws stag events
SEE ALSO
Data::Stag
perl v5.10.0 2008-12-23 STAG-FILTER(1p)