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
muscle
MUSCLE(1) Muscle Manual MUSCLE(1)NAME
muscle - Multiple Protein Sequence Alignment
SYNOPSIS
muscle -in input file (fasta) [-out output file (default fasta)] [-diags] [-log log file] [-maxiters n] [-maxhours n] [-maxmb m] [-html]
[-msf] [-clw] [-clwstrict] [-log[a] logfile] [-quiet] [-stable] [-group] [-version]
DESCRIPTION
This manual page documents briefly the muscle command.
muscle aligns protein sequences and is considered superior and faster than Clustal W.
OPTIONS -in input file
Path to FASTA formatted input file
-out output file
Path to output file, FASTA formatted by default
-diags
Find diagonals (faster for similar sequences)
-maxiters n
Maximum number of iterations (integer, default 16)
-maxhours n
Maximum time to iterate in hours (default no limit)
-maxmb m
Maximum memory to allocate in Mb (default 80% of RAM)
-html
Write output in HTML format (default FASTA)
-msf
Write output in MSF format (default FASTA)
-clw
Write output in Clustal W format (default FASTA)
-clwstrict
As -clw, with 'CLUSTAL W (1.81)' header
-log[a] logfile
Log to file (append if -loga, overwrite if -log)
-quiet
Do not write progress messages to stderr
-stable
Output sequences in input order (default is -group)
-group
Group sequences by similarity (this is the default)
-version
Display version information and exit
SEE ALSO clustalw(1), seaview(1), t_coffee(1).
AUTHORS
Robert Elgar
Wrote Muscle.
Steffen Moeller <moeller@debian.org>
Wrote this manpage.
Charles Plessy <charles-debian-nospam@plessy.org>
Updated this manpage.
COPYRIGHT
Copyright (C) 2003, 2004 Steffen Moeller (manpage)
Copyright (C) 2007, 2008 Charles Plessy (manpage)
Muscle is in the public domain, and therefore not subjected to copyright.
This manual page was written by Steffen Moeller moeller@debian.org for the Debian(TM) system (but may be used by others). Permission is
granted to copy, distribute and/or modify this document as if it were in public domain.
muscle 3.7 02/06/2008 MUSCLE(1)