How can I extract paragaphs and selected lines with Perl?
- by neversaint
I have a text where I need to:
to extract the whole paragraph under
the section "Aceview summary" until the line that starts with "Please quote" (not to be included).
to extract the line that starts with "The closest human gene".
to store them into array with two elements.
The text looks like this (also on pastebin):
AceView: gene:1700049G17Rik, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView.
<META NAME="title"
CONTENT="
AceView: gene:1700049G17Rik a comprehensive annotation of human, mouse and worm genes with mRNAs or EST">
<META NAME="keywords"
CONTENT="
AceView, genes, Acembly, AceDB, Homo sapiens, Human,
nematode, Worm, Caenorhabditis elegans , WormGenes, WormBase, mouse,
mammal, Arabidopsis, gene, alternative splicing variant, structure,
sequence, DNA, EST, mRNA, cDNA clone, transcript, transcription, genome,
transcriptome, proteome, peptide, GenBank accession, dbest, RefSeq,
LocusLink, non-coding, coding, exon, intron, boundary, exon-intron
junction, donor, acceptor, 3'UTR, 5'UTR, uORF, poly A, poly-A site,
molecular function, protein annotation, isoform, gene family, Pfam,
motif ,Blast, Psort, GO, taxonomy, homolog, cellular compartment,
disease, illness, phenotype, RNA interference, RNAi, knock out mutant
expression, regulation, protein interaction, genetic, map, antisense,
trans-splicing, operon, chromosome, domain, selenocysteine, Start, Met,
Stop, U12, RNA editing, bibliography">
<META NAME="Description"
CONTENT= "
AceView offers a comprehensive annotation of human, mouse and nematode genes
reconstructed by co-alignment and clustering of all publicly available
mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable
up-to-date resource on the genes, their functions, alternative variants,
expression, regulation and interactions, in the hope to stimulate
further validating experiments at the bench
">
<meta name="author"
content="Danielle Thierry-Mieg and Jean Thierry-Mieg,
NCBI/NLM/NIH, [email protected]">
<!--
var myurl="av.cgi?db=mouse" ;
var db="mouse" ;
var doSwf="s" ;
var classe="gene" ;
//-->
However I am stuck with the following script logic. What's the right way to achieve that?
#!/usr/bin/perl -w
my $INFILE_file_name = $file; # input file name
open ( INFILE, '<', $INFILE_file_name )
or croak "$0 : failed to open input file $INFILE_file_name : $!\n";
my @allsum;
while ( <INFILE> ) {
chomp;
my $line = $_;
my @temp1 = ();
if ( $line =~ /^ AceView summary/ ) {
print "$line\n";
push @temp1, $line;
}
elsif( $line =~ /Please quote/) {
push @allsum, [@temp1];
@temp1 = ();
}
elsif ($line =~ /The closest human gene/) {
push @allsum, $line;
}
}
close ( INFILE ); # close input file
# Do something with @allsum
There are many files like that I need to process.
