Thank you Don. I corrected "cnt[$5]" to "c[5]" and it worked (on bash in OS X 10.6).
---------- Post updated at 02:08 PM ---------- Previous update was at 02:03 PM ----------
Thanks Rudi. That works great. So far I avoided learning awk except for the simplest tasks, because the flow control in snippets I've grabbed here and there is so terse (to me it appears non-existent in your and Don Cragun's solutions). But I've just got hold of Dale Dougherty's book on sed and awk, and I'll be learning how this works now. (Where's the loop for reading the file on the first pass? Where's the conditional print? Etc... I can already see from looking over Dougherty's book that the answers are there, no need to answer.)
Hi uncleMonty,
I apologize for the typo. It has now been corrected in my earlier post. Note that cnt[$5] should have been changed to c[$5] (NOT c[5])!.
The general form of an awk command (as I'm sure you will find in your book (or the [codei]awk[/icode] man page on your system) is:
If the condition is not present, the given action is applied to every input line that gets to that statement. If action and the surrounding braces are not present, a default action of print (which prints the current input line after any modifications to that line's contents applied by any previous statements have been applied) is taken for any line in which condition evaluates to a non-zero, non-empty string value. So, the awk statement:
prints any line for which the count of the number of times the contents of fields 1, 3, 5, and 7 have all all been seen cnt or more times.
i have a file a.txt and following is only one portion.
I want to search <branch value="/dev36/AREA/" include="yes"></branch> present in between
<template_file name="Approve External" path="core/approve/bin" and </template_file>
where the no of lines containing "<branch value= " is increasing ... (2 Replies)
My sql file xyz_abc.sql in this file there are multiple sql block in this block I need to find the following block
rem Subset Rows (&&tempName.*)
CREATE VIEW &&tempName.* AS
SELECT *
FROM &&tempName.*
WHERE f is not null
and replace with following code
rem Subset Rows... (9 Replies)
Hi,
I would like to know how to solve one of my problems using expert unix commands.
I have a file with occasional blank lines;
for example;
dertu
frthu
fghtu
frtty
frtgy
frgtui
frgtu
ghrye
frhutp
frjuf
I need to edit the file so that the file looks like this; (10 Replies)
Hello all, new to unix and have just found the forum.
I think I will be here quite often, and hope that in time i will be able to provide soem help, role on not being a newbie anymore :)
I have a question which iI am hoping someone could help me with.
If i have a file with lines in in thus... (8 Replies)
i have a file containing over 1 million records,and i want to print about 300,000 line containing a some specific words.
file has content.
eg
1,rrt,234
3,fgt,678
4,crf,456
5,cde,drt
6,cfg,123
and i want to print the line with the word fgt,crf
this is just an example,my file is so... (2 Replies)
Hi Experts,
I have a file which contains some text. i need to print the word next to a given keyword. Please help.
Ex: test.txt
=====================
NEXT HOST
=====================
AEADBAS001
access-list 1 permit xxxxxxxxxxxxxx
ip access-list extended BLA_Outgoing_Filter... (6 Replies)
i need to get least lines of file after last word TEST in file, and send that lines to mail
example of file structure:
TEST 10.10.2010
jdfjdnjfndjfndnfkdk
djfjdnfjkdjkfnjkdfk
jdfjdjfnjdjnfjkdnfjk
TEST 11.10.2010
jdjfnjdnfdkdfjdfjdnk
jdnfjdnjkfndnfjdnfjk
fjdnfjkndnfdfnjdnfjk
TEST... (6 Replies)
Hi All,
I want to read all lines after a perticular string {SET UP VALUES}apprears in the file.
SET UP values contains direcory, number of days and file type.
Step1: Read all lines below SET UP VALUES string.
Step2: If set up values are not present in each record then read from default... (4 Replies)
Hi ,
i have a file with data as below.This is same file. But actual file contains to many rows.
i want to search for a string "Field 039 00" and delete that line and previous 3 lines in that file.. Can some body suggested me how can i do using either sed or awk command ?
Field 004... (7 Replies)
Guys i need an idea for one logic..in shell scripting am struggling with a logic...So the thing is... i need to search for a word in a huge log file and i need to continue to print few more lines from that line and the consecutive line has to end when it finds the line with date..because i know... (1 Reply)
Discussion started by: Prathi
1 Replies
LEARN ABOUT DEBIAN
bio::structure::atom
Bio::Structure::Atom(3pm) User Contributed Perl Documentation Bio::Structure::Atom(3pm)NAME
Bio::Structure::Atom - Bioperl structure Object, describes an Atom
SYNOPSIS
#add synopsis here
DESCRIPTION
This object stores a Bio::Structure::Atom
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 - Kris Boulez
Email kris.boulez@algonomics.com
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new()
Title : new()
Usage : $struc = Bio::Structure::Atom->new(
-id => 'human_id',
);
Function: Returns a new Bio::Structure::Atom object from basic
constructors. Probably most called from Bio::Structure::IO.
