FileA
FileB
FileC
FileD
I want a script (awk preferably or python) that will look for common lines in the 4 different files. Files are sorted on Col1, but can be resorted if necessary.
I want to have three output files
1) Commonlines in all 4 files
2) Common lines in any 3 files
3) Common lines in any 2 files. Getting which files have the common-line would be nice too.
Hi,
I have one situation. I have some 6-7 no. of files in one directory & I have to extract all the lines which exist in all these files. means I need to extract all common lines from all these files & put them in a separate file.
Please help. I know it could be done with the help of... (11 Replies)
Hello guys,
I need a script to get the common lines from two files with a criteria that if the first two columns match then I keep the maximum value of the 3rd column.(tab separated columns)
Sample input:
file1:
111 222 0.1
333 444 0.5
555 666 0.4
file 2:
111 222 0.7
555 666... (5 Replies)
Hello guys,
I need a script to get the common lines from two files with a criteria that if the first two columns match then I keep the maximum value of the 5th column.(tab separated columns) . 3rd and 4th columns corresponds to the row which has highest value for the 5th column.
Sample... (2 Replies)
I've been a Unix admin for nearly 30 years and never learned AWK. I've seen several similar posts here, but haven't been able to adapt the answers to my situation. AWK is so damn cryptic! ;)
I have a single file with ~900 lines (CSV list). Each line starts with an ID, but with different stuff... (6 Replies)
Hello everyone
A few years Ago the user radoulov posted a fancy solution for a problem, which was about finding common lines (gene variation names) between multiple samples (files). The code was:
awk 'END {
for (R in rec) {
n = split(rec, t, "/")
if (n > 1)
dup = dup ?... (5 Replies)
I have this code
awk 'NR==FNR{a=$1;next} a' file1 file2
which does what I need it to do, but for only two files. I want to make it so that I can have multiple files (for example 30) and the code will return only the items that are in every single one of those files and ignore the ones... (7 Replies)
Thanks everyone. I got that problem solved.
I require one more help here. (Yes, UNIX definitely seems to be fun and useful, and I WILL eventually learn it for myself. But I am now on a different project and don't really have time to go through all the basics. So, I will really appreciate some... (6 Replies)
Hi
I have a file like
1 2
1 2 3
1 5 6
11 12
10 2
7 5
17 12
I would like to have an output as
1 2 3 5 6 10 7
11 12 17
any help would be highly appreciated
Thanks (4 Replies)
Hello,
I have a file with 2 columns ( tableName , ColumnName) delimited by a Pipe like below . File is sorted by ColumnName.
Table1|Column1
Table2|Column1
Table5|Column1
Table3|Column2
Table2|Column2
Table4|Column3
Table2|Column3
Table2|Column4
Table5|Column4
Table2|Column5
From... (6 Replies)
Could it be possible to find common lines between all of the files in one folder? Just like comm -12 . So all of the files two at a time. I would like all of the outcomes to be written to a different files, and the file names could be simply numbers - 1 , 2 , 3 etc. All of the file names contain... (19 Replies)
Discussion started by: Eve
19 Replies
LEARN ABOUT DEBIAN
bio::graphics::glyph::wiggle_xyplot
Bio::Graphics::Glyph::wiggle_xyplot(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::wiggle_xyplot(3pm)NAME
Bio::Graphics::Glyph::wiggle_xyplot - An xyplot plot compatible with dense "wig"data
SYNOPSIS
See <Bio::Graphics::Panel> and <Bio::Graphics::Glyph>.
DESCRIPTION
This glyph works like the regular xyplot but takes value data in Bio::Graphics::Wiggle file format:
reference = chr1
ChipCHIP Feature1 1..10000 wigfile=./test.wig
ChipCHIP Feature2 10001..20000 wigfile=./test.wig
ChipCHIP Feature3 25001..35000 wigfile=./test.wig
The "wigfile" attribute gives a relative or absolute pathname to a Bio::Graphics::Wiggle format file. The data consist of a packed binary
representation of the values in the feature, using a constant step such as present in tiling array data. Wigfiles are created using the
Bio::Graphics::Wiggle module or the wiggle2gff3.pl script, currently both part of the gbrowse package.
Alternatively, you can place an array of quantitative data directly in the "wigdata" attribute. This can be an arrayref of quantitative
data starting at feature start and ending at feature end, or the data string returned by
Bio::Graphics::Wiggle->export_to_wif64($start,$end).
OPTIONS
In addition to all the xyplot glyph options, the following options are recognized:
Name Value Description
--------------------
basedir path Path to be used to resolve "wigfile" and "densefile"
tags giving relative paths. Default is to use the
current working directory. Absolute wigfile &
densefile paths will not be changed.
autoscale "local" or "global"
If one or more of min_score and max_score options
are absent, then these values will be calculated
automatically. The "autoscale" option controls how
the calculation is done. The "local" value will
scale values according to the minimum and maximum
values present in the window being graphed. "global"
will use chromosome-wide statistics for the entire
wiggle or dense file to find min and max values.
smoothing method name Smoothing method: one of "mean", "max", "min" or "none"
smoothing_window
integer Number of values across which data should be smoothed.
variance_band boolean If true, draw a grey band across entire plot showing mean
and +/- 1 standard deviation (for wig files only).
bicolor_pivot
name Where to pivot the two colors when drawing bicolor plots.
Options are "mean" and "zero". A numeric value can
also be provided.
pos_color color When drawing bicolor plots, the fill color to use for values
that are above the pivot point.
neg_color color When drawing bicolor plots, the fill color to use for values
that are below the pivot point.
SPECIAL FEATURE TAGS
The glyph expects one or more of the following tags (attributes) in feature it renders:
Name Value Description
--------------------
wigfile path name Path to the Bio::Graphics::Wiggle file or object
for quantitative values.
wigdata string Data exported from a Bio::Graphics::Wiggle in WIF
format using its export_to_wif64() method.
densefile path name Path to a Bio::Graphics::DenseFeature object
(deprecated)
denseoffset integer Integer offset to where the data begins in the
Bio::Graphics::DenseFeature file (deprecated)
densesize integer Integer size of the data in the Bio::Graphics::DenseFeature
file (deprecated)
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
Lincoln Stein <steinl@cshl.edu>.
Copyright (c) 2007 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::wiggle_xyplot(3pm)