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Top Forums UNIX for Dummies Questions & Answers Probably some stupid mistake... Post 302491722 by sluvah on Friday 28th of January 2011 06:09:37 AM
Old 01-28-2011
[solved]Probably some stupid mistake...

Hi everyone !

I have a file wich look like this :

>Sis01
[lots of ATCG stuff]

> Sis02
[lots of ATCG stuff]

...

>Sis44
[lots of ATCG stuff]


I want to separe each paragraphe in a different file, so I decide to use the "FOR" loop + sed.

Code:
for f in {01..44}
do
(
   sed -n '/^>Sis `echo $f'/,/^>/p' Sis_110125.fasta | sed '$d' > Sis_110125_contig`echo $f`
)
done

I get empty files, i think due to the space between ^> and the echoed $f


I try a lot of thing, but I was unable to find a solution !

Thanks for your help !

Last edited by sluvah; 01-28-2011 at 02:10 PM.. Reason: Solved
 

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MooseX::AttributeHelpers::MethodProvider::List(3pm)	User Contributed Perl Documentation    MooseX::AttributeHelpers::MethodProvider::List(3pm)

NAME
MooseX::AttributeHelpers::MethodProvider::List - method generator for MooseX::AttributeHelpers::Collection::List SYNOPSIS
package Stuff; use Moose; use MooseX::AttributeHelpers; has 'options' => ( metaclass => 'Collection::List', is => 'rw', isa => 'ArrayRef[Str]', default => sub { [] }, auto_deref => 1, provides => { elements => 'all_options', map => 'map_options', grep => 'filter_options', find => 'find_option', first => 'first_option', last => 'last_option', get => 'get_option', join => 'join_options', count => 'count_options', empty => 'do_i_have_options', sort => 'sorted_options', } ); no Moose; 1; DESCRIPTION
This is a role which provides the method generators for MooseX::AttributeHelpers::Collection::List. METHODS
meta PROVIDED METHODS
count Returns the number of elements in the list. $stuff = Stuff->new; $stuff->options(["foo", "bar", "baz", "boo"]); my $count = $stuff->count_options; print "$count "; # prints 4 empty If the list is populated, returns true. Otherwise, returns false. $stuff->do_i_have_options ? print "Good boy. " : die "No options! " ; find This method accepts a subroutine reference as its argument. That sub will receive each element of the list in turn. If it returns true for an element, that element will be returned by the "find" method. my $found = $stuff->find_option( sub { $_[0] =~ /^b/ } ); print "$found "; # prints "bar" grep This method accepts a subroutine reference as its argument. This method returns every element for which that subroutine reference returns a true value. my @found = $stuff->filter_options( sub { $_[0] =~ /^b/ } ); print "@found "; # prints "bar baz boo" map This method accepts a subroutine reference as its argument. The subroutine will be executed for each element of the list. It is expected to return a modified version of that element. The return value of the method is a list of the modified options. my @mod_options = $stuff->map_options( sub { $_[0] . "-tag" } ); print "@mod_options "; # prints "foo-tag bar-tag baz-tag boo-tag" sort Sorts and returns the elements of the list. You can provide an optional subroutine reference to sort with (as you can with the core "sort" function). However, instead of using $a and $b, you will need to use $_[0] and $_[1] instead. # ascending ASCIIbetical my @sorted = $stuff->sort_options(); # Descending alphabetical order my @sorted_options = $stuff->sort_options( sub { lc $_[1] cmp lc $_[0] } ); print "@sorted_options "; # prints "foo boo baz bar" elements Returns all of the elements of the list my @option = $stuff->all_options; print "@options "; # prints "foo bar baz boo" join Joins every element of the list using the separator given as argument. my $joined = $stuff->join_options( ':' ); print "$joined "; # prints "foo:bar:baz:boo" get Returns an element of the list by its index. my $option = $stuff->get_option(1); print "$option "; # prints "bar" first Returns the first element of the list. my $first = $stuff->first_option; print "$first "; # prints "foo" last Returns the last element of the list. my $last = $stuff->last_option; print "$last "; # prints "boo" BUGS
All complex software has bugs lurking in it, and this module is no exception. If you find a bug please either email me, or add the bug to cpan-RT. AUTHOR
Stevan Little <stevan@iinteractive.com> COPYRIGHT AND LICENSE
Copyright 2007-2009 by Infinity Interactive, Inc. <http://www.iinteractive.com> This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.10.1 2010-01-02 MooseX::AttributeHelpers::MethodProvider::List(3pm)
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