01-03-2012
Did you make sure you've used the right threshold in your code (depending on your input file) ?
0.8 vs 80
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#! /usr/local/bin/perl -w
$ip = "$ARGV";
$rw = "$ARGV";
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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.
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3. Shell Programming and Scripting
Hello, all!
I am struggling with a short script to read a diagonal matrix for later retrieval.
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4. Shell Programming and Scripting
Hi All
I would like to merge multiple files with the same row and column size into a matrix format
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vi 12.txt
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5. Ubuntu
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
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Hi everyone
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Hi,
I do have couple of files in a folder. The names of each of the files have a pattern.
ahet_005678.txt
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...
ahet_002378.txt
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Hi All
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I do have a large matrix of the following format and it is tab delimited
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LEARN ABOUT DEBIAN
bp_search2tribe
BP_SEARCH2TRIBE(1p) User Contributed Perl Documentation BP_SEARCH2TRIBE(1p)
NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
SYNOPSIS
Usage:
search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..
DESCRIPTION
This script is probably too slow for most people's uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
with the mcxdeblast script and the --m9 option.
This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.
The options are:
-o filename - the output filename [default STDOUT]
-f format - search result format (blast, fasta)
(ssearch is fasta format). default is blast.
-w or --weight VALUE - Change the default weight for E(0.0) hits
to VALUE (default=200 (i.e. 1e-200) )
-h - this help menu
Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You
specify this by doing: search2tribe < file1 file2 file3
AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_SEARCH2TRIBE(1p)