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setting up webapollo_1.0 branch for release
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webapollo_1.0 is branched off of jbrowse_1.7 branch
but want Perl data generation code (in ./bin and ./lib) from master
so, pulling in ./bin and ./lib directories from master via:
    git checkout master -- bin lib
and now committing
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@GreggHelt2
GreggHelt2 committed Dec 21, 2012
1 parent d330a57 commit 05ef386
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Showing 42 changed files with 7,312 additions and 127 deletions.
167 changes: 167 additions & 0 deletions bin/add_bam_track.pl
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#!/usr/bin/env perl

use strict;
use warnings;

use Getopt::Long qw(:config no_ignore_case bundling);
use IO::File;
use File::Basename;
use JSON;

my $STORE_CLASS = "JBrowse/Store/SeqFeature/BAM";
my $ALIGNMENT_TYPE = "WebApollo/View/Track/DraggableAlignments";
my $COVERAGE_TYPE = "JBrowse/View/Track/FeatureCoverage";

my $in_file = "data/trackList.json";
my $out_file = "data/trackList.json";
my $label;
my $bam_url;
my $key;
my $classname = "bam";
my $mismatches = 0;
my $coverage = 0;
my $min_score = undef;
my $max_score = undef;

parse_options();
add_bam_track();

sub parse_options {
my $help;
GetOptions("in|i=s" => \$in_file,
"out|o=s" => \$out_file,
"label|l=s" => \$label,
"bam_url|u=s" => \$bam_url,
"key|k=s" => \$key,
"classname|c=s" => \$classname,
"mismatches|m" => \$mismatches,
"coverage|C" => \$coverage,
"min_score|s=i" => \$min_score,
"max_score|S=i" => \$max_score,
"help|h" => \$help);
print_usage() if $help;
die "Missing label option\n" if !$label;
die "Missing bam_url option\n" if !$bam_url;
die "Missing min_score option\n" if ($coverage && !defined $min_score);
die "Missing max_score option\n" if ($coverage && !defined $max_score);
$key = $label if !$key;
}

sub print_usage {
my $progname = basename($0);
die << "END";
usage: $progname
[-i|--in <input_trackList.json>]
[-o|--out <output_trackList.json>]
-l|--label <track_label>
-u|--bam_url <url_to_bam_file>
[-k|--key <track_key>]
[-c|--classname <css_class>]
[-m|--mismatches]
[-C|--coverage]
[-s|--min_score <min_score>]
[-S|--max_score <max_score>]
[-h|--help]
i: input trackList.json file [default: data/trackList.json]
o: output trackList.json file [default: data/trackList.json]
u: URL to BAM file (can be a relative path)
k: key (display name) for track [default: label value]
c: CSS class for display [default: bam]
m: display mismatches in alignment (generates no subfeatures)
C: display coverage data instead of alignments
s: minimum score to use for generating coverage plot (only applicable
to when the -C option is chosen)
S: maximum score to use for generating coverage plot (only applicable
to when the -C option is chosen)
END
}

sub add_bam_track {
my $json = new JSON;
local $/;
my $in;
$in = new IO::File($in_file) or
die "Error reading input $in_file: $!";
my $track_list_contents = <$in>;
$in->close();
my $track_list = $json->decode($track_list_contents);
my $bam_entry;
my $index;
my $tracks = $track_list->{tracks};
for ($index = 0; $index < scalar(@{$tracks}); ++$index) {
my $track = $tracks->[$index];
if ($track->{label} eq $label) {
$bam_entry = $track;
last;
}
}
if (!$bam_entry) {
$bam_entry = !$coverage ? generate_new_bam_alignment_entry() :
generate_new_bam_coverage_entry();
push @{$track_list->{tracks}}, $bam_entry;
}
else {
if ($coverage) {
if ($bam_entry->{type} eq $ALIGNMENT_TYPE) {
$bam_entry = generate_new_bam_coverage_entry();
$tracks->[$index] = $bam_entry;
}
}
else {
if ($bam_entry->{type} eq $COVERAGE_TYPE) {
$bam_entry = generate_new_bam_alignment_entry();
$tracks->[$index] = $bam_entry;
}
}
}
$bam_entry->{label} = $label;
$bam_entry->{urlTemplate} = $bam_url;
$bam_entry->{key} = $key;
if (!$coverage) {
$bam_entry->{subfeatures} = $mismatches ?
JSON::false : JSON::true;
$bam_entry->{style}->{className} = $classname;
$bam_entry->{style}->{showSubfeatures} = $mismatches ?
JSON::false : JSON::true;
$bam_entry->{style}->{showMismatches} = $mismatches ?
JSON::true : JSON::false;
}
else {
$bam_entry->{min_score} = $min_score;
$bam_entry->{max_score} = $max_score;
}
my $out;
$out = new IO::File($out_file, "w") or
die "Error writing output $out_file: $!";
print $out $json->pretty->encode($track_list);
$out->close();
}

sub generate_new_bam_alignment_entry {
return {
storeClass => $STORE_CLASS,
type => $ALIGNMENT_TYPE,
style => {
arrowheadClass => JSON::null,
featureScale => 0.5,
labelScale => 100,
subfeatureClasses => {
"M" => "cigarM",
"D" => "cigarD",
"N" => "cigarN",
"=" => "cigarEQ",
"E" => "cigarEQ",
"X" => "cigarX",
"I" => "cigarI"
}
}
};
}

sub generate_new_bam_coverage_entry {
return {
storeClass => $STORE_CLASS,
type => $COVERAGE_TYPE
};
}
134 changes: 134 additions & 0 deletions bin/add_bw_track.pl
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#!/usr/bin/env perl

