You haven't specified how your script works. Here is an example based on the assumption that your script is called script.sh and writes output to standard output
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)
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)
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)
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)
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)
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)
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)
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)
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)
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
bp_process_wormbase
BP_PROCESS_WORMBASE(1p) User Contributed Perl Documentation BP_PROCESS_WORMBASE(1p)NAME
process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
SYNOPSIS
% process_wormbase.pl ./WS61 > wormbase.gff
DESCRIPTION
This script massages the Wormbase GFF files located at ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the GFF format
suitable for display by the generic genome browser. It mainly adds comments to the annotations and designates certain well-spaced genetic
loci as framework landmarks.
This script requires the AcePerl distribution, which is available on CPAN (look for the "Ace" module).
To use this script, get the WormBase GFF files from the FTP site listed above and place them in a directory. It might be a good idea to
name the directory after the current release, such as WS61. You do not need to uncompress the files.
Then give that directory as the argument to this script and capture the script's output to a file:
% process_wormbase.pl ./WS61 > wormbase.gff
It may take a while before you see output from this script, since it must first fetch gene and protein database from the remote AceDB
running at www.wormbase.org. The wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command:
% bulk_load_gff.pl -d <databasename> wormbase.gff
SEE ALSO
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
AUTHOR
Lincoln Stein <lstein@cshl.org>
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.2 2012-03-02 BP_PROCESS_WORMBASE(1p)