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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

nps2gps

NPS2GPS(1)						      General Commands Manual							NPS2GPS(1)

NAME

       nps2gps - convert nucleotide-protein sets to ASN.1 genomic product sets

SYNOPSIS

       nps2gps [-] [-D] [-F] [-G str] [-L] [-N] [-P] [-Q] [-R] [-T] [-U] [-f str] [-i filename] [-o filename] [-p path] [-r path] [-x str]

DESCRIPTION

       nps2gps converts NCBI Bioseq-sets from simple nucleotide-protein sets to full genomic product sets complete with mRNA transcripts, which it
       outputs as text ASN.1.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D     RefSeq mRNA Titles

       -F     Map by Feature ID

       -G str General ID database name

       -L     Lock components in advance

       -N     Promote Non-coding RNAs

       -P     mRNA ID from Protein

       -Q     Special mRNA titles

       -R     Enable Remote fetching from ID

       -T     Map by Transcript ID

       -U     Remove Unnecessary gene cross-references

       -f str Substring filter

       -i filename
	      Single input file (default = stdin)

       -o filename
	      Single output file (default = stdout)

       -p path
	      Path to files for batch conversion

       -r path
	      Path for results of batch conversion

       -x str File selection suffix for batch conversion (default = .ent)

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).

NCBI Tools User's Manual					    2012-06-24								NPS2GPS(1)
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