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write POD for flatfile-to-json.pl and migrate to Pod::Usage
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@rbuels
rbuels committed Feb 13, 2012
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203 changes: 170 additions & 33 deletions bin/flatfile-to-json.pl
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#!/usr/bin/env perl

=head1 NAME
flatfile-to-json.pl - format data into JBrowse JSON format from an annotation file
=head1 USAGE
flatfile-to-json.pl \
( --gff <GFF3 file> | --gff2 <GFF2 file> | --bed <BED file> ) \
--tracklabel <track identifier> \
[ --out <output directory> ] \
[ --key <human-readable track name> ] \
[ --cssClass <CSS class name for displaying features> ] \
[ --autocomplete <none|label|alias|all> ] \
[ --getType ] \
[ --getPhase ] \
[ --getSubs ] \
[ --getLabel ] \
[ --urltemplate "http://example.com/idlookup?id={id}" ] \
[ --extraData <attribute> ] \
[ --arrowheadClass <CSS class> ] \
[ --subfeatureClasses '{ JSON-format subfeature class map }' ] \
[ --clientConfig '{ JSON-format extra configuration for this track }' ] \
[ --thinType <BAM -thin_type> ] \
[ --thicktype <BAM -thick_type>] \
[ --type <feature types to process> ] \
[ --nclChunk <chunk size for generated NCLs> ] \
[ --compress ] \
[ --sortMem <memory in bytes to use for sorting> ] \
=head1 ARGUMENTS
=head2 REQUIRED
=over 4
=item --gff <GFF3 file>
=item --gff2 <GFF2 file>
=item --bed <BED file>
Process a GFF3, GFF2, or BED-format file containing annotation data.
=item --tracklabel <track identifier>
Unique identifier for this track.
=back
=head1 OPTIONAL
=over 4
=item --help | -h
Display an extended help screen.
=item --key '<text>'
Human-readable track name.
=item --out <output directory>
Output directory to write to. Defaults to "data/".
=item --cssClass <CSS class name for displaying features>
CSS class for features. Defaults to "feature".
=item --autocomplete <none|label|alias|all>
Make these features searchable by their C<label>, by their C<alias>es,
both (C<all>), or C<none>. Defaults to C<none>.
=item --getType
Include the type of the features in the JSON.
=item --getPhase
Include the phase of the features in the JSON.
=item --getSubs
Include subfeatures in the JSON.
=item --getLabel
Include a label for the features in the JSON.
=item --urltemplate "http://example.com/idlookup?id={id}"
Template for a URL to be visited when features are clicked on.
=item --extraData <attribute>
A map of feature attribute names to perl subs that extract information
from the feature object. Example:
--extraData '{"protein_id" : "sub {shift->attributes(\"protein_id\");} "}'
=item --arrowheadClass <CSS class>
CSS class for arrowheads.
=item --subfeatureClasses '{ JSON-format subfeature class map }'
CSS classes for each subfeature type, in JSON syntax. Example:
--subfeatureClasses '{"CDS": "transcript-CDS", "exon": "transcript-exon"}'
=item --clientConfig '{ JSON-format extra configuration for this track }'
Extra configuration for the client, in JSON syntax. Example:
--clientConfig '{"featureCss": "background-color: #668; height: 8px;", "histScale": 2}'
=item --type <feature types to process>
Only process features of the given type.
=item --nclChunk <chunk size for generated NCLs>
NCList chunk size; if you get "json text or perl structure exceeds
maximum nesting level" errors, try setting this lower (default:
50,000).
=item --compress
Compress the output, making .jsonz (gzipped) JSON files. This can
save a lot of disk space, but note that web servers require some
additional configuration to serve these correctly.
=item --sortMem <bytes>
Bytes of RAM to use for sorting features. Default 512MB.
=back
=head2 BED-SPECIFIC
=over 4
=item --thinType <type>
=item --thickType <type>
Correspond to C<<-thin_type>> and C<<-thick_type>> in
L<Bio::FeatureIO::bed>. Do C<<perldoc Bio::FeatureIO::bed>> for
details.
=back
=cut

use strict;
use warnings;

