--------------------------------------------------------------------------------
Have to check in a file that the lines starting with 620 and 705
are ending at same posiotin.
82012345
62023232323
70523949558
62023255454
9999
In the above lines, i have to check the lines starting... (1 Reply)
I Have to check in a file that all the lines are ending at same posiotin.
Ex : line 1 is ending at position 88
line 2 should at same position i.e 88
Thanks in advance (6 Replies)
I have file format like below and I'm trying to modify this file.
I need to add 'ENDEND' end of each record.
01 ASH01 1CTCTL EDPPOO STAND
01 ASH08 0020 A1TH 101
01 ASH09 0022 A1TH 102
01 ASH09 0022 A1TH 103
01 ASH02 2CTCTL ... (5 Replies)
Hi,
I am a newbie in unix programming so maybe this is a simple question.
I would like to know how can I make a script that outputs only the values that are not between any given start and end positions
Example
file1:
2 30
40 80
82 100
file2:
ID1 1
ID2 35
ID3 80
ID4 81
ID6... (9 Replies)
Hi,
Having a following file's content, lets say:
ABC|ANA|LDJ|||||DKD||||||
AJJ|KKDD||KKDK||||||||||||
KKD||KD|||LLLD||||LLD|||||
Problem:
Need to replace pipes from 8th occurrence of pipe till end.
so the result should be:
ABC|ANA|LDJ|||||DKD
AJJ|KKDD||KKDK||||
-------
-------
... (12 Replies)
I want to remove the trailing spaces at the end of each line starting from a particular position(using ksh script). For example, in the attached file, I want to remove all the spaces starting from the position 430 till the end. The space has to be removed only from the 430th position no matter in... (3 Replies)
I have a need to calculate when British Summer Time starts and ends. After messing around, the following seems to work in Bash.
echo `date +%Y`-03-`cal 3 \`date +%Y\` | grep -oE "^]{2}" | tail
-1`T01:00:00Zand
echo `date +%Y`-03-`cal 10 \`date +%Y\` | grep -oE "^]{2}" | tail ... (10 Replies)
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Hi,
I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below.
Could you please help out to achieve solution through shell script..
File content:
... (2 Replies)
Discussion started by: nani2019
2 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)