Hello Friends,
Input File looks as follows:
Output:
Want something as:
My one line:
This does:
Which I do not want.
So how can I add a "\n" before ">" and after "my lines"
how can read the next line and check if ">" occurs if so need to add "\n" to the end of current line.
Will awk be faster or PERL is the way to go as the file is huge. Thousands of line and more.
One of the programs in perl using arrays went out of memory ,
so need to read and print line by line rather than buffer first.
Thanks
Last edited by Franklin52; 03-19-2010 at 05:31 AM..
Reason: Please use code tags!
Hi,
I'm not very familiar with unix shell. I want to replace the combination of two carriage returns and one newline with one carriage return and one newline. I think the best way to do this is to use sed. I tried something like this:
sed -e "s#\#\#g" file.txt
but it doesn't work.
Thanx... (2 Replies)
I am trying to use sed to replace specific characters at a specific position in the file with a different value... can this be done?
Example:
File:
A0199999123
A0199999124
A0199999125
Need to replace 99999 in positions 3-7 with 88888.
Any help is appreciated. (5 Replies)
Greetings.
I don't have experience programing scripts. I need to insert a string in a specific position of another string on another file (last.cfg), for example:
File last.cfg before using script:
login_interval=1800
lcs.machinename=client04
File last.cfg after using script:... (4 Replies)
I want to remove text from nth position to nth position couple of times in same line
my line is
"hello is there anyone can help me with this question"
I need like this
ello is there anyone can help me with question
'h' is removed and 'this' removed from the line. I want to do this... (5 Replies)
I woud like to substitue a string on a specific position for specific lines
I've got a file and I would like to change a specific string from "TOCHANGE" to "ABCABCAB"
For every line (except 1,2, 3 and the last one) , I need to check between the 9th and the 16th digits.
For the 3rd line, I... (7 Replies)
Hi,
I have file with lines key=val.
For ex(conf.file):-
c=3
ef=78
b=40
ca=40
I want to remove the line with c=3, when I execute the below command it's removing both lines i.e c=3 and ca=40. Could you please correct my command.
/usr/xpg4/bin/awk -v key=c 'match($0,key)... (3 Replies)
I have a file that I need to parse using a script. The dates in the file are displayed in the format:
Mar 2, 2011 9:09:31 PM
I have tried using the date command %e and %l but it pads an extra space for the day and hour if they are single digits.
So this I used a normal date command:
... (6 Replies)
Hi Gurus,
Apologies as I feel like this must be answered already on here somewhere but I just can't find it. I find many people looking to remove all \n and \r (CR and LF) or one or the other but the only times I've found someone trying to remove them only when both are together they've found... (7 Replies)
Hi,
I have a fixed width file.
The way this file works is say for example there are 30 columns in it each with different sizes say 10,5,2, etc...
If data in a field is less than the field size the rest of it is loaded with spaces.
I would like an awk command to that would replace
I have... (8 Replies)
Hi,
I have a file like this (about 8 columns in total, this being the 2nd column)
gi_49482297_ref_YP_039521.1_
gi_49482297_ref_YP_039521.1_
gi_49482315_ref_YP_039539.1_
gi_49482315_ref_YP_039539.1_I want to remove the _ at the end of the line.
And at later stages I would want to replace the... (5 Replies)
Discussion started by: Syeda Sumayya
5 Replies
LEARN ABOUT DEBIAN
bio::index::fasta
Bio::Index::Fasta(3pm) User Contributed Perl Documentation Bio::Index::Fasta(3pm)NAME
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
SYNOPSIS
# Make an index for one or more fasta files
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Once the index is made it can accessed, either in the
# same script or a different one
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',
-fh => *STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq 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 fasta files, and
retrieving the sequence from them. For best results 'use strict'.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl
Additional example code is available in scripts/index/*PLS and in the Bioperl Tutorial (<http://www.bioperl.org/wiki/Bptutorial.pl>)
Note that by default the key for the sequence will be the first continuous string after the '>' in the fasta header. If you want to use a
specific substring of the fasta header you must use the id_parser() method.
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 =~ /^>.+gi|(d+)/;
$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 - James Gilbert
Email - jgrg@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 : 'Fasta'
_index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTA 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 FASTA file.
Returns &default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
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 Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>s*(S+)/
to $header.
Returns : ID string
Args : a fasta header line string
perl v5.14.2 2012-03-02 Bio::Index::Fasta(3pm)