Writing a Perl Script that processes multiple files
I want to write a Perl script that manipulates multiple files. In the directory, I have files 250.*chr$.ped where * is from 1 to 1000 and $ is from 1-22 for a total of 22 x 10,000 = 22,000 files.
I want to write a script that only manipulates files 250.1chr*.ped where * is from 1 to 22. Currently I am using
But it is not working. Could you help? Thanks!
Last edited by Franklin52; 10-06-2011 at 03:21 AM..
Reason: Please use code tags, thank you
All,
I want to combine multiple files in one file.
Something like what we do on the commad line as follows ->
cat file1 file2 file3 > Main_File.
Can something like this be done in a perl script very efficiently?
Thanks,
Rahul. (1 Reply)
Hi All,
I have encountered a problem,please help me.
I have a script in which multiple processes are writing on to the same file .
How should I stop this , I mean lock mechanism can be implemented or we can write the at different files and then concatenate the files.
What would be a better... (1 Reply)
I have a script that runs on one file (at a time).
like this:
$> perl myscript.pl filename > output
How can I run it on >6000 files and have the output sent out into slightly modified file name
$> perl myscript 6000files> output6000files.new extension
Thanks in anticipation (4 Replies)
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)
I would like to write a for loop that does the following:
I have a file called X.txt and other files called 1.txt,2.txt, .....,1000.txt.
I want to substitute the 6th column of the file X.txt with 1.txt and store the output as X.1. Then I want to do the same with X.txt and 2.txt and store the... (1 Reply)
I have a script where the the 9th line looks like this:
$filename=sprintf("250.1chr%d.ped", $N);
I want to modify this script 1000 times, changing 250.1chr%d.ped to 250.2chr%d.ped, 250.3chr%.ped.......and so on all the way to 250.1000chr%d.ped and store each output in files called
... (4 Replies)
I have multiple input files that I want to manipulate using a shell script. The files are called 250.1 through 250.1000 but I only want the script to manipulate 250.300 through 250.1000. Before I was using the following script to manipulate the text files:
for i in 250.*; do
|| awk... (4 Replies)
I am new for Perl I want to ask one question. I have around 50 custom packages which i am using in my Perl script. I want to import all .pm packages in my Perl script in an easy way. Right now i have to import each package individually. So Is there any way to do so??
Right Now i am doing like:
... (1 Reply)
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
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
LEARN ABOUT DEBIAN
bp_fast_load_gff
BP_FAST_LOAD_GFF(1p) User Contributed Perl Documentation BP_FAST_LOAD_GFF(1p)NAME
bp_fast_load_gff.pl - Fast-load a Bio::DB::GFF database from GFF files.
SYNOPSIS
% bp_fast_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
DESCRIPTION
This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files. You must use the
exact variant of GFF described in Bio::DB::GFF. Various command-line options allow you to control which database to load and whether to
allow an existing database to be overwritten.
This script is similar to load_gff.pl, but is much faster. However, it is hard-coded to use MySQL and probably only works on Unix
platforms due to its reliance on pipes. See bp_load_gff.pl for an incremental loader that works with all databases supported by
Bio::DB::GFF, and bp_bulk_load_gff.pl for a fast MySQL loader that supports all platforms.
NOTES
If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically
uncompressed.
FASTA format files are distinguished from GFF files by their filename extensions. Files ending in .fa, .fasta, .fast, .seq, .dna and their
uppercase variants are treated as FASTA files. Everything else is treated as a GFF file. If you wish to load -fasta files from STDIN,
then use the -f command-line swith with an argument of '-', as in
gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -
The nature of the load requires that the database be on the local machine and that the indicated user have the "file" privilege to load the
tables and have enough room in /usr/tmp (or whatever is specified by the $TMPDIR environment variable), to hold the tables transiently.
If your MySQL is version 3.22.6 and was compiled using the "load local file" option, then you may be able to load remote databases with
local data using the --local option.
About maxfeature: the default value is 100,000,000 bases. If you have features that are close to or greater that 100Mb in length, then the
value of maxfeature should be increased to 1,000,000,000. This value must be a power of 10.
If the list of GFF or fasta files exceeds the kernel limit for the maximum number of command-line arguments, use the --long_list
/path/to/files option.
The adaptor used is dbi::mysqlopt. There is currently no way to change this.
COMMAND-LINE OPTIONS
Command-line options can be abbreviated to single-letter options. e.g. -d instead of --database.
--database <dsn> Mysql database name
--create Reinitialize/create data tables without asking
--local Try to load a remote database using local data.
--user Username to log in as
--fasta File or directory containing fasta files to load
--password Password to use for authentication
--long_list Directory containing a very large number of
GFF and/or FASTA files
--maxfeature Set the value of the maximum feature size (default 100Mb; must be a power of 10)
--group A list of one or more tag names (comma or space separated)
to be used for grouping in the 9th column.
--gff3_munge Activate GFF3 name munging (see Bio::DB::GFF)
--summary Generate summary statistics for drawing coverage histograms.
This can be run on a previously loaded database or during
the load.
--Temporary Location of a writable scratch directory
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_FAST_LOAD_GFF(1p)