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.
Hi,
I have file (FILE.tmp) having contents,
FILE.tmp
========
filename=menudata
records=0000000000037
ldbname=pinsys
timestamp=2005/05/14-18:32:33
I want to parse it bring a new file which will look like,
filename records ldbname timestamp... (2 Replies)
Hi,
I have my input as follows :
I have given two entries-
From system Mon Aug 1 23:52:47 2005
Source !100000006!:
Impact !100000005!: High
Status ! 7!: New
Last Name+!100000001!:
First Name+ !100000003!:
... (4 Replies)
I am using Unix on Mac OS X 10.5.6.
I am trying to extract the last entry of a log (text) file. As seen below, each log entry looks like the following (date and time change with each log entry):
I want the script to extract everything quoted above, including the "===" dividers.
... (2 Replies)
Can some one help me with shell script to extract a text block between two known strings.
The given input file is as below:
Name: abs
Some tesxt....
Some tesxt....
Some tesxt....
end of text
Name: xyz
Some tesxt....
Some tesxt....
Some tesxt....
end of text
Name: efg
Some... (5 Replies)
Hi,
I do have a TAB delimted text file with the following format.
1 (- identifier of each group. this text is not present in the file only number)
1 3 4 65 56 WERTF
2 3 4 56 56 GHTYHU
3 3 5 64 23 VMFKLG
2
1 3 4 65 56 DGTEYDH
2 3 4 56 56 FJJJCKC
3 3 5 64 23 FNNNCHD
3
1 3 4 65 56 JDHJDH... (9 Replies)
Hi All
I wanted to know how to effectively delete some columns in a large tab delimited file.
I have a file that contains 5 columns and almost 100,000 rows
3456 f g t t
3456 g h
456 f h
4567 f g h z
345 f g
567 h j k lThis is a very large data file and tab delimited.
I need... (2 Replies)
Hi All
I have two files:
file 1
>AB_1
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2... (5 Replies)
Hi,
I have a folder that contains many (multiple) files
1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files
Each such file have data in the following format
for example:
vi 1.fasta
Code:
>AB_1
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM (6 Replies)
Hi, I need a script that parses and greps data out of a textfile.
I have a text file that has this structure:
File1
host1.localdomain
text random text
Found errors
this text is random (41123) --- random random
at.5165 ---- random random
at.5165 ---- random random
at.5165 ----... (2 Replies)
Hey Guys,
I'm a novice at shell scripts and i need some help parsing file data.
Basically, I want to write a script that retrieves URLs.
Here is what I have so far.
#!/bin/bash
echo "Please enter start date (format: yyyy-mm-dd):\c"
read STARTDATE
echo "Please enter end date... (7 Replies)
Discussion started by: silverdust
7 Replies
LEARN ABOUT MOJAVE
mime::parser::results
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)