Dmb000006: meh

2011-03-02T11:23:04Z

meh

Dmb000006: Yup

2011-03-02T11:05:22Z

Yup

New page

<PRE>
#!/usr/bin/perl -w

## Very simple perl script to drive the Bambus 2.0 pipeline (as I
## currently understand it).

use strict;
use Getopt::Long;

## Configure defaults

my $verbose = 1;

my $contig_file = '';
my $fasta_file = '';
my $mates_file = '';

my $output_prefix = 'out';

## The threshold used to accept or reject a link between contigs
my $link_redundancy = 1;

## Weather or not to run the (crappy) 'repeat filter' code
my $filter_repeats = 0;

## Not running dot saves time on 'big' runs
my $run_dot = 1;

## Process command line arguments

GetOptions
("contig_file=s" => \$contig_file,
"fasta_file=s" => \$fasta_file,
"mates_file=s" => \$mates_file,
"output_prefix=s" => \$output_prefix,

"link_redundancy|r=i" => \$link_redundancy,
"repeat_filter|x" => \$filter_repeats,
"dot|d!" => \$run_dot,
"verbose+" => \$verbose,
)
or die "failure to communicate\n";

die "-c contig file plz!\n" unless -s $contig_file;
die "-f fasta file plz!\n" unless -s $fasta_file;
die "-m mates file plz!\n" unless -s $mates_file;

die "are you crazy?\n"
if $output_prefix eq '';

warn
join("\n",
"contig file : $contig_file",
"fasta file : $fasta_file",
"mates file : $mates_file",
"output prefix : $output_prefix",
"link redundancy : $link_redundancy",
"repeat filter : $filter_repeats",
"run dot? : $run_dot",
"verbose : $verbose",
), "\n"
if $verbose > 0;
#exit;

## Run the pipeline

## Get data into bank format

run(qq/
toAmos
-s $fasta_file
-c $contig_file
-m $mates_file
-o $output_prefix.afg
/);

## Debugging mates file
#exit;

run(qq/
bank-transact -cf
-m $output_prefix.afg
-b $output_prefix.bnk
/);

## Run the new Bambus pipeline

run(qq/
clk
-b $output_prefix.bnk
/);

run(qq/
Bundler
-b $output_prefix.bnk
/);

## Repeat filtering?
my $filter_repeats_option_string = '';
if($filter_repeats){
run(qq/
MarkRepeats
-noCoverageRepeats
-b $output_prefix.bnk
-redundancy $link_redundancy
> $output_prefix.repeats
/);

$filter_repeats_option_string =
"-repeats $output_prefix.repeats";
}

run(qq/
OrientContigs
-noreduce
$filter_repeats_option_string
-b $output_prefix.bnk
-redundancy $link_redundancy
-prefix $output_prefix
/);

## Generate some additional TEXT output

## ouput a fasta sequence for the contigs from the bank (passed to
## printScaff with -f)

#run(qq/
# bank2fasta -iid
# -b $output_prefix.bnk
# > $output_prefix.contig.fasta
#/);

## Generates the useful .details, .oo, .sum and .stats files
# -f $output_prefix.contig.fasta
run(qq/
printScaff -detail -oo -sum
-e $output_prefix.evidence.xml
-s $output_prefix.out.xml
-l $output_prefix.library
-o $output_prefix
/);

run(qq/
mv -f
printScaff.error
$output_prefix.printScaff.error
/)
if -s 'printScaff.error';

## UNTANGLE

run(qq/
untangle
-e $output_prefix.evidence.xml
-s $output_prefix.out.xml
-o $output_prefix.out.untangle.xml
/);

run(qq/
mv -f
untangle.error
$output_prefix.untangle.error
/)
if -s 'untangle.error';

## Generates the useful .details, .oo, .sum and .stats files
# -f $output_prefix.contig.fasta
run(qq/
printScaff -detail -oo -sum -dot
-e $output_prefix.evidence.xml
-s $output_prefix.out.untangle.xml
-l $output_prefix.library
-o $output_prefix.untangle
/);

run(qq/
mv -f
printScaff.error
$output_prefix.untangle.printScaff.error
/)
if -s 'printScaff.error';

## FINALLY, DOT

if($run_dot){
# output before untangle
run(qq/
dot -Tps
$output_prefix.dot
> $output_prefix.ps
/);

# output after untangle
run(qq/
dot -Tps
$output_prefix.untangle.dot
> $output_prefix.untangle.ps
/);
}

warn "OK\n";

## Yup

sub run{
my $cmd = shift;

$cmd =~ s/\n/ /g;

print "\n\n\nRUN: $cmd\n\n"
if $verbose > 0;

`$cmd`;

die if $? != 0;

return 1;
}
</PRE>

← Older revision		Revision as of 11:23, 2 March 2011
Line 1:		Line 1:
		+	:<small>< [[Bambus 2.0]]</small>
	<PRE>		<PRE>
	#!/usr/bin/perl -w		#!/usr/bin/perl -w

Bambus 2.0/goBambus-perl - Revision history

Dmb000006: meh

Dmb000006: Yup