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Changeset 273

Timestamp:

10/03/09 16:26:20 (2 months ago)

Author:

cholt

Message:

fix to check if snap, augustus, exonerate and RepeatMasker?

Files:

r249	r273
116	116
117	117	my %hsps;
	118	my $count; #used to see if file finished
118	119	while (my $line = <$fh>){
	120	$count++;
119	121	next if $line =~ /There were no repetitive sequences detected in/;
120	122	next unless $line =~ /^\s*\d/;
…	…
246	248	}
247	249	$fh->close();
	250
	251	#checks if RepeatMasker really finished
	252	unless($count){
	253	unlink($file);
	254	die "ERROR: The file $file appears to be incomplete\n".
	255	"MAKER will need to delete the file, before trying again\n\n";
	256	}
248	257
249	258	my @keepers;

r216	r273
448	448	$fh->open($report);
449	449
450		<$fh>; # shift off the header
	450	my $header = <$fh>; # shift off the header
	451
	452	#checks if Augustus really finished
	453	unless($header){
	454	unlink($report);
	455	die "ERROR: The file $report appears to be incomplete\n".
	456	"MAKER will need to delete the file, before trying again\n\n";
	457	}
451	458
452	459	my @genes;

r127	r273
39	39	$fh->open($file);
40	40
41		$/ = 'C4 Alignment:';
	41	local $/ = 'C4 Alignment:';
42	42
43	43	my @chunks;
…	…
47	47	$fh->close();
48	48
49		$/ = "\n";
	49	local $/ = "\n";
	50
	51	#checks if exonerate really finished
	52	unless(grep {/completed exonerate analysis/} $chunks[-1]){
	53	unlink($file);
	54	die "ERROR: The file $file appears to be incomplete\n".
	55	"MAKER will need to delete the file, before trying again\n\n";
	56	}
50	57
51	58	return \@chunks;

r127	r273
36	36	$fh->open($file);
37	37
38		$/ = 'C4 Alignment:';
	38	local $/ = 'C4 Alignment:';
39	39
40	40	my @chunks;
…	…
44	44	$fh->close();
45	45
46		$/ = "\n";
	46	local $/ = "\n";
	47
	48	#checks if exonerate realy finished
	49	unless(grep {/completed exonerate analysis/} $chunks[-1]){
	50	unlink($file);
	51	die"ERROR: The file $file appears to be incomplete\n".
	52	"MAKER will need to delete the file, before trying again\n\n";
	53	}
47	54
48	55	return \@chunks;

r222	r273
251	251	$fh->open($report);
252	252
253		<$fh>; # shift off the header
	253	my $header = <$fh>; # shift off the header
	254
	255	#checks if snap really finished
	256	unless($header){
	257	unlink($report);
	258	die "ERROR: The file $report appears to be incomplete\n".
	259	"MAKER will need to delete the file, before trying again\n\n";
	260	}
	261
254	262	my %g;
255	263	my $i = -1;