Hi All,
Below is my requirement. Whatever coming in between ' ', needs to delete.
Input File Contents:
==============
This is nice 'boy'
This 'is
bad
boy.' Got it
Expected Output
===========
This is nice
This
Got it (4 Replies)
Hi guys,
i have the follow problem i need to delete 10 row before the pattern and 1 after and the pattern row itself.
file looks like:
frect 9.8438 25.8681 10.625 25
. dynprop \
(# \
(call fox_execute(__self))) \
(FOX_VAR_29 \
... (4 Replies)
Hello sed gurus. I am using ksh on Sun and have a file created by concatenating several other files. All files contain header rows. I just need to keep the first occurrence and remove all other header rows.
header for file
1111
2222
3333
header for file
1111
2222
3333
header for file... (8 Replies)
i have a file sample.txt containing
i want to delete lines starting with 123 neglecting spaces and tabs.
but not lines containing 123. i.e.
i want files sample.txt as
help me
thanxx (4 Replies)
Hi friends,
I am looking for sed command/script that would search for a given fixed pattern on odd lines and then if it matches, prints the matching pattern and the next line. For example, in the example below, i am looking for pattern 0 and 1011 on odd lines.
########## start of example file... (10 Replies)
Hello,
I am having hard time figuring out how to print/delete the lines between two pattern. Here is the part of the file nastran1.bdf:
RBE3 48729 32232 123456 0.30000 123 59786 59787
60114
RBE3 48732 1330 123 0.30000 123 10107... (4 Replies)
The intended result should be :
PDF converters
'empty line'
gpdftext and pdftotext?xml version="1.0"?>
xml:space="preserve"><note-content version="0.1" xmlns:/tomboy/link" xmlns:size="http://beatniksoftware.com/tomboy/size">PDF converters
gpdftext and pdftotext</note-content>... (9 Replies)
Hi
I need to delete duplicate like pattern lines from a text file containing 2 duplicates only (one being subset of the other) using sed or awk preferably.
Input:
FM:Chicago:Development
FM:Chicago:Development:Score
SR:Cary:Testing:Testcases
PM:Newyork:Scripting
PM:Newyork:Scripting:Audit... (6 Replies)
I have a file
Line 1 a
Line 22
Line 33
Line 1 b
Line 22
Line 1 c
Line 4
Line 5
I want to delete all lines before last occurrence of a line which contains something which is defined in a variable. Say a variable var contains 'Line 1', then I need the following in the output.
... (21 Replies)
In the awk piped to sed below I am trying to format file by removing the odd xxxx_digits and whitespace after, then move the even xxxx_digit to the line above it and add a space between them. There may be multiple lines in file but they are in the same format. The Filename_ID line is the last line... (4 Replies)
Discussion started by: cmccabe
4 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)