12-09-2011
Thank you methyl and Corona !
Unfortunately none of the propositions work.
---------- Post updated at 02:41 PM ---------- Previous update was at 02:19 PM ----------
I was thinking about something like that:
awk '{if ($1 ~/>/) print $0; else (sed 's/[^C]/-/g') print $0}' file.fasta
but it doesn't work.
Syntax error probably !
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
I get a text file with 70+ columns (seperated by Tab) and about 10000 rows. The 58th Column is all numbers. But sometimes 58th columns has "/xxx=##" after the numeric data. I want to truncate this string using the script. Any Ideas...:confused: (3 Replies)
Discussion started by: gagansharma
3 Replies
2. UNIX for Dummies Questions & Answers
how to use sed command to find and replace a directory
i have a file.. which contains lot of paths ...
for eg.. file contains..
/usr/kk/rr/12345/1
/usr/kk/rr/12345/2
/usr/kk/rr/12345/3
/usr/kk/rr/12345/4
/usr/kk/rr/12345/5
/usr/kk/rr/12345/6
/usr/kk/rr/12345/7... (1 Reply)
Discussion started by: wip_vasikaran
1 Replies
3. Shell Programming and Scripting
find . -type f -name "*.sql" -print|xargs perl -i -pe 's/pattern/replaced/g'
this is simple logic to find and replace in multiple files & folders
Hope this helps.
Thanks
Zaheer (0 Replies)
Discussion started by: Zaheer.mic
0 Replies
4. Shell Programming and Scripting
HI,
Please find the text below. I receive a .csv file on server. I need the comma(,) in the second column to be replaced by a semi-colon( ; ).
How to do it. Please help.
Sample text:
"1","lastname1,firstname1","xxxxxx","19/10/2009","23/10/2009","0","N","Leave"... (2 Replies)
Discussion started by: libin4u2000
2 Replies
5. Shell Programming and Scripting
Hi all ,
I'm new to unix
I have a checked project , there exists a file called xxx.config .
now my task is to find all the files in the checked out project which references to this xxx.config file.
how do i use grep or find command . (2 Replies)
Discussion started by: Gangam
2 Replies
6. Shell Programming and Scripting
Hi All,
I have a unix shell script file as below.
My task is
a)to replace 248 to 350 and need to create a new file as BW3_350.sh
b)to replace 248 to 380 and need to create a new file as BW3_380.sh
c)to replace 248 to 320 and need to create a new file as BW3_320.sh
there is no... (6 Replies)
Discussion started by: karthi_mrkg
6 Replies
7. Solaris
hi,
I would like to monitor a log file, which rolls over, everytime a server is restarted.
I would like to grep for a string, and to be more efficient i'd like to grep only newly appended data. so something like a 'tail -f' would do, however, as the log rolls over i think a 'tail -F' is... (2 Replies)
Discussion started by: horhif
2 Replies
8. UNIX for Dummies Questions & Answers
Hi
I am looking to rename the contents of this dir, each one with a new timestamp, interval of a second for each so it the existing format is on lhs and what I want is to rename each of these to what is on rhs..hopefully it nake sense
CDR.20060505.150006.gb CDR.20121211.191500.gb... (3 Replies)
Discussion started by: rob171171
3 Replies
9. Shell Programming and Scripting
I would like to take a fasta file formated like
>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
and use command line perl to move the all sample gt 8 in length to a new file. the result would be
>0001
agttcgaggtcagaatt
>0003
ggtaacctga
cat ${sample}.fasta | perl -lane... (2 Replies)
Discussion started by: jdilts
2 Replies
10. UNIX for Beginners Questions & Answers
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
LEARN ABOUT MOJAVE
file::find::rule::extending5.18
File::Find::Rule::Extending(3) User Contributed Perl Documentation File::Find::Rule::Extending(3)
NAME
File::Find::Rule::Extending - the mini-guide to extending File::Find::Rule
SYNOPSIS
package File::Find::Rule::Random;
use strict;
# take useful things from File::Find::Rule
use base 'File::Find::Rule';
# and force our crack into the main namespace
sub File::Find::Rule::random () {
my $self = shift()->_force_object;
$self->exec( sub { rand > 0.5 } );
}
1;
DESCRIPTION
File::Find::Rule went down so well with the buying public that everyone wanted to add extra features. With the 0.07 release this became a
possibility, using the following conventions.
Declare your package
package File::Find::Rule::Random;
use strict;
Inherit methods from File::Find::Rule
# take useful things from File::Find::Rule
use base 'File::Find::Rule';
Force your madness into the main package
# and force our crack into the main namespace
sub File::Find::Rule::random () {
my $self = shift()->_force_object;
$self->exec( sub { rand > 0.5 } );
}
Yes, we're being very cavalier here and defining things into the main File::Find::Rule namespace. This is due to lack of imaginiation on
my part - I simply can't find a way for the functional and oo interface to work without doing this or some kind of inheritance, and
inheritance stops you using two File::Find::Rule::Foo modules together.
For this reason try and pick distinct names for your extensions. If this becomes a problem then I may institute a semi-official registry
of taken names.
Taking no arguments.
Note the null prototype on random. This is a cheat for the procedural interface to know that your sub takes no arguments, and so allows
this to happen:
find( random => in => '.' );
If you hadn't declared "random" with a null prototype it would have consumed "in" as a parameter to it, then got all confused as it doesn't
know about a '.' rule.
AUTHOR
Richard Clamp <richardc@unixbeard.net>
COPYRIGHT
Copyright (C) 2002 Richard Clamp. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
SEE ALSO
File::Find::Rule
File::Find::Rule::MMagic was the first extension module, so maybe check that out.
perl v5.18.2 2011-09-19 File::Find::Rule::Extending(3)