I want to count the number of each gene in the file, for example there are 3 of ENSGALG00000000189 and so on. I came up with the code above, but it doesn't work properly, could you please help me with that?
Hello,
I have afile which begins with a few urls on multiple lines and then there is listing of some information on separate lines.
The listing begins with the word Name on a given line followed by teh actual list.
I want to count the number of lines in this file after the line having... (6 Replies)
Hi All,
I have to count the number of occurences of the character " ; " in a given line.
I had used the following awk command to achieve the same
echo $KOP.dat|awk '{split($1,my,";"); for(i in my)c++ }END{print c-1}'
My file KOP.dat had the following data
... (1 Reply)
Hi all,
I use bash shell and I have a problem with wc.
I would like to determine the number of lines in a file so I do
wc -l filename
but I don't want to get the filename again
I just would like to have the number of lines and use it in a variable.
Can anybody help?
Thank you, (7 Replies)
say i've got a text file with >10million sequences:
ssss
ssss
tttttt
uuuuuu
uuuuuu
uuuuuu
...
I'd like to convert the file so that the output will report the number of occurence right by each sequence:
2 ssss
2 ssss
1 tttttt
3 uuuuuu
3 uuuuuu
3 uuuuuu
.... (3 Replies)
Hi all
I want to count total numbers of sentences separated by fullstop (.) in different files under a directory at one go. Any help is appreciated. (3 Replies)
Hi all
I have file with columns
F3 pathway CPS
F2
H2
H4
H5
H6 no pathway CMP
H7
H8
H9
H10
My expected output is
F3 pathway CPS
F2 pathway CPS (10 Replies)
So I have several files (35000, to be exact) in the format rmsd_protein_*.dat each with 2 columns and 35000 rows.
I would like to count how many values in the second column are less than 3 for each file, and output it into a new file so that it ultimately appears as:
1 14057
2 ... (12 Replies)
Hi,
could you help me in processing this file under bash?
I need to add some text to the first line and then append the last element of the second columns.
The input file is tab separated while the output should be space separated.
input file is
1.00E-02 2.00E-02 4.465E+17
2.00E-02 3.00E-02... (4 Replies)
Discussion started by: f_o_555
4 Replies
LEARN ABOUT DEBIAN
ace::sequence::gene
Ace::Sequence::Gene(3pm) User Contributed Perl Documentation Ace::Sequence::Gene(3pm)NAME
Ace::Sequence::Gene - Simple "Gene" Object
SYNOPSIS
# open database connection and get an Ace::Object sequence
use Ace::Sequence;
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);
# get all the genes
@genes = $seq->genes;
# get the exons from the first one
@exons = $genes[0]->exons;
# get the introns
@introns = $genes[0]->introns
# get the CDSs (NOT IMPLEMENTED YET!)
@cds = $genes[0]->cds;
DESCRIPTION
Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability
to retrieve the annotated introns and exons of the gene.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a genes() call to
an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
exons()
@exons = $gene->exons;
Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.
introns()
@introns = $gene->introns;
Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.
cds()
@cds = $gene->cds;
Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.
relative()
$relative = $gene->relative;
$gene->relative(1);
This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used
by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first
exon will (usually) be 1.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 148:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-02-18 Ace::Sequence::Gene(3pm)