Thank you for trying. I have got to go and teach now though. I had to resave both files on this mac using TextEdit and whatever the default encoding was (UTF-8 I think). I made the awk one with ancient dredged up emacs muscle memories. Thanks - to be honest the subject id is good enough and it's not hard to get rid of a leading , which why I marked it solved. The files (not big) are attached - I had to edit the original output to remove potential identifier (hastily after I had posted it including it..).
Hi
I have requirement to find nth occurrence in a file and capture data from with in lines (between lines)
Data in File.
<QUOTE>
<SESSION>
<ATTRIBUTE NAME='Parameter Filename' VALUE='file1.parm'/>
<ATTRIBUTE NAME='Service Name' VALUE='None'/>
</SESSION>
<SESSION>
<ATTRIBUTE... (6 Replies)
Hi,
For my reuirement, I have to read a file from the 2nd line till the last line<EOF>.
Say,
I have a file as test.txt, which as a header record in the first line followed by records in rest of the lines.
for i in `cat test.txt`
{
echo $i
}
While doing the above loop, I have read... (5 Replies)
Hi ,
I want to print the nth and n+1 lines from a file once it gets a pattern match.
For eg:
aaa
bbb
ccc
ddd
gh
jjjj
If I find a match for bbb then I need to print bbb as well as 3rd and 4th line from the match.. Please help..Is it possible to get a command using sed :) (6 Replies)
Hi,
I am trying to remove lines once a string is found till another string is found including the start string and end string. I want to basically grab all the lines starting with color (closing bracket). PS: The line after the closing bracket for color could be anything (currently 'more').... (1 Reply)
Hello fellow awkers and seders:
need to figure out a way to ensure a software deployment has completed by checking its trace file in which I can store the deployment results as follows:
echo $testvar
===== Summary - Deploy Result - Start ===== ===== Summary - Deploy Result - End =====... (1 Reply)
Dear All
I am having a text file which is having more than 200 lines.
EX:
001010122 12000 BIB 12000 11200 1200003
001010122 2000 AND 12000 11200 1200003
001010122 12000 KVB 12000 11200 1200003
In the above file i want to search for string KVB... (5 Replies)
I have a need to print nth field based on the parameter passed. Suppose I have 3 fields in a file, passing 1 to the function should print 1st field and so on.
I have attempted below function but this throws an error due to incorrect awk syntax.
function calcmaxlen
{
FIELDMAXLEN=0
... (5 Replies)
Hi All,
I am very new to shell scripting and tried to search this in the forum but no luck.
Requirment:
I have an input file which is comma separated. I need to replace the value in 4th column with another value. This has to happen for all the lines in the file.
Sample data:
Input... (2 Replies)
I cannot seem to get what should be a simple awk one-liner to work correctly and cannot figure out why. I would like to use patterns from a specific field in one file as regex to search for matching strings in the entire line ($0) of another file.
I would like to output the lines of File2 which... (1 Reply)
Discussion started by: jvoot
1 Replies
LEARN ABOUT DEBIAN
theseus_align
THESEUS_ALIGN(1) General Commands Manual THESEUS_ALIGN(1)NAME
theseus_align - quick-and-dirty way to superimpose proteins
SYNOPSIS
theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...
OPTIONS
The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).
DESCRIPTION
This manual page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
different sequences. It should work very well when the protein sequences are relatively similar, although the ML method will still give
much better results than least-squares when the sequences are moderately divergent. Technically, this procedure gives a structure-based
superposition of a sequence-based alignment. It does not perform a structure-based alignment.
First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
that you supply.
Second, these sequences are aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it can generate clustal-
formatted files. However, I highly recommend Bob Edgar's MUSCLE program for both its speed and accuracy. (For more info see
http://www.drive5.com/muscle/ .)
Third, theseus performs a superposition of the structures using the sequence alignment as a guide.
The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other pro-
grams mentioned above, you'll have to copy the script to your own directory and edit it.
SEE ALSO
theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1). All of these programs can be installed on Debian
or Ubuntu systems using apt-get (8).
AUTHOR
theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.
November, 2008 THESEUS_ALIGN(1)