FASTA_NUCLEOTIDE_CHANGER(1) User Commands FASTA_NUCLEOTIDE_CHANGER(1)NAME
fasta_nucleotide_changer - Convets FASTA sequences from/to RNA/DNA
DESCRIPTION
usage: fasta_nucleotide_changer [-h] [-z] [-v] [-i INFILE] [-o OUTFILE] [-r] [-d] Part of FASTX Toolkit 0.0.13.2 by A. Gordon (gor-
don@cshl.edu)
[-h] = This helpful help screen.
[-z] = Compress output with GZIP.
[-v] = Verbose mode. Prints a short summary.
with [-o], summary is printed to STDOUT. Otherwise, summary is printed to STDERR.
[-i INFILE]
= FASTA/Q input file. default is STDIN.
[-o OUTFILE] = FASTA/Q output file. default is STDOUT. [-r] = DNA-to-RNA mode - change T's into U's. [-d] =
RNA-to-DNA mode - change U's into T's.
SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
fasta_nucleotide_changer 0.0.13.2 May 2012 FASTA_NUCLEOTIDE_CHANGER(1)
Check Out this Related Man Page
FASTQ_QUALITY_TRIMMER(1) User Commands FASTQ_QUALITY_TRIMMER(1)NAME
fastq_quality_trimmer - Filters sequences based on quality
DESCRIPTION
usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon (gor-
don@cshl.edu)
[-h] = This helpful help screen.
[-t N] = Quality threshold - nucleotides with lower
quality will be trimmed (from the end of the sequence).
[-l N] = Minimum length - sequences shorter than this (after trimming)
will be discarded. Default = 0 = no minimum length.
[-z] = Compress output with GZIP.
[-i INFILE]
= FASTQ input file. default is STDIN.
[-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose - report number of sequences.
If [-o] is specified,
report will be printed to STDOUT.
If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.
SEE ALSO
The quality of this automatically generated manpage might be insufficient. It is suggested to visit
http://hannonlab.cshl.edu/fastx_toolkit/commandline.html
to get a better layout as well as an overview about connected FASTX tools.
fastq_quality_trimmer 0.0.13.1 April 2012 FASTQ_QUALITY_TRIMMER(1)
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)