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Full Discussion: Parse and Join in a text file
Top Forums Shell Programming and Scripting Parse and Join in a text file Post 302521908 by ctsgnb on Thursday 12th of May 2011 05:22:30 PM
Old 05-12-2011
Give a try to
Code:
nawk '{x=y;y=$0}/^ID/{if (w) print w;sub(".*"$2,">"$2);w=$0}/^P[AT]/{sub(".*"$2,$2);w=w?w" \; "$0:$0}/^\/\//{print w"\n" x;w=z}' infile

or
Code:
nawk '{x=y;y=$0}/^ID|^P[AT]/{sub(".*"$2,$2);v=$0;w=w?w" \; "v:">"v}/^\/\//{print w"\n" x;w=z}' infile

Code:
# cat tst
ID US88811111-0005
OO giensis
OS giensis
SN US74811111
PT I-008, testing for the second phase
PA sandiego group, NC
PI Carozzi; Nadine (Raleigh, NC); Hargiss; Tracy (Cary, NC); Koziel; Michael G. (Raleigh, NC); Duck; Nicholas B. (Apex, NC); Carr; Brian (Raleigh, NC);
PR 20030828 US20030498518P; 20040826 US20040926819; 20070620 US20070765494;
PE US200304985AN 20070765494
P1 Compositions and methods and seeds are provided.
QAISRLEGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSEQLINQRIEEFARNQAISRLEGLSNLYVTIHEIENNTDEL KFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYT
//
ID US74811111-0005
OO giensis
OS giensis
SN US74811111
PT I-003, a gene and methods for its use
PA NIX CORPORATION RESEARCH TRIANGLE PARK, NC
PI Carozzi; Nadine (Raleigh, NC); Hargiss; Tracy (Cary, NC); Koziel; Michael G. (Raleigh, NC); Duck; Nicholas B. (Apex, NC); Carr; Brian (Raleigh, NC);
PR 20030828 US20030498518P; 20040826 US20040926819; 20070620 US20070765494;
PE US200304985AN 20070765494
P1 Compositions and methods and seeds are provided.
MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQIEQLINQRIEEFARNQAISRL EGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYTDGRRENPCEFNRGYRDYTPLP VGYVTKELEYFPETDKVWIEIGETEGTFIVDSVELLLMEE
//

Code:
# nawk '{x=y;y=$0}/^ID/{if (w) print w;sub(".*"$2,">"$2);w=$0}/^P[AT]/{sub(".*"$2,$2);w=w?w" \; "$0:$0}/^\/\//{print w"\n" x ;w=z}' tst
>US88811111-0005 ; I-008, testing for the second phase ; sandiego group, NC
QAISRLEGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSEQLINQRIEEFARNQAISRLEGLSNLYVTIHEIENNTDEL KFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYT
>US74811111-0005 ; I-003, a gene and methods for its use ; NIX CORPORATION RESEARCH TRIANGLE PARK, NC
MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQIEQLINQRIEEFARNQAISRL EGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYTDGRRENPCEFNRGYRDYTPLP VGYVTKELEYFPETDKVWIEIGETEGTFIVDSVELLLMEE

Code:
# nawk '{x=y;y=$0}/^ID|^P[AT]/{sub(".*"$2,$2);v=$0;w=w?w" \; "v:">"v}/^\/\//{print w"\n"x;w=z}' tst
>US88811111-0005 ; I-008, testing for the second phase ; sandiego group, NC
QAISRLEGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSEQLINQRIEEFARNQAISRLEGLSNLYVTIHEIENNTDEL KFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYT
>US74811111-0005 ; I-003, a gene and methods for its use ; NIX CORPORATION RESEARCH TRIANGLE PARK, NC
MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQIEQLINQRIEEFARNQAISRL EGLSNLYVTIHEIENNTDELKFSNCVEEEIYPNNTVTCNDYTVNQEEYGGAYTSRNRGYNEAPSVPADYASVYEEKSYTDGRRENPCEFNRGYRDYTPLP VGYVTKELEYFPETDKVWIEIGETEGTFIVDSVELLLMEE

Last edited by ctsgnb; 05-12-2011 at 06:38 PM..
 

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