What Scrutinizer suggested will work if your "file with DNA" is a UNIX formatted text file that contains zero or more lines where each line contains a DNA string of zero or more characters.
If the files contain a single DNA string with no terminating <newline> character (which is what is specified in post #1), you'll need something more like:
This script requires one operand that is a pathname of the file you want to test.
Hi,
Can someone help me with creating a bash shell script.
I need to create a script that gets a positive number n as an argument.
The script must create n directories in the current directory with names like map_1, map_2 etcetera. Each directory must be contained within its predecessor. So... (7 Replies)
Hi,
I am new to shell-scripting, and doing a lot of reading. I am having some trouble getting started with a simple testing of scripting. I have been experimenting with if, loops, for, test, etc., but still unsure. I seem to have the hang of it when it comes to creating a single file or... (6 Replies)
Hi.
I have two text files(tables) which include some information and I want to make some query codes using them.
First of all, I want to create bash script that read this two tables, create/open database and insert data from files into database.
#!/bin/bash
while read line; do
... (1 Reply)
Hi, I am a new on this forum but i like :) I need a script in bash which will be crating a new user with folder for websites. For example: I will run this program and he creating a new user(with my name) and folder whcich name like user and if i will localho/~user in browser, she show me files from... (1 Reply)
Hello Everyone,
I am currently trying to write a Bash Script to call a PCAP file. The command I will use in the script will be the following:
tshark -r test.pcap -T fields -e frame.number -e frame.time -e eth.src -e eth.dst -e ip.src -e ip.dst -r ip.proto -E header=y -E separator=, quote=d -E... (4 Replies)
I've got this script to loop through all folders and move files that are more than 2 years old. I'm using the install command because it creates the necessary directories on the destination path and then I remove the source. I'd like to change the script to use the mv command since it is much... (4 Replies)
Hi,
I need to perform the untar and rm operation if the file found is a .tar and does not have test.tar or hello.tar as the file names.
Below is the loop to check the same.
for tf in *.tar
do if ]
then found=1
... (1 Reply)
Hey, im fairly new to unix and Im trying to make this unix project that would display a menu and do the following.
MENU
===========================
(p, P) Print users info
(a, A) Add new user
(s, S) Search user
(d, D) Delete user
(x,X) Exit
Enter your choice:
Trying to... (3 Replies)
I want get from user and pass these parameters to bash script. script should copy files in user home directory.
FYI: each file might be exist or not, might be one of them exist or four of them.
Here is my script, it always copy file1 and seems only one of them execute!
#!/bin/bash
for... (6 Replies)
Discussion started by: indeed_1
6 Replies
LEARN ABOUT DEBIAN
bio::liveseq::gene
Bio::LiveSeq::Gene(3pm) User Contributed Perl Documentation Bio::LiveSeq::Gene(3pm)NAME
Bio::LiveSeq::Gene - Range abstract class for LiveSeq
SYNOPSIS
# documentation needed
DESCRIPTION
This is used as storage for all object references concerning a particular gene.
AUTHOR - Joseph A.L. Insana
Email: Insana@ebi.ac.uk, jinsana@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $gene = Bio::LiveSeq::Gene->new(-name => "name",
-features => $hashref
-upbound => $min
-downbound => $max);
Function: generates a new Bio::LiveSeq::Gene
Returns : reference to a new object of class Gene
Errorcode -1
Args : one string and one hashreference containing all features defined
for the Gene and the references to the LiveSeq objects for those
features.
Two labels for defining boundaries of the gene. Usually the
boundaries will reflect max span of transcript, exon... features,
while the DNA sequence will be created with some flanking regions
(e.g. with the EMBL_SRS::gene2liveseq routine).
If these two labels are not given, they will default to the start
and end of the DNA object.
Note : the format of the hash has to be like
DNA => reference to LiveSeq::DNA object
Transcripts => reference to array of transcripts objrefs
Transclations => reference to array of transcripts objrefs
Exons => ....
Introns => ....
Prim_Transcripts => ....
Repeat_Units => ....
Repeat_Regions => ....
Only DNA and Transcripts are mandatory
verbose
Title : verbose
Usage : $self->verbose(0)
Function: Sets verbose level for how ->warn behaves
-1 = silent: no warning
0 = reduced: minimal warnings
1 = default: all warnings
2 = extended: all warnings + stack trace dump
3 = paranoid: a warning becomes a throw and the program dies
Note: a quick way to set all LiveSeq objects at the same verbosity
level is to change the DNA level object, since they all look to
that one if their verbosity_level attribute is not set.
But the method offers fine tuning possibility by changing the
verbose level of each object in a different way.
So for example, after $loader= and $gene= have been retrieved
by a program, the command $gene->verbose(0); would
set the default verbosity level to 0 for all objects.
Returns : the current verbosity level
Args : -1,0,1,2 or 3
perl v5.14.2 2012-03-02 Bio::LiveSeq::Gene(3pm)