Hi!
I'm using SunOS 5.7 w/ Bash 2.01.
Currently, I'm working on a script that will make it possible to find textfiles which match certain criteria. While I write this message, I had some brainfarts, found the answer myself :D and the question I had in mind is now no longer the question I... (3 Replies)
hi,
I have some 50 C files in which for indentation of code some devlopers used tabs, but we dont want any tab used for indentation.
I have following 2 need.
1) find tabs from all 50 files (which are in one directory )
2) replace them with 4 spaces.
Thanks
Rishi (6 Replies)
When formatting a script let's say for instance the following:
case ${choice} in
1)
vi ${tmp1}.tmp
# overwrite the tmp1 var with any user changes
cp ${tmp1}.tmp ${tmp1}
;;
... (2 Replies)
Hi All,
I am facing issues converting white spaces and tabs together in a file I am reading. Here is the command I am trying:
tr -s ' '@ | sort -t@ +1n filename
I guess the problem is that it is not converting the tabs to another delimiter. Also, I am supposed to accomplish this only using... (5 Replies)
I want my program to replace tabs with spaces.1tab=4spaces.When i write aa(tab)aaa(tab)(tab)a(tab) it must show me aaxxaaaxxxxxaxxx. I think that my program works corectly but when a write aaa(tab)a it must show aaaxa but it is aaaxxxxxa.Please for help!!! That is my code:
#include <stdio.h>
... (3 Replies)
Hi,
I'm looking for a command that replaces spaces/tabs with pipe symbol and store the result to the same file instead of routing it to another file.
infile
outfile
Thanks. (11 Replies)
I want to remove extra spaces from variable in aix script.
We retrieve the data from oracle database and then print the values. We have a value on 90th position.
When we execute the query on sqlplus it shows the length of 90th position as 3, but when we use the same query in aix script it shows... (5 Replies)
I'm having trouble getting my vimrc to work the way I want it. For some reason after I hit enter it is creating tabs instead of spaces like I would expect. Here is an example of what I am talking about. $ = newline, ^I = tab. On the line of struct EDGETAG* q; I hit enter and it created a tab... (2 Replies)
so i have a data file that has various lines which may or may not end with spaces or tabs.
data.file:
, \t \t
{sample} <spaces> <spaaces> several more spaces....
{"resemble"}, <nospaces>
Command i'm using:
sed -n 8p data.file | egrep "\],$|\],\ $"
or
egrep "\],$|\],\ $"... (1 Reply)
Discussion started by: SkySmart
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)