|
|
Sponsored Content
Top Forums
Shell Programming and Scripting
Run one script on multiple files and print out multiple files.
Post 302860863 by grace_shen on Monday 7th of October 2013 11:10:59 AM
10-07-2013
|
|
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hello
when I try to run rm on multiple files I have problem to delete files with space.
I have this command :
find . -name "*.cmd" | xargs \rm -f
it doing the work fine but when it comes across files with spaces like : "my foo file.cmd"
it refuse to delete it
why? (1 Reply)
Discussion started by: umen
1 Replies
2. Shell Programming and Scripting
Question for anyone that might be able to help:
My objective is to eheck if a file (a source file) exists in a directory. If it does then, I'd like to call an application (Informatica ETL file...not necessary to know) to run a program which extracts data and loads it into multiple targets.
... (6 Replies)
Discussion started by: jnanasakti
6 Replies
3. UNIX for Dummies Questions & Answers
Hi,
I have thousands of files in a directory that have the following 2 formats:
289620178.aln
289620179.aln
289620180.aln
289620183.aln
289620184.aln
289620185.aln
289620186.aln
289620187.aln
289620188.aln
289620189.aln
289620190.aln
289620192.aln....
and:
alnCDS_1.fasta (1 Reply)
Discussion started by: greptastic
1 Replies
4. Shell Programming and Scripting
Hi,
I want to run a Perl script on multiple files, with same name ("Data.txt") but in different directories (eg : 2010_06_09_A/Data.txt, 2010_06_09_B/Data.txt).
I know how to run this perl script on files in the same directory like:
for $i in *.txt
do
perl myscript.pl $i > $i.new... (8 Replies)
Discussion started by: ad23
8 Replies
5. UNIX for Dummies Questions & Answers
Hi
I have 1000 files labelled data1.txt through data1000.txt. I want to write a script that prints out the number of lines in each txt file and outputs it in the following format:
Column 1: number of data file (1 through 1000)
Column 2: number of lines in the text file
Thanks! (2 Replies)
Discussion started by: evelibertine
2 Replies
6. Shell Programming and Scripting
Hi everyone,
I'm new to the forums, as you can probably tell... I'm also pretty new to scripting and writing any type of code.
I needed to know exactly how I can grep for multiple strings, in files located in one directory, but I need each string to output to a separate file.
So I'd... (19 Replies)
Discussion started by: LDHB2012
19 Replies
7. Shell Programming and Scripting
Hi
I have 100 files under file A labled 1.txt 2.txt.....100.txt(made up name)
I have 1 files under file B labled name.txt
How can i run the same perl script on 100 files and file name.txt
I want to run
perl script.pl A/1.txt B/name.txt
perl script.pl A/2.txt B/name.txt
.......
perl... (3 Replies)
Discussion started by: grace_shen
3 Replies
8. UNIX for Dummies Questions & Answers
How can I run the following command on multiple files and print out the corresponding multiple files.
perl script.pl genome.gff 1.txt > 1.gff
However, there are multiples files of 1.txt, from 1----100.txt
Thank you so much.
No duplicate posting! Continue here. (0 Replies)
Discussion started by: grace_shen
0 Replies
9. Shell Programming and Scripting
I have a script that I need to run on one file at a time. Unfortunately using for i in F* or cat F* is not possible. When I run the script using that, it jumbles the files and they are out of order. Here is the script:
gawk '{count++; keyword = $1}
END {
for (k in count)
{if (count == 2)... (18 Replies)
Discussion started by: newbie2010
18 Replies
10. UNIX for Dummies Questions & Answers
Hi Guys,
I've been having a look around to try and understand how i can do the below however havent come across anything that will work.
Basically I have a parser script that I need to run across all files in a certain directory, I can do this one my by one on comand line however I... (1 Reply)
Discussion started by: mutley2202
1 Replies
LEARN ABOUT DEBIAN
bio::graphics::glyph::vista_plot
Bio::Graphics::Glyph::vista_plot(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::vista_plot(3pm) NAME
Bio::Graphics::Glyph::vista_plot - The "vista_plot" glyph SYNOPSIS
See Bio::Graphics::Glyph, Bio::Graphics::Glyph::wiggle_xyplot and Bio::Graphics::Glyph::heat_map. DESCRIPTION
This glyph draws peak calls (features with discreet boundaries, i.e. putative transcription sites, over signal graph (wiggle_xyplot) requires a special load gff file that uses attributes 'wigfile' and 'peak_type' Example: 2L chip_seq vista 5407 23011573 . . . Name=ChipSeq Exp 1;wigfile=SomeWigFile.wigdb;peak_type=binding_site:exp1 The glyph will draw the wiggle file first, than overlay the peaks (if there are any) over signal graph. Elsewhere in the GFF3 file, there should be one or more features of type "binding_site:exp1", e.g.: 2L exp1 binding_site 91934 92005 . . . Options like 'balloon hover' and 'link' are available to customize interaction with peaks in detail view. BigWig support: Supported bigwig format also requires another attribute to be supplied in load gff file (fasta) which specifies sequence index file for the organism in use. The data file should have the 'bw' extension - it is used to detect the BigWig format by vista_plot 3L chip_seq vista 1 24543530 . . . Name=ChipSeq Exp 2;wigfile=SomeBigWigFile.bw;peak_type=binding_site:exp2;fasta=YourOrganism.fasta Note that all attributes should be present in load gff, as the code currently does not handle situation when only some of the attributes are in gff. To omit peak or signal drawing use "" (i.e. peak_type="") In both cases, the stanza code will look the same (only essential parameters shown): [VISTA_PLOT] feature = vista:chip_seq glyph = vista_plot label = 1 smoothing = mean smoothing_window = 10 bump density = 250 autoscale = local variance_band = 1 max_peak = 255 min_peak = 1 peakwidth = 3 start_color = lightgray end_color = black pos_color = blue neg_color = orange bgcolor = orange alpha = 80 fgcolor = black database = database_with_load_gff_data box_subparts = 1 bicolor_pivot = min key = VISTA plot OPTIONS
Options are the same as for wiggle_xyplot and heat_map Additional parameters: alpha set transparency for peak area. glyph_subtype Display only 'peaks', 'signal', 'density' or 'peaks+signal'. Aliases for 'peaks+signal' include "both" and "vista". Recommended global settings: for proper peak drawing transparency should be enabled by setting truecolors=1 in GBrowse.conf file BUGS
Please report them. SEE ALSO
Bio::Graphics::Panel Bio::Graphics::Glyph Bio::Graphics::Glyph::wiggle_xyplot Bio::Graphics::Glyph::heat_map GD AUTHOR
Peter Ruzanov pruzanov@oicr.on.ca Copyright (c) 2010 Ontario Institute for Cancer Research 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::vista_plot(3pm)