11-05-2009
Hi,
I just found out that the code that you suggested also will print out the content of seq_81,seq_800,etc
Do you have any idea just only specific and only print out the content that matched with seq_8?
Thanks a lot ^^
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Hi,
I got a long list of contents:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
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My input file:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
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My input:
Data name: ABC001
Data length: 1000
Detail info
Data Direction Start_time End_time Length
1 forward 10 100 90
1 forward 15 200 185
2 reverse 50 500 450
Data name: XFG110
Data length: 100
Detail info
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Input file:
#abc_1
SAASFASFGGDSGDSGDSGSDGSDGSDGSDGSDGSDGSDGDS
Output file:
FASFGGDSGDS
I just want to print out the read from position 5 until position 15 from the data.
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>position_10 sample:68711 coords:5453-8666 number:3 type:complete len:344
MSINQYSSDFHYHSLMWQQQQQQQQHQNDVVEEKEALFEKPLTPSDVGKLNRLVIPKQHA
ERYFPLAAAAADAVEKGLLLCFEDEEGKPWRFRYSYWNSSQSYVLTKGWSRYVKEKHLDA
NRTS*
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Input file 1:
>pattern_5
GAATTCGTTCATGTAGGTTGASDASFGDSGRTYRYGHDGSDFGSDGGDSGSDGSDFGSDF
ATTTAATTATGATTCATACGTCATATGTTATTATTCAATCGTATAAAATTATGTGACCTT
SDFSDGSDFKSDAFLKJASLFJASKLFSJAKJFHASJKFHASJKFHASJKFHSJAKFHAW
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HS04636 PROGRAM source 836 7001 + ID=g1
HS04636 PROGRAM beginner 836 7001 + ID=g1.t1;Parent=g1
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HS04636 PROGRAM type 836 1017 + Parent=g1.t1
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21 templeta parent 35718 36554 . - . ID=parent_cluster_50.21.11; Name=Partial%20parent%20for%20training%20set;
21 templeta kids 35718 36554 . - . ID=_52; Parent=parent_cluster_5085.21.11;
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data.txt has several information like the below..
<SERVER>:WEB:MYDOM01:/tmp/cong/MYDOM01,/tmp/app/MYDOM01
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LEARN ABOUT MOJAVE
ppi::dumper5.18
PPI::Dumper(3) User Contributed Perl Documentation PPI::Dumper(3)
NAME
PPI::Dumper - Dumping of PDOM trees
SYNOPSIS
# Load a document
my $Module = PPI::Document->new( 'MyModule.pm' );
# Create the dumper
my $Dumper = PPI::Dumper->new( $Module );
# Dump the document
$Dumper->print;
DESCRIPTION
The PDOM trees in PPI are quite complex, and getting a dump of their structure for development and debugging purposes is important.
This module provides that functionality.
The process is relatively simple. Create a dumper object with a particular set of options, and then call one of the dump methods to
generate the dump content itself.
METHODS
new $Element, param => value, ...
The "new" constructor creates a dumper, and takes as argument a single PPI::Element object of any type to serve as the root of the tree to
be dumped, and a number of key->value parameters to control the output format of the Dumper. Details of the parameters are listed below.
Returns a new "PPI::Dumper" object, or "undef" if the constructor is not passed a correct PPI::Element root object.
memaddr
Should the dumper print the memory addresses of each PDOM element. True/false value, off by default.
indent
Should the structures being dumped be indented. This value is numeric, with the number representing the number of spaces to use when
indenting the dumper output. Set to '2' by default.
class
Should the dumper print the full class for each element. True/false value, on by default.
content
Should the dumper show the content of each element. True/false value, on by default.
whitespace
Should the dumper show whitespace tokens. By not showing the copious numbers of whitespace tokens the structure of the code can often
be made much clearer. True/false value, on by default.
comments
Should the dumper show comment tokens. In situations where you have a lot of comments, the code can often be made clearer by ignoring
comment tokens. True/value value, on by default.
locations
Should the dumper show the location of each token. The values shown are [ line, rowchar, column ]. See "location" in PPI::Element for a
description of what these values really are. True/false value, off by default.
print
The "print" method generates the dump and prints it to STDOUT.
Returns as for the internal print function.
string
The "string" method generates the dump and provides it as a single string.
Returns a string or undef if there is an error while generating the dump.
list
The "list" method generates the dump and provides it as a raw list, without trailing newlines.
Returns a list or the null list if there is an error while generation the dump.
SUPPORT
See the support section in the main module.
AUTHOR
Adam Kennedy <adamk@cpan.org>
COPYRIGHT
Copyright 2001 - 2011 Adam Kennedy.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
The full text of the license can be found in the LICENSE file included with this module.
perl v5.18.2 2011-02-25 PPI::Dumper(3)