I am trying to write a script that will look for a file in a directory, then remove it. I need it to loop until it has removed a certain number of files. Is it better to do a repeat or to list each file in a pattern? Files will be numbered like RAF.01.*, RAF.02.*, etc. Thanks, James (6 Replies)
When you run a script, how will you know the directory for the actual file that contains the script. The code should be like .Me in VB. I dont know how we do it in unix. Is it possible? (8 Replies)
I am trying to write a script that loops through all the files in the current directory that end in '.slg.gz' and runs a parser on each file. Here is my code:
#!/bin/bash
FILES_HOME = 'dirname $0'
for i in $(ls $FILES_HOME/.slg.gz$);do
./run-feature-parser $(i) > OUTPUT.csv
done ... (1 Reply)
Hello, I'm trying to create a script that sorts documents by author (found in file name) and then create a directory for that author. For example,
Input:
John - Paper_1.txt
John - Paper_2.txt
Mark - Paper_1.txt
Jill - Paper_1.txt
Output:
dir/John/Paper_1.txt
dir/John/Paper_2.txt... (1 Reply)
I have a script that runs fine under my home directory. No syntax errors, runs and returns as expected.
When I migrate the script to the UAT directories on the same server for User testing, I get a syntax error.
I've checked to make sure the .profile I'm using is the same in the UAT... (1 Reply)
Greetings all,
We have an older environment that we are trying to bring up to par with our current Production and Test servers. We have a command on our production boxes, UniqueScriptName.sh, and we can issue that command from any directory and it works.
On our older environment, our... (1 Reply)
Hi Gurus,
t=`ps -u irb|grep -v grep|grep BSNL_PAYMENT_C`
echo $t
if
then
echo $?
echo "Process Creation is Running ...."
else
echo "Process went down at $dat $tim"
fi
How would i use loop so that the script continously checks for the current status of this process.... (1 Reply)
I am trying to run a script from crontab but the entire script (which is 70+ lines) is written in bash and I need it to run from a certain directory.
So when I run it manually I cd to /local/mnt/scr and then type ./reordersc and it works fine.
However, I want it to run from the crontab and I... (20 Replies)
Discussion started by: newbie2010
20 Replies
LEARN ABOUT DEBIAN
bio::seqio::kegg
Bio::SeqIO::kegg(3pm) User Contributed Perl Documentation Bio::SeqIO::kegg(3pm)NAME
Bio::SeqIO::kegg - KEGG sequence input/output stream
SYNOPSIS
# It is probably best not to use this object directly, but
# rather go through the SeqIO handler system. Go:
use Bio::SeqIO;
$stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
DESCRIPTION
This class transforms KEGG gene records into Bio::Seq objects.
Mapping of record properties to object properties
This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It
is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the
Bio::Seq::RichSeqI implementing object returned by the parser for each record.
'ENTRY'
$seq->primary_id
'NAME'
$seq->display_id
'DEFINITION'
$seq->annotation->get_Annotations('description');
'ORTHOLOG'
grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink')
'CLASS'
grep {$_->database eq 'PATH'}
$seq->annotation->get_Annotations('dblink')
'POSITION'
FIXME, NOT IMPLEMENTED
'PATHWAY'
for my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
#
}
'DBLINKS'
$seq->annotation->get_Annotations('dblink')
'CODON_USAGE'
FIXME, NOT IMPLEMENTED
'AASEQ'
$seq->translate->seq
'NTSEQ'
$seq-E<gt>seq
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 one
of 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 - Allen Day
Email allenday@ucla.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq::RichSeq object
Args :
write_seq
Title : write_seq
Note : write_seq() is not implemented for KEGG format output.
perl v5.14.2 2012-03-02 Bio::SeqIO::kegg(3pm)