Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bp_blast2tree(1p) [debian man page]

BP_BLAST2TREE(1p)					User Contributed Perl Documentation					 BP_BLAST2TREE(1p)

NAME
tree_from_seqsearch - builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER) DESCRIPTION
This script requires that the bioperl-run pkg be also installed. perl v5.14.2 2012-03-02 BP_BLAST2TREE(1p)

Check Out this Related Man Page

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)
Man Page

13 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Adding the individual columns of a matrix.

I have a huge matrix file containing some 1.5 million rows and 6000 columns. The matrix looks something like this: 1 2 3 4 5 6 7 8 9 3 4 5 I want to add all the numbers in the columns of this matrix and display the result to my stdout. This means that the numbers in the first column are: ... (2 Replies)
Discussion started by: shoaibjameel123
2 Replies

2. Shell Programming and Scripting

awk or sed - Convert 2 lines to 1 line

Hi, Just trying to get to grips with sed and awk for some reporting for work and I need some assistance: I have a file that lists policy names on the first line and then on the second line whether the policy is active or not. Policy Name: Policy1 Active: yes Policy... (8 Replies)
Discussion started by: guinch
8 Replies

3. Shell Programming and Scripting

How can I do this in VI editor?

version info : vi availabe with RHEL 5.4 I have a text file with 10,000 lines. I want to copy lines from 5000th line to 7000th and redirect to a file. Any idea how I can do this? Note: The above scenario is just an example. In my actual requirement, the file has 14 million lines and I want... (9 Replies)
Discussion started by: kraljic
9 Replies

4. Fedora

Is UNIX an open source OS ?

Hi everyone, I know the following questions are noobish questions but I am asking them because I am confused about the basics of history behind UNIX and LINUX. Ok onto business, my questions are-: Was/Is UNIX ever an open source operating system ? If UNIX was... (21 Replies)
Discussion started by: sreyan32
21 Replies

5. What is on Your Mind?

Introduction

Hello, I couldn't find an actual introduction thread, so I decided to just put this here. I go by d0wngrade online. I have been programming in multiple languages for about 15+ years. I started with standard web design languages like HTML and CSS, but I then advanced from design to development... (2 Replies)
Discussion started by: d0wngrade
2 Replies

6. UNIX for Advanced & Expert Users

Detecting unused variables...

Hi guys... The first active code line in AudioScope.sh is set -u . This causes a complete exit if a variable is used/found but has not been allocated at the start of the program. However, apart from writing code to do the task, is there a switch to to check which variables have been... (17 Replies)
Discussion started by: wisecracker
17 Replies

7. Shell Programming and Scripting

One instance of comparing grep and awk

Hi. In thread https://www.unix.com/shell-programming-and-scripting/267833-grouping-counting.html rovf and I had a mini-discussion on grep and awk. Here is a demo script that compares the awk and grep approaches for this single problem: #!/usr/bin/env bash # @(#) s2 Demonstrate group... (1 Reply)
Discussion started by: drl
1 Replies

8. Shell Programming and Scripting

Find columns in a file based on header and print to new file

Hello, I have to fish out some specific columns from a file based on the header value. I have the list of columns I need in a different file. I thought I could read in the list of headers I need, # file with header names of required columns in required order headers_file=$2 # read contents... (11 Replies)
Discussion started by: LMHmedchem
11 Replies

9. OS X (Apple)

Installing Dash Shell on OS X Lion

For those interested in installing dash shell on OSX Lion to help test POSIX compliancy of shell scripts, it is quite easy. I did it like this: If you don't have gcc on your system: 0. Download and install the Command Line Tools for Xcode package from Sign In - Apple * 1. Download the dash... (2 Replies)
Discussion started by: Scrutinizer
2 Replies

10. UNIX for Beginners Questions & Answers

Weird 'find' results

Hello and thanks in advance for any help anyone can offer me I'm trying to learn the find command and thought I was understanding it... Apparently I was wrong. I was doing compound searches and I started getting weird results with the -size test. I was trying to do a search on a 1G file owned by... (14 Replies)
Discussion started by: bodisha
14 Replies

11. UNIX for Beginners Questions & Answers

How to copy a column of multiple files and paste into new excel file (next to column)?

I have data of an excel files as given below, file1 org1_1 1 1 2.5 100 org1_2 1 2 5.5 98 org1_3 1 3 7.2 88 file2 org2_1 1 1 2.5 100 org2_2 1 2 5.5 56 org2_3 1 3 7.2 70 I have multiple excel files as above shown. I have to copy column 1, column 4 and paste into a new excel file as... (26 Replies)
Discussion started by: dineshkumarsrk
26 Replies

12. What is on Your Mind?

New UNIX and Linux History Sections

Dear All, Taking a break from Vue.js coding for the site, SEO and YT videos; and hopefully addressing some well deserved criticism from some here that I have been too focused on the visual aspects of the forums versus the substance and the community.... While the "current generation... (9 Replies)
Discussion started by: Neo
9 Replies

13. Programming

My first PERL incarnation... Audio Oscillograph

Hi all... Well guys and gals, I jumped in at the deep end and found things that PERL cannot do by default. Many tricky terminal escape codes are not catered for so I had to create workarounds. One thing I searched for was this: Passing perl variable to shell command AND, @Neo this was... (15 Replies)
Discussion started by: wisecracker
15 Replies

Featured Tech Videos