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Full Discussion: Add static text in perl
Top Forums Shell Programming and Scripting Add static text in perl Post 302965991 by cmccabe on Friday 5th of February 2016 06:05:05 PM
Old 02-05-2016
The input that goes into the perl is:

Code:
Chr	Start	End	Ref	Alt	Func.refGene	Gene.refGene	GeneDetail.refGene	ExonicFunc.refGene	AAChange.refGene	PopFreqMax	1000G2012APR_ALL	1000G2012APR_AFR	1000G2012APR_AMR	1000G2012APR_ASN	1000G2012APR_EUR	ESP6500si_ALL	ESP6500si_AA	ESP6500si_EA	CG46	common	clinvar	clinvarsubmit	clinvarreference
4	41748130	41748130	G	C	exonic	PHOX2B		synonymous SNV	PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G	0.0007	.	.	.	.	.	0.0005	0.0002	0.0007	.

Code:
my @colsleft = map "Null",(1..$#left);	  
my @colsright = map "Null",(0..$#right);

provided the additional columns to the left and right. Basically, the file that is used is only 24 columns (represented by $_) and @colsleft put 18 columns before them with values of Null and @colsright put 8 additional columns after with values of Null. The total is now 50 and that is what is expected. So basically it is my @out=($.,@colsleft,$_,@colsright); unique entry, followed by 18 columns, then 24, then 8.

The split of column 10 [9] provides the arrays that are used in the $out. grep {$transcript eq $_} keys %nms or next; is a special case that matches the Stranscript with the nms in the beginning. This actually all seems to work.

The loop doesn't get refreshed because if there are multiple enteries then they are on separate rows.

I can not seem to figure out why VUS doesn't populate in $out[45] as that is the only part that doesn't seem to work.

I hope this helps a bit and thank you for all your help Smilie.
 

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SQL::Translator::Filter::Globals(3pm)			User Contributed Perl Documentation		     SQL::Translator::Filter::Globals(3pm)

NAME
SQL::Translator::Filter::Globals - Add global fields and indices to all tables. SYNOPSIS
# e.g. Add timestamp field to all tables. use SQL::Translator; my $sqlt = SQL::Translator->new( from => 'MySQL', to => 'MySQL', filters => [ Globals => { fields => [ { name => 'modified' data_type => 'TIMESTAMP' } ], indices => [ { fields => 'modifed', }, ] constraints => [ { } ] }, ], ) || die "SQLFairy error : ".SQL::Translator->error; my $sql = $sqlt->translate || die "SQLFairy error : ".$sqlt->error; DESCRIPTION
Adds global fields, indices and constraints to all tables in the schema. The globals to add can either be defined in the filter args or using a _GLOBAL_ table (see below). If a table already contains a field with the same name as a global then it is skipped for that table. The _GLOBAL_ Table An alternative to using the args is to add a table called "_GLOBAL_" to the schema and then just use the filter. Any fields and indices defined on this table will be added to all the tables in the schema and the _GLOBAL_ table removed. The name of the global can be changed using a "global_table" arg to the filter. SEE ALSO
perl(1), SQL::Translator BUGS
Will generate duplicate indices if an index already exists on a table the same as one added globally. Will generate duplicate constraints if a constraint already exists on a table the same as one added globally. TODO
Some extra data values that can be used to control the global addition. e.g. 'skip_global'. AUTHOR
Mark Addison <grommit@users.sourceforge.net> perl v5.14.2 2012-01-18 SQL::Translator::Filter::Globals(3pm)
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