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Full Discussion: how to fetch substring from records into another file
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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LEARN ABOUT XFREE86

comm

COMM(1) 							   User Commands							   COMM(1)

NAME

       comm - compare two sorted files line by line

SYNOPSIS

       comm [OPTION]... FILE1 FILE2

DESCRIPTION

       Compare sorted files FILE1 and FILE2 line by line.

       When FILE1 or FILE2 (not both) is -, read standard input.

       With  no  options,  produce three-column output.  Column one contains lines unique to FILE1, column two contains lines unique to FILE2, and
       column three contains lines common to both files.

       -1     suppress column 1 (lines unique to FILE1)

       -2     suppress column 2 (lines unique to FILE2)

       -3     suppress column 3 (lines that appear in both files)

       --check-order
	      check that the input is correctly sorted, even if all input lines are pairable

       --nocheck-order
	      do not check that the input is correctly sorted

       --output-delimiter=STR
	      separate columns with STR

       --total
	      output a summary

       -z, --zero-terminated
	      line delimiter is NUL, not newline

       --help display this help and exit

       --version
	      output version information and exit

       Note, comparisons honor the rules specified by 'LC_COLLATE'.

EXAMPLES

       comm -12 file1 file2
	      Print only lines present in both file1 and file2.

       comm -3 file1 file2
	      Print lines in file1 not in file2, and vice versa.

AUTHOR

       Written by Richard M. Stallman and David MacKenzie.

REPORTING BUGS

       GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
       Report comm translation bugs to <http://translationproject.org/team/>

COPYRIGHT

       Copyright (C) 2017 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       join(1), uniq(1)

       Full documentation at: <http://www.gnu.org/software/coreutils/comm>
       or available locally via: info '(coreutils) comm invocation'

GNU coreutils 8.28						   January 2018 							   COMM(1)
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