Sponsored Content
Full Discussion: extract data from 2 files
Top Forums Shell Programming and Scripting extract data from 2 files Post 302597502 by Diya123 on Friday 10th of February 2012 01:19:52 PM
Old 02-10-2012
extract data from 2 files

file 1
Code:
WASH7P        17232,18267,18500,20564            17368,18362,18554,21139

file 2


Code:
chr1	14969	15038	Exon	WASH7P
chr1	17232	17368	Exon	WASH7P
chr1	17258	17368	Exon	WASH7P
chr1	17605	17742	Exon	WASH7P
chr1	18267	18362	Exon	WASH7P
chr1	18267	18366	Exon	WASH7P
chr1	18267	18369	Exon	WASH7P
chr1	18267	18379	Exon	WASH7P
chr1	18496	18554	Exon	WASH7P
chr1	18500	18554	Exon	WASH7P
chr1	18912	19139	Exon	WASH7P

What I need to check is for each gene if column 2 of file 2 is present in column 2 of file 1 and column 3 of file 2 is present in column 3 of file 1 . If so then these two are supposed to be placed in column 4 and 5 of file 1. I just explained one example here. I have 15000 entries with different genes(column5 of file 2). so a for loop should be there to iterate..

o/p

Code:
 WASH7P        17232,18267,18500,20564            17368,18362,18554,21139  17232,18267,18500   17232,18267,18500

Thanks,

Last edited by Franklin52; 02-11-2012 at 08:59 AM.. Reason: Adding code tags
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Perl script for extract data from xml files

Hi All, Prepare a perl script for extracting data from xml file. The xml data look like as AC StartTime="1227858839" ID="88" ETime="1227858837" DSTFlag="false" Type="2" Duration="303" /> <AS StartTime="1227858849" SigPairs="119 40 98 15 100 32 128 18 131 23 70 39 123 20 120 27 100 17 136 12... (3 Replies)
Discussion started by: allways4u21
3 Replies

2. Shell Programming and Scripting

extract the relevant data files for a quarter

CTB_KT_OllyotLvos_20081204_164352_200811.txt CTB_KT_LN_utahfwd_20081204_164352_200811.txt CTB_KT_LN_utahfwd_Summ_20081204_164352_200811.txt CTB_KT_PML_astdt_prFr_20081204_210153_200811.txt CTB_KT_PML_astdt_prOt_20081204_210153_200811.txt CTB_KT_PML_astdt_Nopr_20081204_210153_200811.txt... (7 Replies)
Discussion started by: w020637
7 Replies

3. UNIX for Dummies Questions & Answers

AWK, extract data from multiple files

Hi, I'm using AWK to try to extract data from multiple files (*.txt). The script should look for a flag that occurs at a specific position in each file and it should return the data to the right of that flag. I should end up with one line for each file, each containing 3 columns:... (8 Replies)
Discussion started by: Liverpaul09
8 Replies

4. Shell Programming and Scripting

How to extract data from indexed files (ISAM files) maintained in an unix server.

Hi, Could someone please assist on a quick way of How to extract data from indexed files (ISAM files) maintained in an UNIX(AIX) server.The file data needs to be extracted in flat text file or CSV or excel format . Usually we have programs in microfocus COBOL to extract data, but would like... (2 Replies)
Discussion started by: devina
2 Replies

5. Shell Programming and Scripting

extract data with awk from html files

Hello everyone, I'm new to this forum and i am new as a shell scripter. my problem is to have html files in a directory and I would like to extract from these some data that lies between two different lines Here's my situation <td align="default"> oxidizability (mg / l): data_to_extract... (6 Replies)
Discussion started by: sbobotex
6 Replies

6. Shell Programming and Scripting

Extract data with awk and write to several files

Hi! I have one file with data that looks like this: 1 data data data data 2 data data data data 3 data data data data . . . 1 data data data data 2 data data data data 3 data data data data . . . I would like to have awk to write each block to a separate file, like this: 1... (3 Replies)
Discussion started by: LinWin
3 Replies

7. Shell Programming and Scripting

How to extract information from two files with data range

Hi, I want to make a query about extracting data from two files that both have data ranges. the data that i want to extract; when there is matching between file1 column 2 is equal to file2 column2 , and file1 column 3 and column 4 is within the range of file2 columns 3 and 4. I would like rows... (1 Reply)
Discussion started by: houkto
1 Replies

8. UNIX for Dummies Questions & Answers

Extract common data out of multiple files

I am trying to extract common list of Organisms from different files For example I took 3 files and showed expected result. In real I have more than 1000 files. I am aware about the useful use of awk and grep but unaware in depth so need guidance regarding it. I want to use awk/ grep/ cut/... (7 Replies)
Discussion started by: macmath
7 Replies

9. Shell Programming and Scripting

Extract data in tabular format from multiple files

Hi, I have directory with multiple files from which i need to extract portion of specif lines and insert it in a new file, the new file will contain a separate columns for each file data. Example: I need to extract Value_1 & Value_3 from all files and insert in output file as below: ... (2 Replies)
Discussion started by: belalr
2 Replies

10. Shell Programming and Scripting

Match and extract data using two files

Hello, Using the information in file 1, I would like to extract from file2 all rows which matchs in column 3. file 1 1233 1230 1231 1232 file2 65733.00 19775.00 1220 65733.00 19793.00 1220 65733.00 19801.00 1220 65733.00 19809.00 1231 65733.00 19817.00 ... (2 Replies)
Discussion started by: jiam912
2 Replies
Graph(3pm)						User Contributed Perl Documentation						Graph(3pm)

