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Full Discussion: Match first pattern first then extract second pattern match
Top Forums Shell Programming and Scripting Match first pattern first then extract second pattern match Post 302377981 by rdcwayx on Sunday 6th of December 2009 07:12:47 AM
Old 12-06-2009
Debian
patrick87, your sample input file make us confused. So I have to guess.

I change your input file, in number two session, there is no keyword accession. Please confirm, if this is your desired output.

Code:
$ cat input.txt
<accession>Q91G55</accession>
<name>043L_IIV6</name>
<protein>
<recommendedName>
<location>
<position position="294"/>
</location>
<fullName>Uncharacterized protein 043L</fullName>

<name>1106L_ASFB7</name>
<protein>
<recommendedName>
<fullName>Protein MGF 110-6L</fullName>

<accession>O55734</accession>
<name>120L_IIV6</name>
<fullName>Uncharacterized protein 120L</fullName>

$  awk 'BEGIN {RS=""; FS="\n"} /<accession>/ {for (i=1;i<=NF;i++) {if ($i~/<fullName>/) {print $i}}}' input.txt
<fullName>Uncharacterized protein 043L</fullName>
<fullName>Uncharacterized protein 120L</fullName>

 

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LEARN ABOUT DEBIAN

bp_aacomp

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)
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