I have a little problem with the following perl script that is supposed to remove gaps (dashes) from a sequence alignment:
The thing is that when the gap is at the beggining of the sequence, the script will remove it along with the character in the sequence ID, example:
Unfortunately, that's enough to mess up the FASTA format which completely stops me from doing any further analysis.
Any help will be greatly appreciated!
I have a question regarding running perl in the current process.
I shall demonstrate with an example.
Look at this.
sh-2.05b$ pwd
/tmp
sh-2.05b$ cat test.sh
#! /bin/sh
cd /etc
sh-2.05b$ ./test.sh
sh-2.05b$ pwd
/tmp
sh-2.05b$ . ./test.sh
sh-2.05b$ pwd
/etc
sh-2.05b$
So... (10 Replies)
I am trying to use a script to replace the header of each file, whose filename are stored within the array $test, using the sed command within a Perl script as follows:
$count = 0;
while ( $count < $#test )
{
`sed -e 's/BIOGRF 321/BIOGRF 332/g' ${test} > 0`;
`cat 0 >... (2 Replies)
so in unix this command works works and shows me a list of directories
find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt
but when i try running a perl script to run this command
my $query = 'find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt';... (2 Replies)
How can i print the output of a perl script on a unix console and redirect the same in a log file under same directory simultaneously ?
Like in Shell script, we use tee, is there anything in Perl or any other option ? (2 Replies)
Hi all,
Not sure if this should be in the programming forum, but I believe it will get more response under the Shell Programming and Scripting FORUM.
Am trying to write a customized df script in Perl and need some help with regards to using arrays and file handlers.
At the moment am... (3 Replies)
I am trying to run a perl script which needs input arguments from a parent perl script, but doesn't seem to work. Appreciate your help in this regard.
From parent.pl
$input1=123;
$input2=abc;
I tried calling it with
system("/usr/bin/perl child.pl $input1 $input2");
and
`perl... (1 Reply)
Hi Folks,
I have 2 perl scripts and I need to execute 2nd perl script from the 1st perl script in WINDOWS.
In the 1st perl script that I had, I am calling the 2nd script
main.pl
===========
print "This is my main script\n";
`perl C:\\Users\\sripathg\\Desktop\\scripts\\hi.pl`;
... (3 Replies)
Hi All,
I am aware that html tags can be embedded in cgi script as below.. In the same way is it possible to embed the below javascript in perl cgi script ??
print("<form action="action.htm" method="post" onSubmit="return submitForm(this.Submitbutton)">");
print("<input type = "text"... (1 Reply)
Not sure what I am doing wrong here, but I can print the list with no issue. Just a blank screen with the 'do'.
#!/usr/bin/perl
open FILE, "upslist.txt";
while ($line=<FILE>){
if ($line=~/^(.*?),(.*?)$/){
#print "ups:$1 string:$2\n";
do 'check_snmp_mgeups-0.1.pl -H $1 -C $2';
} ... (1 Reply)
I have reviewed many examples on-line about running another process (either PERL or shell command or a program), but do not find any usefull for my needs way. (Reviewed and not useful the system(), 'back ticks', exec() and open())
I would like to run another PERL-script from first one, not... (1 Reply)
Discussion started by: alex_5161
1 Replies
LEARN ABOUT DEBIAN
build-lives-rfx-plugin
build-lives-rfx-plugin(1) General Commands Manual build-lives-rfx-plugin(1)NAME
build-lives-rfx-plugin - builds rendered effects for LiVES
SYNOPSIS
build-lives-rfx-plugin script_name [plugin_dir] -get section file
DESCRIPTION
This perl script is used by LiVES to compile an RFX (rendered effect) plugin for LiVES. It is generally called from build-lives-rfx-plugin-
multi for a script which has a language code representing LiVES-perl. The script_name must be the full (absolute) path to the plugin
script, and plugin_dir can be used to specify the output directory where the compiled plugin should be generated. If plugin_dir is not
defined then /tmp is assumed.
The second variant with -get is used to print out a script section from a plugin script to stdout. It is generally only used internally by
LiVES.
Return values The script returns the following values
0 - success 1 - the value of a trigger was greater than the number of parameters 2 - a value could not be read from the script file 3 - the
language code of the plugin script was not equivalent to LiVES-perl 4 - the API version level of the plugin script was invalid 5 - the
<define> section was missing from the plugin script
SEE ALSO build-lives-rfx-plugin-multi(1), lives(1)AUTHOR
Gabriel Finch a.k.a Salsaman (salsaman@xs4all.nl)
May 9 2010 build-lives-rfx-plugin(1)