Hi,
filenames:
contains name of list of files to search in.
placelist
contains the names of places to be searched in all files in "filenames"
for i in $(<filenames)
do
egrep -f placelist $i
if ]
then
echo $i
fi
done >> outputfile
Output i am getting: (0 Replies)
Hello,
I am new to unix and need help with a problem. I have 2 files each containing multiple columns of information ie;
File 1 :
A B C D E
1 2 3 4 5
File 2 :
F G
6 7
I would like to merge the information from File 2 to File 1 so that the data reads as follows;
File 1:
A... (4 Replies)
Hi,
I have to write one script that has to search a list of numbers in certain zipped files.
For eg. one file file1.txt contains the numbers. File1.txt contains 5,00,000 numbers and I have to search each number in zipped files(The number of zipped files are around 1000 each file is 5 MB)
I have... (10 Replies)
Hi,
I want to find for a particular word which is existing in different files and folders under the parent directory. What command can I use to retrieve all the file names which is having the word. (1 Reply)
Hello there,
I am trying to extract (string) information ( a list words) from 4 files and then put the results into 1 file. Currently I am doing this using grep -f list.txt file1 . and repeat the process for the other 3 files. The reasons i am doing that (a) I do know how to code (b) each file... (4 Replies)
Hey gyuz,
I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :
samtools view input.bam chrname:region1 > region1.txt
This will store all the reads from given bam file within the region of interest in region1.txt
Now I have... (5 Replies)
I have a list of files all over a file system e.g.
/home/1/foo/bar.x
/www/sites/moose/foo.txtI'm looking for strings in these files and want to replace each occurrence with a replacement string, e.g.
if I find: '#@!^\&@ in any of the files I want to replace it with: 655#@11, etc.
There... (2 Replies)
Hello,
I have hundreds of files in which I need to change email address. Here is what I am trying to do:
1. All text files are in a directory "a"
2. In the text file, I want to replace email address for preparer. All these lines start with {{PreparerEmail and end with }}. The email... (3 Replies)
I need to look for 3 files in a particular directory, if they are > 0kb. If files exist proceed further, if not mail out saying one of the file is missing. All the 3 files should be present.
Please see my script below and correct if needed. Anyway, it is not working.
#! /bin/bash... (13 Replies)
Im having an issue when trying to replace the first column with a new set of values in multiple files. The results from the following code only replaces the files with the last set of values in val.txt. I want to replace all the files with all the values.
for date in {1..31}
do
for val in... (1 Reply)
Discussion started by: ncwxpanther
1 Replies
LEARN ABOUT DEBIAN
bio::index::genbank
Bio::Index::GenBank(3pm) User Contributed Perl Documentation Bio::Index::GenBank(3pm)NAME
Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
SYNOPSIS
# Complete code for making an index for one or more GenBank files
use strict;
use Bio::Index::GenBank;
my $Index_File_Name = shift;
my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name,
-write_flag => 'WRITE');
$inx->make_index(@ARGV);
# Print out sequences present in the index in gcg format
use Bio::Index::GenBank;
use Bio::SeqIO;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name);
my $seqio = Bio::SeqIO->new(-format => 'gcg');
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq object
$seqio->write_seq($seq);
}
# alternatively
my ($locus, $acc);
my $seq1 = $inx->get_Seq_by_id($locus);
my $seq2 = $inx->get_Seq_by_acc($acc);
DESCRIPTION
By default the index that is created uses the LOCUS, ACCESSION, and VERSION identifiers as keys. Inherits functions for managing dbm files
from Bio::Index::Abstract.pm, and provides the basic functionality for indexing GenBank files, and retrieving the sequence from them. For
best results 'use strict'.
You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For
example:
$inx->id_parser(&get_id);
# make the index
$inx->make_index($file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /clone="(S+)"/;
$1;
}
FEED_BACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Email - birney@ebi.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_index_file
Title : _index_file
Usage : $index->_index_file($file_name, $i)
Function: Specialized function to index GenBank format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parser
Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string.
Returns &default_id_parser (see below) if not
set. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : reference to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser($line)
Function: The default parser for GenBank.pm
Returns : Array of specified ids
Args : a line string
_file_format
Title : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Index::GenBank(3pm)