10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
see I have a text like:
27-MAY 14:00 4 aaa 5.30 0.01
27-MAY 14:00 3 aaa 0.85 0.00
27-MAY 14:00 2 aaa 1.09 0.00
27-MAY 14:00 5 aaa 0.03 0.00
27-MAY 14:00... (3 Replies)
Discussion started by: netbanker
3 Replies
2. Shell Programming and Scripting
Hi All,
Need help to grep blank and copy to file. I have a file in below format
dns1dm06_10,
dns2dm02_04,
dbidub,10000000c9a46d0c
gbpuhci,10000000c948b00a
ibtur001,10000000c9a1ccda
yubkbtp1,10000000c93fec5b
I need to copy to all lines which doesn't have wwn >> no-wwn.txt
1... (2 Replies)
Discussion started by: ranjancom2000
2 Replies
3. Shell Programming and Scripting
here in the below code just a space between 'Info' and '(' is showing that the patter doesnt match...
echo "CREATE TABLE Info (" | grep -i "CREATE TABLE Info (" | wc | awk -F' ' '{print $1}'
1
echo "CREATE TABLE Info (" | grep -i "CREATE TABLE Info (" | wc | awk -F' ' '{print $1}'
0
... (9 Replies)
Discussion started by: vivek d r
9 Replies
4. Shell Programming and Scripting
Hey guys,
I'm having a bit of trouble getting this to work using either sed or grep. It's possible awk might be the ticket I need as well, but my regulat expression skills aren't quite up to the task for doing this.
I'm looking to grep for the string ERROR from the following log up until any... (6 Replies)
Discussion started by: terrell
6 Replies
5. Shell Programming and Scripting
Hi Expert,
Kindly request for your expertise in this matter.
I have below output:
12.125.124.173,xx1.common.com
12.125.124.174,xx2.common.com
12.125.124.175,xx3.common.com
12.125.124.176,
12.125.124.177,
12.125.124.178,
12.125.124.179,xx4.common.com
12.125.124.180,xx5.common.com... (8 Replies)
Discussion started by: regmaster
8 Replies
6. Shell Programming and Scripting
Hi,
I want to know how to grep space.
Eg: input file contains
1565432 432 546
3514432 432 545
6541332 432 354
5464412 565 355
8456145 546 534
5632465 432 654
From this i need output of the lines which has 432 which are bold.
My requirement is whenever 432 comes... (3 Replies)
Discussion started by: rakeshbharadwaj
3 Replies
7. Shell Programming and Scripting
Hello All,
I am trying to match white space in patterns through - Grep
I tried ] & ] but none of them worked.
Then I tried Perl extension '\s' and it worked.
So just wanted to know if ] & ] are still supported or have they become deprecated.
However they have been mentioned in the... (3 Replies)
Discussion started by: paragkalra
3 Replies
8. Shell Programming and Scripting
Hi,
i have to search for a char like that :
export var1="i am not happy /not happy"
with a command like :
grep $var1 file
but this not working with me !!!
thank you in advance. (2 Replies)
Discussion started by: tizilfin
2 Replies
9. Shell Programming and Scripting
Hii... Every One......
I want to grep multiple patterns with space in between them.
For eg : I have a file which contains following :
red cat
every one
new one
you are
an ox
take one
Now, what I want to do is to grep " you are" , "an ox" and "red cat" from this file.
Any help........ (5 Replies)
Discussion started by: prashantshukla
5 Replies
10. UNIX for Dummies Questions & Answers
Hi, All,
I wonder how to change the field separator of grep from : to space when use grep to display.
for example when I use
grep -e 'pattern1' -e 'pattern2' -n filename
to find patterns, it use : to separate patterns, but I want to use blank space. is there an option I can set to... (2 Replies)
Discussion started by: Jenny.palmy
2 Replies
POA(1) POA(1)
NAME
poa - align a set of sequences or alignments.
SYNOPSIS
poa [OPTIONS] [MATRIXFILE]
One of the -read_fasta, -read_msa, or -read_msa_list arguments must be used, since a sequence or alignment file is required.
DESCRIPTION
POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed,
scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to
MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can
be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10 to 30 times faster than
CLUSTALW.
EXAMPLES
poa -read_fasta multidom.seq -clustal m.aln blosum80.mat
On Debian systems, poa can be tested using the following command:
poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat
OPTIONS
INPUT
-read_fasta FILE
Read in FASTA sequence file.
-read_msa FILE
Read in MSA alignment file.
-read_msa2 FILE
Read in second MSA file.
-subset FILE
Filter MSA to include list of seqs in file.
-subset2 FILE
Filter second MSA to include list of seqs in file.
-remove FILE
Filter MSA to include list of seqs in file.
-remove2 FILE
Filter second MSA to include list of seqs in file.
-read_msa_list FILE
Read an MSA from each filename listed in file.
-tolower
Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files).
-toupper
Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files).
ALIGNMENT
-do_global
Do global alignment.
-do_progressive
Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores.
-read_pairscores FILE
Read tab-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment.)
-fuse_all
Fuse identical letters on align rings.
ANALYSIS
-hb
Perform heaviest bundling to generate consensi.
-hbmin VALUE
Include in heaviest bundle sequences with percent ID (as a fraction) >= VALUE.
OUTPUT
-pir FILE
Write out MSA in PIR format.
-clustal FILE
Write out MSA in CLUSTAL format.
-po FILE
Write out MSA in PO format.
-preserve_seqorder
Write out MSA with sequences in their input order.
-printmatrix LETTERS
Print score matrix to stdout.
-best
Restrict MSA output to heaviest bundles (PIR only).
-v
Run in verbose mode (e.g. output gap penalties).
REFERENCE
Please cite Grasso C, Lee C.(2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed
and scalability to very large alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12.
SEE ALSO
The homepage of POA is http://www.bioinformatics.ucla.edu/poa
COPYRIGHTS
Copyright (C) 2001, 2006 Christopher Lee <leec@mbi.ucla.edu>. POA is free software. You can redistribute it and/or modify it under the
terms of the GNU General Public License as published by the Free Software Foundation.
This manual page was written by Charles Plessy <charles-debian-nospam@plessy.org> for the Debian(TM) system (but may be used by others).
Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any
later version published by the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
COPYRIGHT
Copyright (C) 2006 Charles Plessy
september 26, 2006 POA(1)