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Top Forums Shell Programming and Scripting how to fetch substring from records into another file Post 302220575 by smriti_shridhar on Friday 1st of August 2008 07:32:50 AM
Old 08-01-2008
One more thing Jean..

I run that script on files which need to extract longer substrings and the format of output file is getting disturbed. I tried some options of printf but coudn't correct it. Please help me out.

===FILE1====
>bi|37779709|geb|AAP20876.1| kinetic [ ternata]
MASKLLLFLLPAILGLIIPRPAVAVGTNYLLSGETLDTDGHLKNGDFDFIMQEDCNAVLYNGNWQSNTAN
KGRDCKLTLTDRGELVINNGEGSAVWRSGSQSAKGNYAAVLHPEGKLVIYGPSVFKINPWVPGLNSLRLG
NVPFTCNMLFSGQVLYGDGKITARNHMLVMQGDCNLVLYGGKCDWQSNTHGNGEHCFLRLNHKGELIIKD
DDFKSIWSSQSSSKQGDYVFILQDNGYGVIYGPAIWATSSKRSVAAQETMIGMVTEKVN
>bi|146403769|geb|ABQ32294.1| pure [an eg]
MAKLLLFLLPAILGLLIPRSAVALGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANN
GRDCKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWVPGLNSLRFRN
IPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDD
DFRPSGAAVPAPSR

===FILE2====
bi|37779709|geb|AAP20876.1| 28 264
bi|146403769|geb|ABQ32294.1| 27 224

===OUTPUTFILE===
>gi|37779709|gb|AAP20876.1| lectin [Pinellia ternata] (28-264)
NYLLSGETLDTDGHLKNGDFDFIMQEDCNAVLYNGNWQSNTANKGRDCKLTLTDRGELVINNGEGSAVWRSGSQSAKGNYAAVLHPEGKLVIYGPSVFKI NPWVPGLNSLRLGNVPFTCNMLFSGQVLYGDGKITARNHMLVMQGDCNLVLYGGKCDWQSNTHGNGEHCFLRLNHKGELIIKDDDFKSIWSSQSSSKQGD YVFILQDNGYGVIYGPAIWATSSKRSVAAQETMIGM
>gi|146403769|gb|ABQ32294.1| lectin [Colocasia esculenta] (27-224)
NYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKI DPWVPGLNSLRFRNIPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFRPSGAAVPAPS


where as the output should be like this:
>gi|37779709|gb|AAP20876.1| lectin [Pinellia ternata] (28-264)
NYLLSGETLDTDGHLKNGDFDFIMQEDCNAVLYNGNWQSNTANKGRDCKLTLTDRGELVINNGEGSAVWR
SGSQSAKGNYAAVLHPEGKLVIYGPSVFKINPWVPGLNSLRLGNVPFTCNMLFSGQVLYGDGKITARNHML
VMQGDCNLVLYGGKCDWQSNTHGNGEHCFLRLNHKGELIIKDDDFKSIWSSQSSSKQGDYVFILQDNGY
GVIYGPAIWATSSKRSVAAQETMIGM
>gi|146403769|gb|ABQ32294.1| lectin [Colocasia esculenta] (27-224)
NYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGELVIKNGDGSTVWR
SRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWVPGLNSLRFRNIPFTDNLLFSGQVLYGDGRLTAKNHQLV
MQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFRPSGAAVPAPS

where each line after header line should not have more than 70 characters.

I will be thankful to you. Smilie
-smriti
 

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MELD(1) 						      General Commands Manual							   MELD(1)

NAME
meld - Visual diff and merge tool for the GNOME Desktop SYNOPSIS
meld [options] meld [options] FILE1 meld [options] DIR1 meld [options] FILE1 FILE2 [FILE3] meld [options] DIR1 DIR2 [DIR3] DESCRIPTION
Meld is a graphical diff viewer and merge application for the Gnome desktop. It supports 2 and 3-file diffs, recursive directory diffs, diffing of directories under version control (Arch, Bazaar, Codeville, CVS, Darcs, Git, Mercurial, Monotone, RCS), as well as the ability to manually and automatically merge file differences. OPTIONS
--auto-compare, -a Automatically compare all differing files on startup. --diff FILE1|DIR1 FILE2|DIR2 [FILE3|DIR3] Create a diff tab for the given files or directories. Note that "meld --diff FILE1 FILE2" is functionally equivalent to "meld FILE1 FILE2". However, the --diff argument can be given multiple times for one invocation of meld which allows the user to automatically initiate multiple diffs when meld starts. See examples below. --help, -h Print application help and usage. --LABEL=<label>, -L <label> Set application window title to <label>. --version Print application version and exit. EXAMPLES
meld Run meld without initiating a diff. meld FILE1 Initiate a diff between FILE1 and the version-controlled copy of FILE1. meld DIR1 Initiate a recursive diff between DIR1 and the version-controlled copy of DIR1. meld FILE1 FILE2 Initiate a diff between FILE1 and FILE2. meld FILE1 FILE2 FILE3 Initiate a 3-way diff between FILE1, FILE2, and FILE3. meld DIR1 DIR2 Initiate a recursive diff between directory DIR1 and DIR2. meld DIR1 DIR2 DIR3 Initiate a recursive 3-way diff between directory DIR1, DIR2, and DIR3. meld --diff FILE1 FILE2 --diff FILE3 FILE4 Initiate a diff between FILE1 and FILE2, and a separate diff between FILE3 and FILE4. BUGS
If you find a bug, please report it at https://bugzilla.gnome.org/buglist.cgi?product=meld or mail a description of the issue to meld- list@gnome.org. AUTHORS
See the AUTHORS text file in meld's source code (http://git.gnome.org/browse/meld/tree/AUTHORS). 26 Sept 2010 MELD(1)
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