Dear Corona688,
Below the word by word execution of program from terminal: I have the executable set in the path:
Above options comes up when trying to execute the program from terminal. I am trying to run this program automatically so that I don't have to do this interactively for 1000 of sequences.
I really appreciate your time and response Corona688.
Regards
I've written a script (bgrep) for a more advanced grep command (& attached a cut down version below). I'm trying allow all grep options to be used, or in any combination.
The script works fine if I type say
bgrep -i -files product
it will return a non-case sensitive list of matches for... (3 Replies)
Hey guys,
I have an interactive script that is quite critical to our production environmentl thus updating it to run non-interactively is not an option.
The script takes a varying number of arguments, which it ques untill user confirm end of data entry
e.g of user input :
1
2
y ... (3 Replies)
The following bash script does not work because the java/groovy code always thinks there are four arguments even if there are only 1 or 2. As you can see from my hideous backslashes, I am using cygwin bash on windows.
export... (1 Reply)
Hi!
I have a python script that requires arguments and these arguments are file paths. This script works fine when executed like this:
/my_python_script "file_path1" "file_path2"
(i added quotes as some file names may have weird characters)
the issue happens when i launch my python script... (14 Replies)
I'm pretty new to bash scripting and I've found myself writing things like this (and the same with even more nesting):
if $CATEGORIES; then
if $LABEL_SLOTS; then
$pyth "$wd/texify_grammar.py" "$input" "$texfile" "--label-slots" "--categories" "$CATEGORY_LIST"
... (9 Replies)
I've tried to find a solution to this, but I"m stumped.
OS - RH Linux 5.9
I have a bash script <myProgram.sh> that gets executed manually and creates a small response file. I'm trying to automate the running of this script.
When myProgram.sh runs, it prompts the user to enter 2 pieces of... (13 Replies)
Hi,
I wanted to pass an argument to a bash script. So that the argument is used inside the awk command inside the bash script.
I know the noraml way of passing argument to a bash script as below :
sh myScript.sh abc
Inside the bash script i can use like this
myArg1=$1
wc $myArg
But... (8 Replies)
I have a script test.sh which reads various inputs from a user.
#!/bin/ksh
read x
read y
read z
echo x: $x y: $y z: $z
# read few more things again
read a
read b
echo a: $a b: $b
When i run this script as
test.sh << EOF
1
2
EOF (3 Replies)
Hi,
I have a requirement for creating a MQ (queue) where the inputs has to be passed as arguments.
Running the script as below
./hi.sh "Servername" "QueueManagername" "QueuecreationCommand"
cat hi.sh
echo "Welcome to $1"
runmqsc $2 < $3
But the queue creation command is... (9 Replies)
I at the moment, making a simple bash script, capable of setting up an workspace for me, so i don't have to do it manually.. Problem is though i can't seem to provide the bash script any argument, without running into my error checks, checking for input...
Here is the code:
#!/bin/bash... (7 Replies)
Discussion started by: kidi
7 Replies
LEARN ABOUT DEBIAN
bio::map::relativei
Bio::Map::RelativeI(3pm) User Contributed Perl Documentation Bio::Map::RelativeI(3pm)NAME
Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are
relative to.
SYNOPSIS
# do not use this module directly
# See Bio::Map::Relative for an example of
# implementation.
DESCRIPTION
A Relative object is used to describe what the co-ordinates (numerical(), start(), end()) of a Position are relative to. By default they
are implicitly assumed to be relative to the start of the map the Position is on. But setting the relative() of a Position to one of these
objects lets us define otherwise.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
absolute_conversion
Title : absolute_conversion
Usage : my $absolute_coord = $relative->absolute_conversion($pos);
Function: Convert the start co-ordinate of the supplied position into a number
relative to the start of its map.
Returns : scalar number
Args : Bio::Map::PositionI object
type
Title : type
Usage : my $type = $relative->type();
Function: Get the type of thing we are relative to. The types correspond
to a method name, so the value of what we are relative to can
subsequently be found by $value = $relative->$type;
Note that type is set by the last method that was set, or during
new().
Returns : the string 'map', 'element' or 'position', or undef
Args : none
map
Title : map
Usage : my $int = $relative->map();
$relative->map($int);
Function: Get/set the distance from the start of the map that the Position's
co-ordiantes are relative to.
Returns : int
Args : none to get, OR
int to set; a value of 0 means relative to the start of the map.
element
Title : element
Usage : my $element = $relative->element();
$relative->element($element);
Function: Get/set the map element (Mappable) the Position is relative to. If
the Mappable has more than one Position on the Position's map, we
will be relative to the Mappable's first Position on the map.
Returns : Bio::Map::MappableI
Args : none got get, OR
Bio::Map::MappableI to set
position
Title : position
Usage : my $position = $relative->position();
$relative->position($position);
Function: Get/set the Position your Position is relative to. Your Position
will be made relative to the start of this supplied Position. It
makes no difference what maps the Positions are on.
Returns : Bio::Map::PositionI
Args : none got get, OR
Bio::Map::PositionI to set
description
Title : description
Usage : my $description = $relative->description();
$relative->description($description);
Function: Get/set a textual description of what this relative describes.
Returns : string
Args : none to get, OR
string to set
perl v5.14.2 2012-03-02 Bio::Map::RelativeI(3pm)