Hi all,
I'm newbi in scripting.
could someone tell how to delete the ^M at the end of the linie with an awk command.
many thanks in advance. (2 Replies)
Any clues on how to parse a line returned from an ls command that allows for the filename to be fully passed even if it includes spaces? What I got close with is:
ls -ltra | awk '{print $1 "|" $3 "|" $4 "|" $5 "|" $6 "|" $7 "|" $8 "|" $9 $10 $11 $12 ... (etc)}'
However this clears the spaces in... (6 Replies)
Hi to all! I 'm new in unix programing so... may be I decided a wrong tool to solve the problem but anyway... all road goes to rome jajaja.
My question is: There is any way to print date at the END clause of an AWK script. I mean, I'm writing a tool with AWK and the results are redirected to a... (4 Replies)
Hello.
I'm using a file to "grep" in a 2nd one (with awk)
cat file1
2 first user
9 second user
1 third user (with a space after user)
I want to get the line except the 1st field so I do :
field=$(gawk '{$1 =""; print $0}' file | sed 's/^ //')
It works but it deletes... (5 Replies)
I have a textfile which I am parsing with awk. The lines do not have the same number of fields, so sometimes $3 is the last field, sometimes not.
When I do a 'printf("%s, %s\n", $2, $3)', if $3 is the last field in the line, when I cat the file the output looks something like this:... (3 Replies)
I'm new to awk, trying to understand the basics.
I'm trying to reset the counter everytime the program gets a new file to check.
I figured in the BEGIN part it would work, but it doesn't.
#!/bin/awk -f
BEGIN {counter=0}
{
sum=0
for ( i=1; i<=NF;... (1 Reply)
Hello,
I have another problem with my script. Please accept my apologies, but I am really nooby in sh scripts. I am writing it for first time.
My script:
returned=`tail -50 SapLogs.log | grep -i "Error"`
echo $returned
if ; then
echo "There is no errors in the logs"
fi
And after... (10 Replies)
Hi,
I tried to use a code to awk until the end of file. I not sure what is the syntax so my last paragraph is \n
`var=$(awk '/\n/ {P=0} /Policy Change/ {P=1} P' (2 Replies)
Discussion started by: alvinoo
2 Replies
LEARN ABOUT DEBIAN
bio::graphics::glyph::allele_tower
Bio::Graphics::Glyph::allele_tower(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::allele_tower(3pm)NAME
Bio::Graphics::Glyph::allele_tower - The "allele_tower" glyph
SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
DESCRIPTION
This glyph draws a letter for each allele found at a SNP position, one above the other (i.e. in a column). For example:
A
G
See also http://www.hapmap.org/cgi-perl/gbrowse/gbrowse 'genotyped SNPs' for an example.
The common options are available (except height which is calculated based on the number of alleles). In addition, if you give the glyph
the minor allele frequency (MAF) and indicate which is the minor allele, the glyph will display these differences.
GETTING THE ALLELES
To specify the alleles, create an "Alleles" attribute for the feature. There should be two such attributes. For example, for a T/G
polymorphism, the GFF load file should look like:
Chr3 . SNP 12345 12345 . . . SNP ABC123; Alleles T ; Alleles G
Alternatively, you can pass an "alleles" callback to the appropriate section of the config file. This option should return the two alleles
separated by a slash:
alleles = sub {
my $snp = shift;
my @d = $snp->get_tag_values('AllelePair');
return join "/",@d;
}
OPTIONS
. Glyph Colour
. Different colour for alleles on the reverse strand
. Print out the complement for alleles on the reverse strand
. Major allele shown in bold
. Horizontal histogram to show allele frequency
GLYPH COLOR
The glyph color can be configured to be different if the feature is on the plus or minus strand. Use fgcolor to define the glyph color for
the plus strand and bgcolor for the minus strand. For example:
fgcolor = blue
bgcolor = red
For this option to work, you must also set ref_strand to return the strand of the feature:
ref_strand = sub {shift->strand}
REVERSE STRAND ALLELES
If the alleles on the negative strand need to be the complement of what is listed in the GFF files, (e.g. A/G becomes T/C), set the
complement option to have value 1
complement = 1
For this option to work, you must also set ref_strand to return the strand of the feature:
ref_strand = sub {shift->strand}
MAJOR/MINOR ALLELE
Use the 'minor_allele' option to return the minor allele for the SNP. If you use this option, the major allele will appear in bold type.
ALLELE FREQUENCY HISTOGRAMS
Use the 'maf' option to return the minor allele frequency for the SNP. If you use this option, a horizontal histogram will be drawn next
to the alleles, to indicate their relative frequencies. e.g.
A______
C__
Note: The 'label' option must be set to 1 (i.e. on) and the 'minor_allele' option must return a valid allele for this to work.
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::allele_tower,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Fiona Cunningham <cunningh@cshl.edu> in Lincoln Stein's lab <steinl@cshl.edu>.
Copyright (c) 2003 Cold Spring Harbor Laboratory
This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either
version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition,
please see DISCLAIMER.txt for disclaimers of warranty.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::allele_tower(3pm)
01-11-2018
