Basically what I am trying to do is match the exact gene name in the input (panel_genes.txt) with the gene names in column M of the attached hg19_refGene.txt. Thank you.
hi all
i have directory
/usr
under this directory i have subdirectories
tmp1,tmp2,tmp3
like this
/usr/tmp1
/usr/tmp2
/usr/tmp3
and so on
i want to search string in files (i don't know the name of the files)and i want to serch it in all the directories under the /usr
how shell i do... (3 Replies)
I am doing "ps -f" to see my process.
but I get lines that one of it represents the ps command itself.
I want to grep it out using -v flag, but than I get another process that belongs to the GREP itself :
I would like to exclude
# ps -f
UID PID PPID C STIME TTY TIME CMD... (2 Replies)
Hi guys, i wondering with any1 could help me with this.
I have this script will i need to "grep" an integer form a file x2. If the value is 0 then it's ok. But anything greater then 0, i'll ask the script to echo an error message. This is how the script looks like:
MESSAGEFILE=x2
STRING="0"
... (5 Replies)
i want to search in the current directory all the files that contain one word for example "hello"
i want to achieve it with the grep command but not with the grep * (2 Replies)
Hi, im taking an entry Unix class, and as part of my lab assignment I have to copy all files in the /home/david/lab3 directory that have the file extension .save to your lab3/temp directory. I'm having trouble getting the grep to do anything worth while
I've been trying to do:
cp... (6 Replies)
Hi,
I have around 500 Text files and Each file will be having either
String1 or String2.
I want to list the file only which has String1 and Sting2 in a single command.. (5 Replies)
Hi
I have lots of file in on folder and i want to egrep from only few files.
List of files......
Polt_KJ_430_OutputRBS_istUt_CR2.log
Polt_KN_4122_OutputRBS_ncChk_CR.log
Polt_LN_2230_OutputRNC_Hth_CLKLKL.log
Solt_KJ_430_OutputRBS_istUt_CR2.log
Solt_KN_4122_OutputRBS_ncChk_CR3.log... (2 Replies)
Hello,
I am running below command as root user
#nodetool cfstats tests | grep "Memtable switch count"
Memtable switch count: 12
Where as when I try to run same command as another user it gives different result.
#su -l zabbix -s /bin/bash -c "nodetool cfstats tests | grep "Memtable switch... (10 Replies)
for example i have a directory
home/solaris/unix/samplefiles/
with defaults files in it.. those default files have 1 word in common "UNIX". how can i list the files without "UNIX" words in it using grep command
thanks,
im using unix solaris, korn shell.. (1 Reply)
Discussion started by: daveaztig14
1 Replies
LEARN ABOUT DEBIAN
ace::sequence::gappedalignment
Ace::Sequence::GappedAlignment(3pm) User Contributed Perl Documentation Ace::Sequence::GappedAlignment(3pm)NAME
Ace::Sequence::GappedAlignment - Gapped alignment object
SYNOPSIS
# open database connection and get an Ace::Sequence object
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 gapped alignments
@alignments = $seq->alignments('EST_GENOME');
# get the aligned segments from the first one
@segs = $alignments[0]->segments;
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);
DESCRIPTION
Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds
the ability to retrieve the positions of the aligned segments. Each segment is an Ace::Sequence::Feature, from which you can retrieve the
source and target coordinates.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::GappedAlignment object directly. Instead, objects will be created in response to a
alignments() call to an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
segments()
@segments = $gene->segments;
Return a list of Ace::Sequence::Feature objects corresponding to similar segments.
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 166:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-11-10 Ace::Sequence::GappedAlignment(3pm)