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Full Discussion: Help Parsing Sequence File
Top Forums UNIX for Dummies Questions & Answers Help Parsing Sequence File Post 302436858 by Fahmida on Tuesday 13th of July 2010 10:10:43 AM
Old 07-13-2010
Many Thanks for your reply. However, for input parameters "len=100 limit=20 testseq.txt", I get the following output:
HTML Code:
>1630 length 144 cvg_0.0_tip_0
TGTCTTCTTAAATCTTTATTAGCACgAATCCTGTGACGTAA
>1655 length 128 cvg_0.0_tip_0
aTGTGCTGGgTGGGTGCCTGtGTCTGTG
>1662 length 142 cvg_0.0_tip_0
cttcttaaatctttattctcTAGCAATATCCTGTGACGTAC
Length of the extracted sequences are 41, 28, and 41 respectively, which should be 40 for all of them. The expected output, considering 20 characters each taken from the start and end of each sequence is:

HTML Code:
>1630 length 144 cvg_0.0_tip_0
TGTCTTCTTAAATCTTTATTGCACgAATCCTGTGACGTAA
>1655 length 128 cvg_0.0_tip_0
aTGTGCTGGgTGGGTGCCTGtGGGAAGTGAGCtGTCTGTG
>1662 length 142 cvg_0.0_tip_0
cttcttaaatctttattctcAGCAATATCCTGTGACGTAC
All of them are 040 characters long. Thanks.
 

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LEARN ABOUT DEBIAN

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
       to standard output.

   Document Title
       The first line of the file is used for the HTML document title.

   Bookmarks
       The last line of the file is examined and, if it contains a string enclosed between < and >, that is taken to be the bookmark marker.   The
       entire file is then scanned looking for lines beginning with it (ignoring leading whitespace).  These lines are converted to HTML headings.

       The  number  of whitespace characters after the first bookmark marker is used for heading level 1.  The level of subsequent headings is set
       to the number of whitespace characters between the bookmark marker and the bookmark text minus the number for the first bookmark plus one.

   Embedded URLs
       Valid URLs (according to RFC 1630) embedded in the text are turned into hyperlinks.  The ftp, gopher, http, https,  mailto,  news,  telnet,
       and wais URLs are recognized.

OPTIONS

       -t   Compile a table of contents and insert it between the first heading and the body.

       -v   Print the version number to standard output and exit.

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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