Help with AWK and Scripting! Post: 302445626

Sponsored Content

Top Forums Shell Programming and Scripting Help with AWK and Scripting! Post 302445626 by SriJit on Monday 16th of August 2010 11:12:15 AM

08-16-2010

Registered User

Incorrect Ouput

Hi Agama,

I ran yoyour second code. It gives me the wrong output. It even prints the texts in the input.

Here is a sample input,

Code:

#### ACGG_NNNP.pairwiseRMSDs.txt
#### Output from pdb_extract.py
#### Created 2010-08-12 13:59:31.122708

5 structures aligned

1OSW_0002_ACGG_NNNP_A_10_13.pdb.pdb most representative structure of pool
 with lowest average pair-wise RMSD of 0.81

    Mean global RMSD: 0.91  (0.81 to 0.98A)
 Mean global bb RMSD: 0.72  (0.65 to 0.82A)

                                 Avg  Avgbb  Pair-Wise RMSD Matrix:
Structure:                       RMSD RMSD  (Top-Right=Heavy atom alignment, Bottom-Left=Backbone atom alignment)
-------------------------------  ---- ----   0_13 0_13 0_13 0_13 0_13
1OSW_0002_ACGG_NNNP_A_10_13.pdb  0.81 0.65  [     0.84 0.77 0.95 0.70]
1OSW_0005_ACGG_NNNP_A_10_13.pdb  0.85 0.76  [0.85      1.01 0.59 0.94]
1OSW_0015_ACGG_NNNP_A_10_13.pdb  0.98 0.68  [0.43 0.83      1.10 1.04]
1OSW_0019_ACGG_NNNP_A_10_13.pdb  0.95 0.82  [0.91 0.51 0.94      1.14]
1OSW_0021_ACGG_NNNP_A_10_13.pdb  0.95 0.67  [0.42 0.83 0.52 0.91     ]

END

Can you please try to run the code for this and see if it works perfectly with just printing the matrix with 0 inserted in the spaces along the diagonal? If not can you make what changes I should make to get that output? It is 5*5 matrix in the above input. There is space along the diagonal.

Thanks,
Srijit

Last edited by Scott; 08-17-2010 at 03:49 AM.. Reason: Code tags, please...

SriJit

View Public Profile for SriJit

Find all posts by SriJit

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Awk scripting

Hi, I'm new to unix and i am kind of familiar with the basic commands. can anyone suggest some good books especially for AWK scripting and SHELL scripting thanks, Hari

2. Shell Programming and Scripting

AWK scripting

I have a text file in which the text has been divided into paragraphs (two line breaks or tab marks a new paragraph) and I want to make a script which output would delete line breaks within the paragraph and the different paragraphs would be separated by two line breaks. So, if my input file...

3. Shell Programming and Scripting

Scripting via awk

Hi, I am trying to understand what is happening here, new to scripting: I have a couple of these, but if I knew what was going on in one I can figure out the rest: awk '/rpc-100083/ { $2 = "enable -r" } $3 ~ /.NOS99dtlogin/ { $t = $2; $2 = $3; $3 = $t } { print }' /var/svc/profile/upgrade...

4. Shell Programming and Scripting

awk scripting

Hi I have 2 files of large size( 10 Miilions) , i want to join 2 files based on some condition . for this taking lot of time and 100 cpu .i want to iterate the based on some value (like 1 lakh) I put the 2 files in the associative arrays . if the array limit reaches the 1 lach join the with...

5. Shell Programming and Scripting

scripting/awk help : awk sum output is not comming in regular format. Pls advise.

Hi Experts, I am adding a column of numbers with awk , however not getting correct output: # awk '{sum+=$1} END {print sum}' datafile 2.15291e+06 How can I getthe output like : 2152910 Thank you.. # awk '{sum+=$1} END {print sum}' datafile 2.15079e+06

6. Shell Programming and Scripting

Need help with awk scripting.

Hi, i am newbie to this site and hope to learn but problem is s but need help urgently. Plz pm me if you are good at this. Help will be appreciated.

7. Shell Programming and Scripting

Need help with awk scripting

hi all, I am working on awk scripting.I have created two awk files and now have a requirement of replacing the contents of first file with some contents of second file. Please find below the two files created.File1 has 3 records and File2 has 4 records. cat File1 111,0165,CB21031251,0165,...

8. Shell Programming and Scripting

Need help in awk scripting

Hi I am beginner of shell/AWK scripting , can you please help me in select particular column and column between two pattern from a multiple column file. file1.txt number status date1 date2 description category ...

9. Shell Programming and Scripting

awk Scripting

Hey guys, I want to get all the columns in this input file tab-delimited, i need to get the column send them to a variable. From there i could print them in shuffle and pick and select columns i want. Here is the input sample 2013/08/05 06:50:38:067 MINOR SiteScope ...

10. Shell Programming and Scripting

New at scripting awk with variable

I am trying to write a shell script that will add a date to and awk command from the command prompt. here is the line I am having difficulties. zgrep -i playback $dir/$1-*-errors.out.gz |cut -d '|' -f 1,11,12,15 | awk -v start=${start} -v end=${end} -F '|' '{$1>=start && $1 <=end} {print $2...

LEARN ABOUT DEBIAN

g_anadock

g_anadock(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_anadock(1)

NAME

       g_anadock - cluster structures from Autodock runs

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_anadock  -f  eiwit.pdb  -ox  cluster.pdb  -od	edocked.xvg -of efree.xvg -g anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free
       -[no]rms -cutoff real

DESCRIPTION

	g_anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked  energy  and
       free energy estimates are analysed, and for each cluster the energy statistics are printed.

       An  alternative	approach to this is to cluster the structures first using  g_cluster and then sort the clusters on either lowest energy or
       average energy.

FILES

       -f eiwit.pdb Input
	Protein data bank file

       -ox cluster.pdb Output
	Protein data bank file

       -od edocked.xvg Output
	xvgr/xmgr file

       -of efree.xvg Output
	xvgr/xmgr file

       -g anadock.log Output
	Log file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]freeno
	Use Free energy estimate from autodock for sorting the classes

       -[no]rmsyes
	Cluster on RMS or distance

       -cutoff real 0.2
	Maximum RMSD/distance for belonging to the same cluster

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						      g_anadock(1)

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Awk scripting

Discussion started by: rharee

2. Shell Programming and Scripting

AWK scripting

Discussion started by: Muki101

3. Shell Programming and Scripting

Scripting via awk

Discussion started by: ulemsee

4. Shell Programming and Scripting

awk scripting

Discussion started by: kiranmosarla