Hi All,
I need to pass a variable to perl script from bash script, where in perl i am using if condition. Here is the cmd what i am using in perl
FROM_DATE="06/05/2008"
TO_DATE="07/05/2008"
"perl -ne ' print if ( $_ >="$FROM_DATE" && $_ <= "$TO_DATE" ) ' filename"
filename has... (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)
I am fiddling with a little script that will issue a shutdown command if the temperature on the CPU goes above a certain level. I started writing the script in Bash, and then thought I would like to use Perl to extract the detailed bits, but I am not sure if this is really practical. Basically I... (2 Replies)
Hi Everyone,
i have a string 00:44:40
so:
$tmp=~ s/://gi;
$tmp=~s/({2})({2})({2})/$1*3600+$2*60+$3/e;
the output is 2680.
Any way to combine this two lines into a single line?
Thanks (4 Replies)
Hi,
I have tried several times but failed, I need to call this script from the perl script. This one line script will be sent to /var/tmp/error
Bash command:
/usr/openv/netbackup/bin/admincmd/bperror -backstat -l -hoursago 12 |awk '{ print $19, $12, $14, $16}'|grep -vi default|sort >... (12 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)
Server: IBM p770
OS: AIX 6.1 TL5 SP1
When one of our develoeprs types "bash" on the command line to switch shells, it hangs. For some reason, two bash processes are created....the first bash process spawns a second bash process in the same console, causing a hang. Anyone have any idea what... (2 Replies)
I'm reading about debugging aids in bash and have come across the set command. It says in my little book that an addition to typing
set
you can also use them "on the command line when running a script..." and it lists this in a small table:
set -o option Command Line... (5 Replies)
In a bash script, one can call a perl command in the following manner, where "myperlcommand" is a perl command.
perl -e 'myperlcommand(arguments)'
perl -e 'print("UUUU"x4)'
Now, how can one call a bash command from within a perl script? (Suppose that mybashcommand is a bash... (1 Reply)
How to run several bash commands put in bash command line without needing and requiring a script file.
Because I'm actually a windows guy and new here so for illustration is sort of :
$ bash "echo ${PATH} & echo have a nice day!"
will do output, for example:... (4 Replies)
Discussion started by: abdulbadii
4 Replies
LEARN ABOUT DEBIAN
bio::variation::aachange
Bio::Variation::AAChange(3pm) User Contributed Perl Documentation Bio::Variation::AAChange(3pm)NAME
Bio::Variation::AAChange - Sequence change class for polypeptides
SYNOPSIS
$aamut = Bio::Variation::AAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-proof' => $proof,
'-isMutation' => 1,
'-mut_number' => $mut_number
);
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$aamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$aachange->add_Allele($a2);
$aachange->allele_mut($a2);
print "
";
# add it to a SeqDiff container object
$seqdiff->add_Variant($rnachange);
# and create links to and from RNA level variant objects
$aamut->RNAChange($rnachange);
$rnachange->AAChange($rnachange);
DESCRIPTION
The instantiable class Bio::Variation::RNAChange describes basic sequence changes at polypeptide level. It uses methods defined in
superclass Bio::Variation::VariantI, see Bio::Variation::VariantI for details.
If the variation described by a AAChange object has a known Bio::Variation::RNAAChange object, create the link with method AAChange(). See
Bio::Variation::AAChange for more information.
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 lists 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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
RNAChange
Title : RNAChange
Usage : $mutobj = $self->RNAChange;
: $mutobj = $self->RNAChange($objref);
Function: Returns or sets the link-reference to a mutation/change object.
If there is no link, it will return undef
Returns : an obj_ref or undef
label
Title : label
Usage : $obj->label();
Function:
Sets and returns mutation event label(s). If value is not
set, or no argument is given returns false. Each
instantiable subclass of L<Bio::Variation::VariantI> needs
to implement this method. Valid values are listed in
'Mutation event controlled vocabulary' in
http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
Example :
Returns : string
Args : string
similarity_score
Title : similarity_score
Usage : $self->similarity_score
Function: Measure for evolutionary conservativeness
of single amino substitutions. Uses BLOSUM62.
Negative numbers are noncoservative changes.
Returns : integer, undef if not single amino acid change
trivname
Title : trivname
Usage : $self->trivname
Function:
Given a Bio::Variation::AAChange object with linked
Bio::Variation::RNAChange and Bio::Variation::DNAMutation
objects, this subroutine creates a string corresponding to
the 'trivial name' of the mutation. Trivial name is
specified in Antonorakis & MDI Nomenclature Working Group:
Human Mutation 11:1-3, 1998.
Returns : string
perl v5.14.2 2012-03-02 Bio::Variation::AAChange(3pm)