I am using awk as part of and if then else statement. I am trying to have the user enter a gene name and then a variant or variants and have a specific transcript assigned to the variants depending on the gene. Below is my code but the if then else statement is wrong. Basically, the gene name would be the condition that assigns a particular transcript to a variant.
The desired output would be, if the user enters GJB2 as the gene name and then c.283G>A for the variant there is a statement for that condition that saves a file with NM_004004.5:c.283G>A . However if MECP2 is entered as the gene name and c.48delC,c.255G>T are entered as the variants, the a file is saved:
Code:
NM_004992.3:c.48delC
NM_004992.3:c.255G>T
Thank you .
Code:
syntax() {
printf "\n\n"
printf "Please enter the gene name : "; read gene
printf "Enter variant(s): "; IFS="," read -a variants
[ -z "$gene" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
[ "$gene" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
awk '{
if(${gene} = "GJB2")
for ((i=0; i<${#variants[@]}; i++))
do printf "NM_004004.5:%s\n" "${variants}" >> c:/Users/cmccabe/Desktop/Python27/$gene.txt >> c:/Users/cmccabe/Desktop/Python27/out.txt;
done
else if(${gene} = "MECP2")
for ((i=0; i<${#variants[@]}; i++))
do printf "NM_004992.3:%s\n" "${variants}" >> c:/Users/cmccabe/Desktop/Python27/$gene.txt >> c:/Users/cmccabe/Desktop/Python27/out.txt;
done
else if(${gene} = "Phox2B")
for ((i=0; i<${#variants[@]}; i++))
do printf "NM_003924.3:%s\n" "${variants}" >> c:/Users/cmccabe/Desktop/Python27/$gene.txt >> c:/Users/cmccabe/Desktop/Python27/out.txt
}'
name
}
Hi Friends
How do I do two things from one if statement inside awk? I want to run a script and create a new file from the same condition.
awk '{ if ($2 == ""){print " "|"cd /local/test; ./script.ksh"}{cat > ran_true.txt}}' $IN_FILE
Bolded are the two things I want to be done.
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LEARN ABOUT DEBIAN
ace::sequence::gappedalignment
Ace::Sequence::GappedAlignment(3pm) User Contributed Perl Documentation Ace::Sequence::GappedAlignment(3pm)NAME
Ace::Sequence::GappedAlignment - Gapped alignment object
SYNOPSIS
# open database connection and get an Ace::Sequence object
use Ace::Sequence;
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);
# get all the gapped alignments
@alignments = $seq->alignments('EST_GENOME');
# get the aligned segments from the first one
@segs = $alignments[0]->segments;
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);
DESCRIPTION
Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds
the ability to retrieve the positions of the aligned segments. Each segment is an Ace::Sequence::Feature, from which you can retrieve the
source and target coordinates.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::GappedAlignment object directly. Instead, objects will be created in response to a
alignments() call to an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
segments()
@segments = $gene->segments;
Return a list of Ace::Sequence::Feature objects corresponding to similar segments.
relative()
$relative = $gene->relative;
$gene->relative(1);
This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used
by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first
exon will (usually) be 1.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 166:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-11-10 Ace::Sequence::GappedAlignment(3pm)
04-02-2015
.