Hi All,
I have an input below. I tried to use the awk below but it seems that it ;s not working. Can anybody help ?
My concept here is to find the 2nd field of the last occurrence of such pattern " ** XXX ccc ccc cc cc ccc 2007 " . In this case, the 2nd field is " XXX ". With this "XXX" term... (20 Replies)
Hi
I have a pattern like :
SYSTEM_NAME-232-S7-200810060949.LOG
Here I need to extract system name and the timestamp and also the numeric number after "-S" i.e 7 here .
I am not very sure of whether I should use sed / awk for this ?:confused:
Thanks,
Priya. (6 Replies)
I have a mail log file and I want to extract some lines belonging to one domain. For example
Input File:
Dec 12 03:15:28 postfix/smtpd: 3F481EB0295: client=unknown, sasl_method=PLAIN, sasl_username=abcd@xyz.com
Dec 12 03:22:08 postfix/smtpd: 60B56EE001D: client=5ad9b9ba.com,... (7 Replies)
This is my first post, please be nice. I have tried to google and read different tutorials.
The task at hand is:
Input file input.txt (example)
abc123defhij-E-1234jslo
456ujs-W-abXjklp
From this file the task is to grep the -E- and -W- strings that are unique and write a new file... (5 Replies)
Hi All,
My file looks like this:
1 2 3
3 4 5
6 7 8
8 7 6
3 4 5
3 6 7
3 4 5
1 2 4
3 4 6
2 4 6
As you can see there are two newlines after the next pattern of numbers begin. (4 Replies)
I have hundreds of files to process. In each file
I need to look for a pattern then
extract value(s) from next line and then
search for value(s) selected from point (2) in the same file at a specific position.
HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V
TITLE CYTOCHROME... (7 Replies)
Hi all,
I got a txt here and I need to extract all D 8888 44 and D 8888 43 + next field
=",g("en")];f._sn&&(f._sn= "og."+f._sn);for(var n in f)l.push("&"),l.push(g(n)),l.push("="),l.push(g(f));l.push("&emsg=");l.push(g(d.name+":"+d.message));var m=l.join("");Ea(m)&&(m=m.substr(0,2E3));c=m;var... (5 Replies)
Hi All,
I am having a file like below . Basically when SB comes in the text with B. I have to take the word till SB. When there only B I should take take till B. Tried for cut it by demilter but not able to build the logic
SB- CD B_RESTO SB_RESTO CRYSTALS BOILERS -->There SB and B so I... (6 Replies)
Hello.
Here is a file contents :
declare -Ax NEW_FORCE_IGNORE_ARRAY=(="§" ="§" ="§" ="§" ="§" .................. ="§"Here is a pattern
=I want to extract 'NEW_FORCE_IGNORE_ARRAY' which is the whole word before the first occurrence of pattern '='
Is there a better solution than mine :... (3 Replies)
Discussion started by: jcdole
3 Replies
LEARN ABOUT DEBIAN
bio::index::fastq
Bio::Index::Fastq(3pm) User Contributed Perl Documentation Bio::Index::Fastq(3pm)NAME
Bio::Index::Fastq - Interface for indexing (multiple) fastq files
SYNOPSIS
# Complete code for making an index for several
# fastq files
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new(
'-filename' => $Index_File_Name,
'-write_flag' => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index
# in Fastq format
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name);
my $out = Bio::SeqIO->new('-format' => 'Fastq','-fh' => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq::Quality object
$out->write_seq($seq);
}
# or, alternatively
my $id;
my $seq = $inx->get_Seq_by_id($id); #identical to fetch
DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fastq files, and
retrieving the sequence from them. Note: for best results 'use strict'.
Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
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 - Tony Cox
Email - avc@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
_file_format
Title : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fastq'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTQ 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. Useful
for (for instance) specifying a different
parser for different flavours of FASTQ file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fastq
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( &my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fastq ID parser for Fastq.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fastq header line string
perl v5.14.2 2012-03-02 Bio::Index::Fastq(3pm)