NAME
SVG::Graph - Visualize your data in Scalable Vector Graphics (SVG) format. SYNOPSIS
use SVG::Graph; use SVG::Graph::Data; use SVG::Graph::Data::Datum; #create a new SVG document to plot in... my $graph = SVG::Graph->new(width=>600,height=>600,margin=>30); #and create a frame to hold the data/glyphs my $frame = $graph->add_frame; #let's plot y = x^2 my @data = map {SVG::Graph::Data::Datum->new(x=>$_,y=>$_^2)} (1,2,3,4,5); my $data = SVG::Graph::Data->new(data => @data); #put the xy data into the frame $frame->add_data($data); #add some glyphs to apply to the data in the frame $frame->add_glyph('axis', #add an axis glyph 'x_absolute_ticks' => 1, #with ticks every one #unit on the x axis 'y_absolute_ticks' => 1, #and ticks every one #unit on the y axis 'stroke' => 'black', #draw the axis black 'stroke-width' => 2, #and 2px thick ); $frame->add_glyph('scatter', #add a scatterplot glyph 'stroke' => 'red', #the dots will be outlined #in red, 'fill' => 'red', #filled red, 'fill-opacity' => 0.5, #and 50% opaque ); #print the graphic print $graph->draw; DESCRIPTION
SVG::Graph is a suite of perl modules for plotting data. SVG::Graph currently supports plots of one-, two- and three-dimensional data, as well as N-ary rooted trees. Data may be represented as: Glyph Name Dimensionality supported 1d 2d 3d tree -------------------------------------------------------- Axis x Bar Graph x Bubble Plot x Heatmap Graph x Line Graph x Pie Graph x Scatter Plot x Spline Graph x Tree x SVG::Graph 0.02 is a pre-alpha release. Keep in mind that many of the glyphs are not very robust. PLOTTING
You need to create a SVG::Graph::Frame instance from the parent SVG::Graph instance for each set of data to be plotted. Datasets can be hierarchical, and to represent this, SVG::Graph::Frame instances can themselves contain subframes. SVG::Graph::Frame can contain: - multiple subframes as instances of SVG::Graph::Frame - a single SVG::Graph::Data instance - multiple SVG::Graph::Glyph instances with which to render the attached SVG::Graph::Data instance, and all SVG::Graph::Data instances attached to SVG::Graph::Frame subinstances See SVG::Graph::Frame and SVG::Graph::Glyph for details. ONE DATA SET 1. create an SVG::Graph instance 2. create an SVG::Graph::Frame instance by calling SVG::Graph::add_frame(); 3. create an SVG::Graph::Data instance, containing an SVG::Graph::Data::Datum instance for each data point. 4. Attach the SVG::Graph::Data instance to your SVG::Graph::Frame using SVG::Graph::Frame::add_data(); 5. Attach glyphs to the SVG::Graph::Frame instance using SVG::Graph::Frame::add_glyph(); 6. Call SVG::Graph::draw(); MULTIPLE DATA SETS 1. create an SVG::Graph instance 2. create an SVG::Graph::Frame instance by calling SVG::Graph::add_frame(); 3. create an SVG::Graph::Data instance, containing an SVG::Graph::Data::Datum instance for each data point. 4. Attach the SVG::Graph::Data instance to your SVG::Graph::Frame using SVG::Graph::Frame::add_data(); 5. Attach glyphs to the SVG::Graph::Frame instance using SVG::Graph::Frame::add_glyph(); 6. repeat [2-5] for each additional data set to be added. add_frame() can be called on SVG::Graph to add top-level data sets, or SVG::Graph::Frame to add hierarchical data sets. 7. Call SVG::Graph::draw(); FEEDBACK
Send an email to the svg-graph-developers list. For more info, visit the project page at http://www.sf.net/projects/svg-graph AUTHORS
Allen Day, <allenday@ucla.edu> Chris To, <crsto@ucla.edu> CONTRIBUTORS
James Chen, <chenj@seas.ucla.edu> Brian O'Connor, <boconnor@ucla.edu> SEE ALSO
SVG METHODS
new Title : new Usage : my $graph = SVG::Graph->new(width=>600, height=>600, margin=>20); Function: creates a new SVG::Graph object Returns : a SVG::Graph object Args : width => the width of the SVG height => the height of the SVG margin => margin for the root frame init Title : init Usage : Function: Example : Returns : Args : width Title : width Usage : $obj->width($newval) Function: Example : Returns : value of width (a scalar) Args : on set, new value (a scalar or undef, optional) height Title : height Usage : $obj->height($newval) Function: Example : Returns : value of height (a scalar) Args : on set, new value (a scalar or undef, optional) margin Title : margin Usage : $obj->margin($newval) Function: Example : Returns : value of margin (a scalar) Args : on set, new value (a scalar or undef, optional) svg Title : svg Usage : $obj->svg($newval) Function: Example : Returns : value of svg (a scalar) Args : on set, new value (a scalar or undef, optional) add_frame Title : add_frame Usage : my $frame = $graph->add_frame Function: adds a Frame to the current Graph Returns : a SVG::Graph::Frame object Args : a hash. usable keys: frame_transform (optional) 'top' default orientation 'bottom' rotates graph 180 deg (about the center) 'right' points top position towards right 'left' points top position towards left frames Title : frames Usage : get/set Function: Example : Returns : Args : xoffset Title : xoffset Usage : $obj->xoffset($newval) Function: Example : Returns : value of xoffset (a scalar) Args : on set, new value (a scalar or undef, optional) yoffset Title : yoffset Usage : $obj->yoffset($newval) Function: Example : Returns : value of yoffset (a scalar) Args : on set, new value (a scalar or undef, optional) draw Title : draw Usage : $graph=>draw Function: depends on child glyph implementations Returns : xmlifyied SVG object Args : none perl v5.10.0 2009-01-07 Graph(3pm)
All times are GMT -4. The time now is 05:50 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy