diff options
Diffstat (limited to 'biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl')
| -rw-r--r-- | biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl | 92 |
1 files changed, 92 insertions, 0 deletions
diff --git a/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl b/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl new file mode 100644 index 000000000000..90bd168cc57e --- /dev/null +++ b/biology/velvet/files/patch-contrib-VelvetOptimiser-VelvetOptimiser.pl @@ -0,0 +1,92 @@ +--- contrib/VelvetOptimiser/VelvetOptimiser.pl.orig 2009-09-14 23:44:19.000000000 +0900 ++++ contrib/VelvetOptimiser/VelvetOptimiser.pl 2009-10-30 22:13:45.000000000 +0900 +@@ -44,9 +44,10 @@ + my @hashvals; + my %assemblies; + my $readfile; ++my $MAXKMERLENGTH = %%MAXKMERLENGTH%%; + my $logfile = "logfile.txt"; + my $hashs = 19; +-my $hashe = 129; ++my $hashe = $MAXKMERLENGTH; + my $ass_num = 1; + my $interested = 1; + +@@ -311,26 +312,26 @@ + my $ass = shift; + print STDERR "\tPlease type in the insert length for the short reads: "; + #my $len = <>; +- my $len = "200"; #do not ask for insert size! ++ my $len = "auto"; #do not ask for insert size! + chomp($len); +- while($len =~ /\D+/){ +- print STDERR "\tThe length needs to be a number, please re-enter: "; +- $len = <>; +- chomp($len); +- } ++ #while($len =~ /\D+/){ ++ # print STDERR "\tThe length needs to be a number, please re-enter: "; ++ # $len = <>; ++ # chomp($len); ++ #} + print STDERR strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n"; + print OUT strftime("%b %e %H:%M:%S", localtime), " Running assembly with short insert length $len\n"; + + #re-write the pstringg with the new velvetg command.. +- my $vg = $ass->{pstringg}; +- if($vg =~ /ins_length /){ +- $vg =~ s/ins_length\s+\d+/ins_length $len/; +- } +- else { +- $vg .= " -ins_length $len"; +- } ++ #my $vg = $ass->{pstringg}; ++ #if($vg =~ /ins_length /){ ++ # $vg =~ s/ins_length\s+\d+/ins_length $len/; ++ #} ++ #else { ++ # $vg .= " -ins_length $len"; ++ #} + +- $ass->{pstringg} = $vg; ++ #$ass->{pstringg} = $vg; + my $worked = VelvetOpt::gwrap::objectVelvetg($ass); + if($worked){ + $ass->getAssemblyDetails(); +@@ -347,8 +348,8 @@ + my $usage = "\nVelvetOptimiser.pl: A script to run the Velvet assembler and optimise its output. Simon Gladman - CSIRO 2008, 2009.\n\n"; + $usage .= "Usage: VelvetOptimiser.pl <-f 'velveth parameters'> [-s <hash start>] [-e <hash end>] [-a <yes>]\n\n"; + $usage .= "Where:\t<-f 'velveth parameters'> is the parameter line normally passed to velveth in quotes.\n"; +-$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=31!\n"; +-$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: 31. MUST BE ODD AND > START & <= 31!\n"; ++$usage .= "\t-s <hash start> The hash value you want velvet to start looking from. Default: 19. MUST BE ODD > 0 & <=$MAXKMERLENGTH!\n"; ++$usage .= "\t-e <hash end> The hash value you want velvet to stop looking at. Default: $MAXKMERLENGTH. MUST BE ODD AND > START & <= $MAXKMERLENGTH!\n"; + $usage .= "\t-a <yes> The final optimised assembly will include read tracking and amos file outputs (however, intermediate assemblies won't.)\n"; + $usage .= "\nIf the optimizer requires an insert length for some paired end data, it will ask for it when it gets to the optimization step.\n"; + +@@ -390,9 +391,9 @@ + $hashs = $opts{'s'}; + print STDERR "\n\t\t's-Param' is >$hashs<\n"; + unless($hashs =~ /^\d+$/){ die "\tFatal error! Start hash not a number!\n$usage";} +- if($hashs > 129){ +- print STDERR "\tStart hash value too high. New start hash value is 129.\n"; +- $hashs = 129; ++ if($hashs > $MAXKMERLENGTH){ ++ print STDERR "\tStart hash value too high. New start hash value is $MAXKMERLENGTH.\n"; ++ $hashs = $MAXKMERLENGTH; + } + if(!&isOdd($hashs)){ + $hashs = $hashs - 1; +@@ -404,9 +405,9 @@ + if($opts{'e'}){ + $hashe = $opts{'e'}; + unless($hashe =~ /^\d+$/){ die "\tFatal error! End hash not a number!\n$usage";} +- if($hashe > 129 || $hashe < 1){ +- print STDERR "\tEnd hash value not in workable range. New end hash value is 129.\n"; +- $hashe = 129; ++ if($hashe > $MAXKMERLENGTH || $hashe < 1){ ++ print STDERR "\tEnd hash value not in workable range. New end hash value is $MAXKMERLENGTH.\n"; ++ $hashe = $MAXKMERLENGTH; + } + if($hashe < $hashs){ + print STDERR "\tEnd hash value lower than start hash value. New end hash value = $hashs.\n"; |