in reply to Re: concatenating identical sequences
in thread concatenating identical sequences
Thanks Limbic~Region and BrowserUk for your good advice. I have had a quick go with BrowserUk's script and it seems to work OK. However, the merge is not so clean and results after the merge seem not to be in equal chunks (I have posted this on to my scratchpad). I am speculating that this will continue as > continue to add more block (i.e thousands). I have adapted your script as follows:
I must also confess I do not understand the last bit of code:#! perl -slw use strict; if (scalar(@ARGV) != 1) { print "\n"; print "Usage: script.pl <alignment file>"; print "\n"; exit(); } my ($FILENAME) = @ARGV; #read in file open(DATA, $FILENAME); my( $id, %accu, @order ); ## remove existing files my $remove = "new_alignment_".$FILENAME; #remove any existing results + file if (unlink($remove) == 1) { print "Existing \"$remove\" file was removed\n +"; } ## generate a temporary storage file my $outputfile = "new_alignment_".$FILENAME; #make a big file in which + the final results will be printed unless ( open(POS, ">>$outputfile") ) { print "Cannot open file \"$outputfile\" to write to!!\n\n"; exit; } while( <DATA> ) { chomp; if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) { $id = $1; unless( exists $accu{ $id } ) { push @order, $id; $accu{ $id } = $2; } else { $accu{ $id } .= ' ' . $2; } } else { $accu{ $id } .= ' ' . $_; } } for my $key ( @order ) { printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' ); print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $ +key }; print POS ''; }
Could you kindly please explain it to me.for my $key ( @order ) { printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' ); print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $ +key }; print POS ''; }
PS: Still thinking of how to implement what Limbic~Region has pointed out.
$new_guy
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