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Full Discussion: Extracting a block of text from a large file using variables?
Top Forums UNIX for Dummies Questions & Answers Extracting a block of text from a large file using variables? Post 302891063 by Klor on Monday 3rd of March 2014 03:21:51 PM
Old 03-03-2014
Extracting a block of text from a large file using variables?
Hi UNIX Members,

I've been tasked with performing the following:
Extract a block of data in column form
#This data changes each time, therefore automating future procedures

Please Note the following:
line = reading a line from a file_list that leads to the data
The filename is called mol_1($line).opt.out, the block of text is in the opt.out file

So far I have:
Set variables to assign line numbers the text I require lies between ( $ORB and $MULL)
######I would like to extract the text between these two variables#####
I'd like to make a seperate file 'HOMO'(Highest Occupied Molecular Orbital) in which is a temporary data file which I can work with.

Scope of file : $ORB = 18172, $MULL = 18278
Line numbers needed to extract is 18172-18278 (however these change therefore are created as variables)



The current script I have is:
Code:
#!/bin/bash -f
while read line
do

#mkdir HOMO
#cd ./B3LYP_631Gstar2.$line

OBEGIN=$(cat -n $line.opt.out | grep "ORBITAL ENERGIES" | tail -1 | cut -f 1)
OEND=4
ORB=$(( $OBEGIN + $OEND ))
#echo $ORB

MBEGIN=$(cat -n $line.opt.out | grep "MULLIKEN POPULATION ANALYSIS" | tail -1 | cut -f 1)
MEND=3
MULL=$(( $MBEGIN - $MEND ))

###### Works up till here, above is to show what i'm working with####
###Below is the 3 methods i've tried

#sed '$ORB,$MULL!d' $line.opt.out > HOMO
#awk 'NR==$ORB,NR==$MULL' $line.opt.out | cut -f1  > HOMO
#grep -E '($ORB: ){5}$MULL' < $line.opt.out > HOMO

#echo $MULL
done<$1

~

Summary of task: Extracting a block of text from a large file using variables $ORB and $MULL as numbers

#######EXTRA#####
If you know how to extract data that is in columns ( Say I need only column 2 and column 4 out of 6 columns) to be in columns in another file (sort of like an excel file) that's be much appreciated!


Warm Regards, Klor
Last edited by Scrutinizer; 03-03-2014 at 04:33 PM.. Reason: code tags
 

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LEARN ABOUT SUNOS

liborbit-2

libORBit-2.3(3) 					 Introduction to Library Functions					   libORBit-2.3(3)

NAME

       libORBit-2 - the GNOME Object Request Broker (ORB)

DESCRIPTION

       libORBit-2  is a CORBA Object Request Broker (ORB) which forms the core of the GNOME component system, Bonobo. ORBit2 conforms to the CORBA
       2.4 specification and provides an implementation of the C language mapping.  ORBit2 also provides some extensions to the  CORBA	specifica-
       tion;  for example, an interface type data representation which can be generated by the IDL compiler or at runtime, and used to dynamically
       invoke CORBA methods and process CORBA requests.

       To access the API documentation, you must install the developer version of the package.

FILES

       The following files are used by this application:

       /usr/lib/libORBit-2.so  GNOME Object Request Broker shared library

       /usr/share/gtk-doc/html Location of developer documentation

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWgnome-component	   |
       +-----------------------------+-----------------------------+
       |Interface stability	     |External			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       orbit-idl-2(1), libORBitCosNaming-2(3), libIDL-2(3), libbonobo-activation(3), libbonobo-2(3)

NOTES

       Written by Mark McLoughlin, Sun Microsystems Inc., 2003, 2004.

SunOS 5.10							    31 Aug 2004 						   libORBit-2.3(3)
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