BP_MRTRANS(1p) User Contributed Perl Documentation BP_MRTRANS(1p)NAME
bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates
SYNOPSIS
Usage:
bp_mrtrans -i inputfile -o outputfile [-if input format] [-of output format] [-s cDNA sequence database] [-sf cDNA sequence format] [-h]
DESCRIPTION
This script will convert a protein alignment back into a cDNA. Loosely based on Bill Pearson's mrtrans.
The options are:
-o filename - the output filename [default STDOUT]
-of format - output sequence format
(multiple sequence alignment)
[default phylip]
-i filename - the input filename [required]
-if format - input sequence format
(multiple sequence alignment)
[ default clustalw]
-s --seqdb filename - the cDNA sequence database file
-sf --seqformat - the cDNA seq db format (flatfile sequence format)
-h - this help menu
AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_MRTRANS(1p)
Check Out this Related Man Page
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)