use strict;
use warnings;

use Getopt::Long qw(:config no_ignore_case bundling);
use IO::File;
use File::Basename;
use JSON;

my $in_file = "data/trackList.json";
my $out_file = "data/trackList.json";
my $label;
my $bw_url;
my $key;
my $bicolor_pivot = "mean";
my $pos_color = undef;
my $neg_color = undef;
my $min_score = undef;
my $max_score = undef;

parse_options();
add_bw_track();

sub parse_options {
my $help;
GetOptions("in|i=s" => \$in_file,
"out|o=s" => \$out_file,
"label|l=s" => \$label,
"bw_url|u=s" => \$bw_url,
"key|k=s" => \$key,
"bicolor_pivot|b=s" => \$bicolor_pivot,
"pos_color|c=s" => \$pos_color,
"neg_color|C=s" => \$neg_color,
"min_score|s=i" => \$min_score,
"max_score|S=i" => \$max_score,
"help|h" => \$help);
print_usage() if $help;
die "Missing label option\n" if !$label;
die "Missing bw_url option\n" if !$bw_url;
$key = $label if !$key;
}

sub print_usage {
my $progname = basename($0);
die << "END";
usage: $progname
[-i|--in <input_trackList.json>]
[-o|--out <output_trackList.json>]
-l|--label <track_label>
-u|--bw_url <url_to_big_wig_file>
[-k|--key <track_key>]
[-b|bicolor_pivot <pivot_for_changing_colors>]
[-c|pos_color <color_for_positive_side_of_pivot>]
[-C|neg_color <color_for_negative_side_of_pivot>]
[-s|min_score <min_score>]
[-S|max_score <max_score>]
[-h|--help]
i: input trackList.json file [default: data/trackList.json]
o: output trackList.json file [default: data/trackList.json]
u: URL to BigWig file (can be a relative path)
k: key (display name) for track [default: label value]
b: point where to set pivot for color changes - can be "mean", "zero",
or a numeric value [default: mean]
c: CSS color for positive side of pivot [default: blue]
C: CSS color for negative side of pivot [default: red]
s: mininum score to be graphed [default: autocalculated]
S: maximum score to be graphed [default: autocalculated]
END
}

sub add_bw_track {
my $json = new JSON;
local $/;
my $in;
$in = new IO::File($in_file) or
die "Error reading input $in_file: $!";
my $track_list_contents = <$in>;
$in->close();
my $track_list = $json->decode($track_list_contents);
my $bw_entry;
foreach my $track (@{$track_list->{tracks}}) {
if ($track->{label} eq $label) {
$bw_entry = $track;
last;
}
}
if (!$bw_entry) {
$bw_entry = generate_new_bw_entry();
push @{$track_list->{tracks}}, $bw_entry;
};
$bw_entry->{label} = $label;
$bw_entry->{urlTemplate} = $bw_url;
$bw_entry->{key} = $key;
$bw_entry->{bicolor_pivot} = $bicolor_pivot;
if (defined $min_score) {
$bw_entry->{min_score} = $min_score;
}
else {
delete $bw_entry->{min_score};
}
if (defined $max_score) {
$bw_entry->{max_score} = $max_score;
}
else {
delete $bw_entry->{max_score};
}
if ($pos_color) {
$bw_entry->{style}->{pos_color} = $pos_color;
}
else {
delete $bw_entry->{style}->{pos_color};
}
if ($neg_color) {
$bw_entry->{style}->{neg_color} = $neg_color;
}
else {
delete $bw_entry->{style}->{neg_color};
}
delete $bw_entry->{style} if !scalar(keys %{$bw_entry->{style}});
my $out;
$out = new IO::File($out_file, "w") or
die "Error writing output $out_file: $!";
print $out $json->pretty->encode($track_list);
$out->close();
}

sub generate_new_bw_entry {
return {
storeClass => "JBrowse/Store/BigWig",
type => "JBrowse/View/Track/Wiggle/Density",
};
}
21 changes: 8 additions & 13 deletions bin/bam-to-json.pl
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Expand Up @@ -8,8 +8,8 @@ =head1 USAGE
bam-to-json.pl \
--bam <bam file> \
--trackLabel <track identifier> \
[ --out <output directory> ] \
[ --trackLabel <track identifier> ] \
[ --key <human-readable track name> ] \
[ --cssClass <class> ] \
[ --clientConfig '{ JSON }' ] \
Expand Down Expand Up @@ -64,7 +64,7 @@ =head1 OPTIONS
use warnings;

use FindBin qw($Bin);
use lib "$Bin/../src/perl5";
use lib "$Bin/../lib";
use JBlibs;

use Pod::Usage;
Expand Down Expand Up @@ -168,10 +168,7 @@ =head1 OPTIONS
my $sorter = NCLSorter->new( 1, 2, sub { $track->addSorted( $_[0]) } );
#$sorter->addSorted( [ 0, 23, 345, 1 ] );
$index->fetch( $bam, $tid, $start, $end,
sub {
my $a = align2array( $_[0] );
$sorter->addSorted( $a ) if $a->[2] - $a->[1] > 1;
}
sub { $sorter->addSorted( align2array( $_[0] )) }
);
$sorter->flush;
$track->finishLoad;
Expand All @@ -186,13 +183,11 @@ =head1 OPTIONS
sub align2array {
my $align = shift;

my $a = [ 0,
$align->pos,
$align->calend + 1,
$align->reversed ? -1 : 1
];
$a->[2]--;
return $a;
return [ 0,
$align->pos,
$align->calend + 1,
$align->reversed ? -1 : 1
];
}

sub slurp {
Expand Down

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