Don
I modified a bit your script to output the total count and give some format:
With the above script I am getting the desired output:
However, I tried to include the END step in your awk script fail miserably. How can I modify the script so I don't have to "stitch" together the two scripts as shown above?
Thanks!
Hi all,
if for example I had a variable containing the string 'hello', is the any way I can output, for example, the e and the 2nd l based on their position in the string not their character (in this case 2 and 4)?
any general pointers in the right direction will be much appreciated, at... (3 Replies)
Hi Please help me to refine my syntax. I want to delete the excess characters from the out put below.
-bash-3.00$ top -b -n2 -d 00.20 |grep Cpu|tail -1 | awk -F ":" '{ print $2 }' | cut -d, -f1
4.4% us
now i want to delete the % and us. How wil i do that to make it just 4.4.
Thanks (7 Replies)
Hi,
I've a csv file seperated by '|' from which I'm trying to remove the excess '|' characters more than the existing fields. My CSV looks like as below.
HRLOAD|Service|AddChange|EN
PERSONID|STATUS|LASTNAME|FIRSTNAME|ITDCLIENTUSERID|ADDRESSLINE1
10000001|ACTIVE|Testazar1|Testore1|20041|||... (24 Replies)
sed -e "s// /g" old.txt > new.txt
While I do know some control characters need to be escaped, can normal characters also be escaped and still work the same way? Basically I do not know all control characters that have a special meaning, for example, ?, ., % have a meaning and have to be escaped... (11 Replies)
helloo
I wonder if there's a way to cut characters out of a string and keep only
the last 2 by using sed.
For example if there's the todays' date:
2012-05-06
and we only want to keep the last 2 characters which are the day.
Is there a quick way to do it with sed? (2 Replies)
Hey guys,
I know that title is a mouthful - I'll try to better explain my struggles a little better...
What I'm trying to do is:
1. Query a db and output to a file, a list of column data.
2. Then, for each line in this file, repeat these values but wrap them with:
ITEM{
... (3 Replies)
Hi,
I have a xml file (Config.xml)
<Header name="" TDate="" PDate="">
<Config>
{"config" { "Nation" "Pri:|Sec:"}}
</Config>
</Header>
Now I wanted to printed all the strings between "". I tried the following
cat Config.xml | sed -n 's/.*\.*//p'
... (8 Replies)
Hi,
I hope you can help me out please?
I need to replace from character 8-16 with AAAAAAAA and the rest should stay the same after character 16
gtwrhtrd11111111rjytwyejtyjejetjyetgeaEHT
wrehrhw22222222hytekutkyukrylryilruilrGEQTH
hrwjyety33333333gtrhwrjrgkreglqeriugn;RUGNEURGU
... (4 Replies)
I have a file that looks like this:
>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT
I am using the following script to report if AATTCCGGATCG is present in any sequence:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t"... (10 Replies)
Discussion started by: Xterra
10 Replies
LEARN ABOUT DEBIAN
bio::tools::geneid
Bio::Tools::Geneid(3pm) User Contributed Perl Documentation Bio::Tools::Geneid(3pm)NAME
Bio::Tools::Geneid - Results of one geneid run
SYNOPSIS
use Bio::Tools::Geneid;
my $gid = Bio::Tools::Geneid(-file => "geneid.out");
while (my $gene = $gid->next_prediction)
{
my @transcripts = $gene->transcripts;
foreach my $t (@transcripts)
{
my @exons = $t->exons;
foreach my $e (@exons)
{
printf("Exon %d..%d
", $e->start, $e->end);
}
}
}
DESCRIPTION
This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It
relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the
default mode of operation which is to predict exons and assemble an optimal gene prediction.
It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.
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 - Keith James
Email: kdj@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $obj->new(-file = "<geneid.out");
$obj->new(-fh => *GI);
Function: Constructor for geneid wrapper. Takes either a file
: or filehandle
Returns : L<Bio::Tools::Geneid>
next_prediction
Title : next_prediction
Usage : while($gene = $geneid->next_prediction)
{
# do something
}
Function: Returns the gene structure prediction of the geneid result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Gene::GeneStructure object
Args : None
_add_exon
Title : _add_exon
Usage : $obj->_add_exon($gene, $transcript, ... exon data ...)
Function: Adds a new exon to both gene and transcript from the data
: supplied as args
Example :
Returns : Nothing
_set_strand
Title : _set_strand
Usage : $obj->_set_strand($gene)
Function: Sets the overall gene strand to the same strand as all
: the exons if they are all on the same strand, or to strand 0
: if the exons are on different strands.
Example :
Returns : Nothing
_target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns : A target ID
perl v5.14.2 2012-03-02 Bio::Tools::Geneid(3pm)