Returns : a new Bio::Structure::Atom object
x()
Title : x
Usage : $x = $atom->x($x);
Function: Set/gets the X coordinate for an Atom
Returns : The value for the X coordinate of the Atom (This is just a number,
it is expected to be in Angstrom, but no garantees)
Args : The X coordinate as a number
y()
Title : y
Usage : $y = $atom->y($y);
Function: Set/gets the Y coordinate for an Atom
Returns : The value for the Y coordinate of the Atom (This is just a number,
it is eypected to be in Angstrom, but no garantees)
Args : The Y coordinate as a number
z()
Title : z
Usage : $z = $atom->z($z);
Function: Set/gets the Z coordinate for an Atom
Returns : The value for the Z coordinate of the Atom (This is just a number,
it is ezpected to be in Angstrom, but no garantees)
Args : The Z coordinate as a number
xyz()
Title : xyz
Usage : ($x,$y,$z) = $atom->xyz;
Function: Gets the XYZ coordinates for an Atom
Returns : A list with the value for the XYZ coordinate of the Atom
Args :
residue()
Title : residue
Usage :
Function: No code here, all parent/child stuff via Entry
Returns :
Args :
icode()
Title : icode
Usage : $icode = $atom->icode($icode)
Function: Sets/gets the icode
Returns : Returns the icode for this atom
Args : reference to an Atom
serial()
Title : serial
Usage : $serial = $atom->serial($serial)
Function: Sets/gets the serial number
Returns : Returns the serial number for this atom
Args : reference to an Atom
occupancy()
Title : occupancy
Usage : $occupancy = $atom->occupancy($occupancy)
Function: Sets/gets the occupancy
Returns : Returns the occupancy for this atom
Args : reference to an Atom
tempfactor()
Title : tempfactor
Usage : $tempfactor = $atom->tempfactor($tempfactor)
Function: Sets/gets the tempfactor
Returns : Returns the tempfactor for this atom
Args : reference to an Atom
segID()
Title : segID
Usage : $segID = $atom->segID($segID)
Function: Sets/gets the segID
Returns : Returns the segID for this atom
Args : reference to an Atom
pdb_atomname()
Title : pdb_atomname
Usage : $pdb_atomname = $atom->pdb_atomname($pdb_atomname)
Function: Sets/gets the pdb_atomname (atomname used in the PDB file)
Returns : Returns the pdb_atomname for this atom
Args : reference to an Atom
element()
Title : element
Usage : $element = $atom->element($element)
Function: Sets/gets the element
Returns : Returns the element for this atom
Args : reference to an Atom
charge()
Title : charge
Usage : $charge = $atom->charge($charge)
Function: Sets/gets the charge
Returns : Returns the charge for this atom
Args : reference to an Atom
sigx()
Title : sigx
Usage : $sigx = $atom->sigx($sigx)
Function: Sets/gets the sigx
Returns : Returns the sigx for this atom
Args : reference to an Atom
sigy()
Title : sigy
Usage : $sigy = $atom->sigy($sigy)
Function: Sets/gets the sigy
Returns : Returns the sigy for this atom
Args : reference to an Atom
sigz()
Title : sigz
Usage : $sigz = $atom->sigz($sigz)
Function: Sets/gets the sigz
Returns : Returns the sigz for this atom
Args : reference to an Atom
sigocc()
Title : sigocc
Usage : $sigocc = $atom->sigocc($sigocc)
Function: Sets/gets the sigocc
Returns : Returns the sigocc for this atom
Args : reference to an Atom
sigtemp()
Title : sigtemp
Usage : $sigtemp = $atom->sigtemp($sigtemp)
Function: Sets/gets the sigtemp
Returns : Returns the sigtemp for this atom
Args : reference to an Atom
aniso()
Title : aniso
Usage : $u12 = $atom->aniso("u12", $u12)
Function: Sets/gets the anisotropic temperature factors
Returns : Returns the requested factor for this atom
Args : reference to an Atom, name of the factor, value for the factor
id()
Title : id
Usage : $atom->id("CZ2")
Function: Gets/sets the ID for this atom
Returns : the ID
Args : the ID
_remove_residue()
Title : _remove_residue
Usage :
Function: Removes the Residue this Atom is atttached to.
Returns :
Args :
_grandparent()
Title : _grandparent
Usage :
Function: get/set a symbolic reference to our grandparent
Returns :
Args :
perl v5.14.2 2012-03-02 Bio::Structure::Atom(3pm)