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Top Forums UNIX for Dummies Questions & Answers bash script to parse sequence... Post 302476726 by Corona688 on Thursday 2nd of December 2010 10:55:07 AM
Old 12-02-2010
I'm sure there's a way to loop over your data files. However you've told us nothing about them other than you have a lot of them so it's a little hard to help. Do they have filenames? Do you have a list of them? Are they organized in any way?

Quote:
Originally Posted by R0H0N
[CODE]listFile="/path/listFile.txt"
dataFile="/path/dataFile.txt"
>outputFile

cat $dataFile | while read line
You've replaced the useless use of grep with a useless use of cat.

I suggest this instead:

Code:
while read RECORD LENGTH NUMREADS
do
        IFS="=" read G LENGTH <<< "${LENGTH}"
        IFS="=" read G NUMREADS <<< "${NUMREADS}"

        ...
done < listfile

Still working on the data processing. Should post in a while.

---------- Post updated at 09:52 AM ---------- Previous update was at 09:43 AM ----------

Does the output data have to be produced in the same order as the input data? That's going to be a royal pain because it's in random order, whereas the input file is sorted. That means starting over at the top of the datafile for every record instead of reading as you go.

---------- Post updated at 09:55 AM ---------- Previous update was at 09:52 AM ----------

Quote:
1. The code produces exactly the similar 'Output' as the input 'DataFile'. The headers are not similar. List file contain less headers. For example 'contig00001 length=477 numreads=22' is not present in the 'list' file and should not be retrieved.
Well, that turns this on its head. I hope you mean data file, because if the list file contains no listings that makes no sense at all... What does the data file look like then? What relationship do the list fields have with the data to be retrieved? Is length bytes? What does numreads mean? How do we calculate some sort of offset from this?
 

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URI::URL(3)						User Contributed Perl Documentation					       URI::URL(3)

NAME
URI::URL - Uniform Resource Locators SYNOPSIS
$u1 = URI::URL->new($str, $base); $u2 = $u1->abs; DESCRIPTION
This module is provided for backwards compatibility with modules that depend on the interface provided by the "URI::URL" class that used to be distributed with the libwww-perl library. The following differences compared to the "URI" class interface exist: o The URI::URL module exports the url() function as an alternate constructor interface. o The constructor takes an optional $base argument. The "URI::URL" class is a subclasses of "URI::WithBase". o The URI::URL->newlocal class method is the same as URI::file->new_abs o URI::URL::strict(1) o $url->print_on method o $url->crack method o $url->full_path; same as ($uri->abs_path || "/") o $url->netloc; same as $uri->authority o $url->epath, $url->equery; same as $uri->path, $uri->query o $url->path and $url->query pass unescaped strings. o $url->path_components; same as $uri->path_segments (if you don't consider path segment parameters). o $url->params and $url->eparams methods. o $url->base method. See URI::WithBase. o $url->abs and $url->rel have an optional $base argument. See URI::WithBase. o $url->frag; same as $uri->fragment o $url->keywords; same as $uri->query_keywords; o $url->localpath with friends map to $uri->file o $url->address and $url->encoded822addr; same as $uri->to for mailto URI. o $url->groupart method for news URI. o $url->article; same as $uri->message SEE ALSO
URI, URI::WithBase COPYRIGHT
Copyright 1998-2000 Gisle Aas. perl v5.8.0 2002-05-09 URI::URL(3)
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