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Full Discussion: Extract regular expression and line below
Top Forums Shell Programming and Scripting Extract regular expression and line below Post 302691809 by pathunkathunk on Saturday 25th of August 2012 07:29:06 PM
Old 08-25-2012
Thanks, agama, but with the following command I get the following error:
Code:
awk -F \| ' /^>gi/ { printf( ">%s\n", $4 ); getline print; }' test3.fa

awk: syntax error at source line 1
context is
/^>gi/ { printf( ">%s\n", $4 ); getline >>> print <<< ; }
awk: illegal statement at source line 1

Code:
cat test3.fa 
>gi|299507456|gb|GL349621.1| Acyrthosiphon pisum unplaced genomic scaffold Scaffold1, whole genome shotgun sequence
TTTACAATTGCTATTGTAACAATATATCAGGAGCCTTGTATTAAATTTTCACGCATTTTTACCAAACAAATAAAATTTTATTGAT
>gi|299507455|gb|GL349622.1| Acyrthosiphon pisum unplaced genomic scaffold Scaffold2, whole genome shotgun sequence
GTATGCGCGCATCTCCATACCGTCCGATAAATTCGCAGTAAAAAAAATGTGATTCACATTGTCGATTATAATAAAAAAAT
>gi|299507454|gb|GL349623.1| Acyrthosiphon pisum unplaced genomic scaffold Scaffold3, whole genome shotgun sequence
AATATTAAATAATTAATCTAAATAAATTAAATACCTCATTAGTCATTAACACACATTTTTTTCTTAGTTTTAATGTAT

 

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LEARN ABOUT DEBIAN

bp_process_gadfly

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

NAME

       process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser

SYNOPSIS

	 % process_gadfly.pl ./RELEASE2 > gadfly.gff

DESCRIPTION

       This script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the
       "correct" version of the GFF format.

       To use this script, download the whole genome FASTA file and save it to disk.  (The downloaded file will be called something like
       "na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename.)  Do the same for the whole genome
       GFF annotation file (the saved file will be called something like "whole-genome_annotation-feature-region_dmel_RELEASE3.GFF".)  If you wish
       you can download the ZIP compressed versions of these files.

       Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:

	% process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff

       The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command:

	 % bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff

       (Where "fly" is the name of the database.  Change it as appropriate.  The database must already exist and be writable by you!)

       The resulting database will have the following feature types (represented as "method:source"):

	 Component:arm		    A chromosome arm
	 Component:scaffold	    A chromosome scaffold (accession #)
	 Component:gap		    A gap in the assembly
	 clone:clonelocator	    A BAC clone
	 gene:gadfly		    A gene accession number
	 transcript:gadfly	    A transcript accession number
	 translation:gadfly	    A translation
	 codon:gadfly		    Significance unknown
	 exon:gadfly		    An exon
	 symbol:gadfly		    A classical gene symbol
	 similarity:blastn	    A BLASTN hit
	 similarity:blastx	    A BLASTX hit
	 similarity:sim4	    EST->genome using SIM4
	 similarity:groupest	    EST->genome using GROUPEST
	 similarity:repeatmasker    A repeat

       IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases.

SEE ALSO

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

AUTHOR

       Lincoln Stein, lstein@cshl.org

       Copyright (c) 2002 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

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