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Add static text in perl
02-04-2016
. I will try again tomorrow and post back.#!/usr/bin/env perl
my @header = (
"Index",
"Chromosome Position",
"Gene",
"Inheritance",
"RNA Accession",
"Chr",
"Coverage",
"Score",
"A(#F,#R)",
"C(#F,#R)",
"G(#F,#R)",
"T(#F,#R)",
"Ins(#F,#R)",
"Del(#F,#R)",
"SNP db_xref",
"Mutation Call",
"Mutant Allele Frequency",
"Amino Acid Change",
"HP",
"SPLICE",
"Pseudogene",
"Classification",
"HGMD",
"Disease",
"Sanger",
"References",
);
# to be inserted after "Amino Acid Change" header member
my $nineteenth_member = "Heredity";
# insert into @header members
splice @header, 18, 0, $nineteenth_member;
$" = "\t"; # output separator for print when interpolating
# every element of @header will be separated by tab
print "@header\n";#!/usr/bin/env perl
my @numbers = qw( 1 2 3 4 );
my @fractions = qw( 3.1 3.2 3.3 3.4 );
splice @numbers, 3, 0, @fractions;
{
local $" = ",";
print "@numbers\n";
}
print "@numbers\n";perl example2.pl 1,2,3,3.1,3.2,3.3,3.4,4 1 2 3 3.1 3.2 3.3 3.4 4
02-04-2016
.#!/bin/perl
use strict;
my %nms=("NM_004004.5"=>"AR","NM_004992.3"=>"XLD","NM_003924.3"=>"AD"); # match NM and inheritence with gene
# Accept the input and output files as parameters
my $input_file = $ARGV[0];
my $output_file = $ARGV[1];
# Set the header columns to be added to the left
# and to the right of the header in the input file
my @left = (
"Index",
"Chromosome Position",
"Gene",
"Inheritance",
"RNA Accession",
"Chr",
"Coverage",
"Score",
"A(#F,#R)",
"C(#F,#R)",
"G(#F,#R)",
"T(#F,#R)",
"Ins(#F,#R)",
"Del(#F,#R)",
"SNP db_xref",
"Mutation Call",
"Mutant Allele Frequency",
"Amino Acid Change"
);
my @right = (
"HP",
"SPLICE",
"Pseudogene",
"Classification",
"HGMD",
"Disease",
"Sanger",
"References"
);
# open the input file, read the header line and sandwich it
# between @left and @right arrays
my $final_header;
open (FH, "<", $input_file) or die "Can't open $input_file: $!";
chomp(my $hdr=<FH>);
$final_header = sprintf("%s\t%s\t%s\n", join("\t", @left), $hdr, join("\t",@right));
# final header is set, print it to the output file
open (OF, ">", $output_file) or die "Can't open $output_file: $!";
print OF "$final_header";
# close (FH) or die "Can't close $output_file: $!";
my @colsleft = map "Null",(1..$#left);
my @colsright = map "Null",(0..$#right);
while(<FH>) { # puts row of input file into $_
chomp;
my @vals = split/\t/; # this splits the line at tabs
my @mutations=split/,/,$vals[9]; # splits on comma to create an array of mutations
my ($gene,$transcript,$exon,$coding,$aa);
for (@mutations)
{
$_ or next; # skip if AB empty
($gene,$transcript,$exon,$coding,$aa) = split/\:/; # this takes col AB and splits it at colons
grep {$transcript eq $_} keys %nms or next;
}
# warn join ("\t",$gene,$transcript,$exon,$coding,$aa);
my @out=($.,@colsleft,$_,@colsright);
$out[2]=$gene;
$out[3]=$nms{$transcript};
$out[4]=$transcript;
$out[15]=$coding;
$out[17]=$aa;
$out[45] = "VUS";
print "$out[45]\n";
#print OF join("\t",$.,@colsleft,$_,@colsright),"\n"; # row data is set, print it to the output file
print OF join("\t",@out),"\n"; # row data is set, print it to the output file
}Classification Null
02-05-2016
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 .
my @colsleft = map "Null",(1..$#left); my @colsright = map "Null",(0..$#right);
.
02-06-2016
Index Chromosome Position Gene Inheritance RNA Accession Chr Coverage Score A(#F,#R) C(#F,#R) G(#F,#R) T(#F,#R) Ins(#F,#R) Del(#F,#R) SNP db_xref Mutation Call Mutant Allele Frequency Amino Acid Change 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 HP SPLICE Pseudogene Classification HGMD Disease Sanger References 1 Null PHOX2B AD NM_003924.3 Null Null Null Null Null Null Null Null Null Null Null Null Null 4 41748071 41748078 GGCCCGGG - exonic PHOX2B frameshift deletion PHOX2B:NM_003924.3:exon3:c.691_698del:p.G231fs Null Null Null VUS Null Null Null Null
print OF join("\t",@out),"\n";.
02-06-2016
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 .
1 Null PHOX2B AD NM_003924.3 Null Null Null Null Null Null Null Null Null Null Null Null Null 4 41748071 41748078 GGCCCGGG - exonic PHOX2B frameshift deletion PHOX2B:NM_003924.3:exon3:c.691_698del:p.G231fs
cat -T desired_output
1^INull^IPHOX2B^IAD^INM_003924.3^INull^INull^INull^INull^INull^INull^INull^INull^INull^INull^INull^INull^INull^I4^I41748071^I41748078^IGGCCCGGG^I-^Iexonic^IPHOX2B^I^Iframeshift deletion^IPHOX2B:NM_003924.3:exon3:c.691_698del:p.G231fs^I^I^I^I^I^I^I^I^I^I^I^I^I^I^INull^INull^INull^IVUS^INull^INull^INull^INull
perl -pe 's/\t/\|/g' desired_output
1|Null|PHOX2B|AD|NM_003924.3|Null|Null|Null|Null|Null|Null|Null|Null|Null|Null|Null|Null|Null|4|41748071|41748078|GGCCCGGG|-|exonic|PHOX2B||frameshift deletion|PHOX2B:NM_003924.3:exon3:c.691_698del:p.G231fs|||||||||||||||Null|Null|Null|VUS|Null|Null|Null|Null
perl -nalF"\t" -e 'for(@F){print $n, ": ", $F[$n++]}' desired_output1: 1 2: Null 3: PHOX2B 4: AD 5: NM_003924.3 6: Null 7: Null 8: Null 9: Null 10: Null 11: Null 12: Null 13: Null 14: Null 15: Null 16: Null 17: Null 18: Null 19: 4 20: 41748071 21: 41748078 22: GGCCCGGG 23: - 24: exonic 25: PHOX2B 26: 27: frameshift deletion 28: PHOX2B:NM_003924.3:exon3:c.691_698del:p.G231fs 29: 30: 31: 32: 33: 34: 35: 36: 37: 38: 39: 40: 41: 42: 43: Null 44: Null 45: Null 46: VUS 47: Null 48: Null 49: Null 50: Null
my @mutations=split/,/,$vals[9];
PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G,PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G,PHOX2B:NM_003924.3:exon3:c.C639G:p.G213G
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