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Top Forums Shell Programming and Scripting parsing a portion of Data from a text file Post 302457343 by Lucky Ali on Monday 27th of September 2010 09:34:06 PM
Old 09-27-2010
parsing a portion of Data from a text file

Hi All,
I need some help to effectively parse out a subset of results from a big results file.

Below is an example of the text file. Each block that I need to parse starts with "Output of GENE for sequence file 100.fasta" (next block starts with another number). I have given the portion of the block that I need to parse out below and rest of the block is incomplete (given only those text thats needed for parsing.)


Code:
# Output of GENE for sequence file 100.fasta
#
#
#
#
# 
# 
# Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     4.145      0.6043        -0.01       0.0274
# OuterSeq
#  frags    0.125      1.0000         0.00       0.0000
#
#
#
#Output of GENE for sequence file 101.fasta
#
#
#
#
#
## Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     2.665      0.8360         0.44       0.0439
# OuterSeq
#  frags  Not found      0.0000         0.00       0.0000
#
#
#
#
#Output of GENE for sequence file 103.fasta
#
#
#
#
#
## Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     3.665      0.8705         1.44       0.0039
# OuterSeq
#  frags  Not found      1.0000         2.00       0.0000

I would like to parse out the number, for example, 100 from the block 'Output of GENE for sequence file 100.fasta" and then the Sim P-values of each block in such a way

Code:
100  0.6043
101 0.8360 
103 0.8705

Please let me know the best and simple way to parse out this using awk or sed.

LA
 

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MIME::Parser::Results(3)				User Contributed Perl Documentation				  MIME::Parser::Results(3)

NAME
MIME::Parser::Results - results of the last entity parsed SYNOPSIS
Before reading further, you should see MIME::Parser to make sure that you understand where this module fits into the grand scheme of things. Go on, do it now. I'll wait. Ready? Ok... ### Do parse, get results: my $entity = eval { $parser->parse(*STDIN); }; my $results = $parser->results; ### Get all messages logged: @msgs = $results->msgs; ### Get messages of specific types (also tests if there were problems): $had_errors = $results->errors; $had_warnings = $results->warnings; ### Get outermost header: $top_head = $results->top_head; DESCRIPTION
Results from the last MIME::Parser parse. PUBLIC INTERFACE
new Constructor. msgs Instance method. Return all messages that we logged, in order. Every message is a string beginning with its type followed by ": "; the current types are "debug", "warning", and "error". errors Instance method. Return all error messages that we logged, in order. A convenience front-end onto msgs(). warnings Instance method. Return all warning messages that we logged, in order. A convenience front-end onto msgs(). top_head Instance method. Return the topmost header, if we were able to read it. This may be useful if the parse fails. SEE ALSO
MIME::Tools, MIME::Parser AUTHOR
Eryq (eryq@zeegee.com), ZeeGee Software Inc (http://www.zeegee.com). All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.18.2 2008-06-30 MIME::Parser::Results(3)
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