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Top Forums UNIX for Dummies Questions & Answers bash script to parse sequence... Post 302476741 by Fahmida on Thursday 2nd of December 2010 11:32:37 AM
Old 12-02-2010
Hi Rohon,

The list fiiles are as follows: List1.txt, List2.txt, ....., List4000.txt
And the corresponding data files are: DataFile1.txt, DataFile2.txt, ...., DataFile4000.txt
List1.txt will be used for DataFaile1.txt and so on.

Contents of both the files are not sorted. For example:
List1.txt
HTML Code:
contig00002 length=653   numreads=34
contig00015 length=636   numreads=21
contig00005 length=662   numreads=51
contig00045 length=584   numreads=24
contig00033 length=539   numreads=19
DataFile1.txt
HTML Code:
>contig00015 length=477   numreads=22
GGGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGTAAGTGAAT
GTCACATCGTTTGGATCAAGACCCATTTGCAGCACAAGCCCTGTTTTGTT
>contig00002 length=530   numreads=27
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGAGGATAGGG
AGCTGAGCAGCCAGTGACAGGATCCAGCTCCAGGGGGTGAATGGGGATGG
>contig00005 length=670   numreads=22
GGGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGATTGTTGAA
GTGGAAAGCCATTTTGACTATTACCGCCCGGTGGCAGAAACCAAACCTGG
>contig00045 length=636   numreads=21
GGGCAGCTGCGGCCGCTAATACGACTCACTATAGGGAGAGATCGTGGCGA
TCGCCAATCACCCAGGTGCCGTTAGCCAGAGCTGGTTTGATGACCGTTTC
>contig00072 length=662   numreads=51
GGGCAGCTGCGGCCGCTAATACGACTCACTATAGGGAGAGAGCTCCAGCA
GAATGGACACGCCTCCTGAGCTGTGATAGGGAGAGCATAAACACGCCTCC
One way would be, read one header from the list file, say 'contig00002 length=653 numreads=34', search for it in the DataFile1.txt and retrieve the following:
'>contig00002 length=530 numreads=27
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGAGGATAGGG
AGCTGAGCAGCCAGTGACAGGATCCAGCTCCAGGGGGTGAATGGGGATGG'

Cheers.
 

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LEARN ABOUT OPENSOLARIS

pdbtxt2html

pdbtxt2html(1)						      General Commands Manual						    pdbtxt2html(1)

NAME

       pdbtxt2html - Doc Text to HTML converter for Palm Pilots

SYNOPSIS

       pdbtxt2html [ -t ] file.txt [ file.html ]
       pdbtxt2html -v

DESCRIPTION

       pdbtxt2html converts text converted from a Doc(4) file via txt2pdbdoc(1) to HTML.  If no HTML filename is given, the generated HTML is sent
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   Document Title
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   Bookmarks
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EXAMPLE

       To convert a Doc file to HTML:

	    txt2pdbdoc alice.pdb alice.txt
	    pdbtxt2html alice.txt alice.html

SEE ALSO

       html2pdbtxt(1), txt2pdbdoc(1), doc(4), pdb(4)

       Tim Berners Lee.  Universal Resource Identifiers in WWW, Network Working Group of the Internet Engineering Task Force, June 1994.
	    http://info.internet.isi.edu/in-notes/rfc/files/rfc1630.txt

AUTHOR

       Paul J. Lucas <pauljlucas@mac.com>

txt2pdbdoc							 January 21, 2005						    pdbtxt2html(1)
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