Hello every body ! I'm a new in this forum and beginner in Perl scripting and I have some problems ! I have a big file like that :
The three column are separated by tabulation (\t)
I want to cluster the IDs that share a identity more than 0.8 using Perl scripting, can someone help me ?
Thanks a lot in advance for your help
Hey guys,
I have this file generated by me... i want to create some HTML output from it.
The problem is that i am really confused about how do I go about reading the file.
The file is in the following format:
TID1 Name1 ATime=xx AResult=yyy AExpected=yyy BTime=xx BResult=yyy... (8 Replies)
Hi All
I would like to merge multiple files with the same row and column size into a matrix format
In a folder I have multiple files in the following format
vi 12.txt
a 1
b 5
c 7
d 0
vi 45.txt
a 3
b 6
c 9
d 2
vi 9.txt
a 4 (7 Replies)
Hi all,
Is there a way to convert full data matrix to linearised left data matrix?
e.g full data matrix
Bh1 Bh2 Bh3 Bh4 Bh5 Bh6 Bh7
Bh1 0 0.241058 0.236129 0.244397 0.237479 0.240767 0.245245
Bh2 0.241058 0 0.240594 0.241931 0.241975 ... (8 Replies)
Hi everyone
I am very new at awk but think that that might be the best strategy for this. I have a matrix very similar to a correlation matrix and in practical terms I need to convert it into a list containing the values from the matrix (one value per line) with the first field of the line (row... (5 Replies)
Hi,
I do have couple of files in a folder. The names of each of the files have a pattern.
ahet_005678.txt
ahet_005898.txt
ahet_007678.txt
ahet_004778.txt
...
...
ahet_002378.txt
Each of the above files have the same pattern of data with 4 columns and have an header for the last 3... (4 Replies)
Hi All
I do have a matrix in the following format
a_2 a_3 s_4 t_6
b 0 0.9 0.004 0
c 0 0 1 0
d 0 0.98 0 0
e 0.0023 0.96 0 0.0034
I have thousands of rows
I would like to parse the maximum value in each of the row and out put that highest value along the column header of... (2 Replies)
I do have a large matrix of the following format and it is tab delimited
ch-ab1-20 ch-bb2-23 ch-ab1-34 ch-ab1-24 er-cc1-45 bv-cc1-78
ch-ab1-20 0 2 3 4 5 6
ch-bb2-23 3 0 5 ... (6 Replies)
Discussion started by: Kanja
6 Replies
LEARN ABOUT DEBIAN
bio::matrix::io
Bio::Matrix::IO(3pm) User Contributed Perl Documentation Bio::Matrix::IO(3pm)NAME
Bio::Matrix::IO - A factory for Matrix parsing
SYNOPSIS
use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'scoring',
-file => 'BLOSUMN50');
my $matrix = $parser->next_matrix;
DESCRIPTION
This is a general factory framework for writing parsers for Matricies. This includes parsing output from distance output like PHYLIP's
ProtDist. Additionally it should be possible to fit parsers for PWM and PSSMs once their Matrix objects are written.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Matrix::IO->new();
Function: Builds a new Bio::Matrix::IO object
Returns : an instance of Bio::Matrix::IO
Args :
newFh
Title : newFh
Usage : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
$matrix = <$fh>; # read a matrix object
print $fh $matrix; # write a matrix object
Returns : filehandle tied to the Bio::SeqIO::Fh class
Args :
fh
Title : fh
Usage : $obj->fh
Function: Get a filehandle type access to the matrix parser
Example : $fh = $obj->fh; # make a tied filehandle
$matrix = <$fh>; # read a matrix object
print $fh $matrix; # write a matrix object
Returns : filehandle tied to Bio::Matrix::IO class
Args : none
next_matrix
Title : next_matrix
Usage : my $matrix = $matixio->next_matrix;
Function: Parse the next matrix from the data stream
Returns : L<Bio::Matrix::MatrixI> type object or undef when finished
Args : none
write_matrix
Title : write_matrix
Usage : $io->write_matrix($matrix)
Function: Writes a matrix out to the data stream
Returns : none
Args : Array of Bio::Matrix::MatrixI object
- note that not all matricies can be converted to
each format, beware with mixing matrix types and output formats
_load_format_module
Title : _load_format_module
Usage : *INTERNAL Matrix::IO stuff*
Function: Loads up (like use) a module at run time on demand
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Returns : guessed format of filename (lower case)
Args : filename
perl v5.14.2 2012-03-02 Bio::Matrix::IO(3pm)