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

use Getopt::Long;
use Pod::Usage;

use Bio::DB::SeqFeature::Store;
use Bio::DB::GFF;
use Bio::FeatureIO;

use JsonGenerator;
use BioperlFlattener;
use ExternalSorter;
Expand All @@ -25,7 +183,8 @@
my $cssClass = "feature";
my ($getType, $getPhase, $getSubs, $getLabel, $compress) = (0, 0, 0, 0, 0);
my $sortMem = 1024 * 1024 * 512;
GetOptions("gff=s" => \$gff,
my $help;
GetOptions("gff=s" => \$gff,
"gff2=s" => \$gff2,
"bed=s" => \$bed,
"bam=s" => \$bam,
Expand All @@ -44,11 +203,16 @@
"subfeatureClasses=s" => \$subfeatureClasses,
"clientConfig=s" => \$clientConfig,
"thinType=s" => \$thinType,
"thicktype=s" => \$thickType,
"thickType=s" => \$thickType,
"type=s@" => \$types,
"nclChunk=i" => \$nclChunk,
"compress" => \$compress,
"sortMem=i" =>\$sortMem);
"sortMem=i" =>\$sortMem,
"help|h" => \$help,
);

pod2usage( -verbose => 2 ) if $help;

# parent path of track-related dirs, relative to $outdir
my $trackRel = "tracks";

Expand All @@ -59,36 +223,9 @@

die "run prepare-refseqs.pl first to supply information about your reference sequences" unless (scalar keys %refSeqs);

if (!(defined($gff) || defined($gff2) || defined($bed) || defined($bam)) || !defined($trackLabel)) {
print "The --tracklabel parameter is required\n"
unless defined($trackLabel);
print "You must supply either a --gff, -gff2, or --bed parameter\n"
unless (defined($gff) || defined($gff2) || defined($bed) || defined($bam));
print <<USAGE;
USAGE: $0 [--gff <gff3 file> | --gff2 <gff2 file> | --bed <bed file>] [--out <output directory>] --tracklabel <track identifier> --key <human-readable track name> [--cssClass <CSS class for displaying features>] [--autocomplete none|label|alias|all] [--getType] [--getPhase] [--getSubs] [--getLabel] [--urltemplate "http://example.com/idlookup?id={id}"] [--extraData <attribute>] [--subfeatureClasses <JSON-syntax subfeature class map>] [--clientConfig <JSON-syntax extra configuration for FeatureTrack>]
--out: defaults to "data"
--cssClass: defaults to "feature"
--autocomplete: make these features searchable by their "label", by their "alias"es, both ("all"), or "none" (default).
--getType: include the type of the features in the json
--getPhase: include the phase of the features in the json
--getSubs: include subfeatures in the json
--getLabel: include a label for the features in the json
--urltemplate: template for a URL that clicking on a feature will navigate to
--arrowheadClass: CSS class for arrowheads
--subfeatureClasses: CSS classes for each subfeature type, in JSON syntax
e.g. '{"CDS": "transcript-CDS", "exon": "transcript-exon"}'
--clientConfig: extra configuration for the client, in JSON syntax
e.g. '{"featureCss": "background-color: #668; height: 8px;", "histScale": 2}'
--type: only process features of the given type
--nclChunk: NCList chunk size; if you get "json text or perl structure exceeds maximum nesting level" errors, try setting this lower (default: $nclChunk)
--extraData: a map of feature attribute names to perl subs that extract information from the feature object
e.g. '{"protein_id" : "sub {shift->attributes(\"protein_id\");} "}'
--compress: compress the output (requires some web server configuration)
--sortMem: the amount of memory in bytes to use for sorting
USAGE
exit(1);
}
pod2usage( "Must provide a --tracklabel parameter." ) unless defined $trackLabel;
pod2usage( "You must supply either a --gff, -gff2, or --bed parameter." )
unless defined $gff || defined $gff2 || defined $bed || defined $bam;

if (!defined($nclChunk)) {
# default chunk size is 50KiB
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