add an example shell script that downloads and formats some fairly bi…

…g tomato data

docs/examples/format_tomato.sh

@@ -0,0 +1,104 @@
+#!/usr/bin/env bash
+
+## example script that fetches and formats large data from the tomato
+## genome (similar in size to Human) using flatfile-to-json
+
+IN='sample_data/raw/tomato';
+OUT='sample_data/json/tomato';
+
+set -e;
+rm -rf $OUT;
+mkdir -p $IN $OUT;
+
+# fetch the tomato data using `wget` (about 1G total)
+for f in ITAG2.3_assembly.gff3        \
+         ITAG2.3_gene_models.gff3     \
+         ITAG2.3_genomic.fasta        \
+         ITAG2.3_cdna_alignments.gff3 \
+         ITAG2.3_sgn_data.gff3        \
+         ; do
+    if [ ! -e $IN/$f ]; then
+        wget -v -O $IN/$f ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/annotation/ITAG2.3_release/$f;
+    fi
+done
+
+# format the reference sequences
+bin/prepare-refseqs.pl --compress --fasta $IN/ITAG2.3_genomic.fasta --out $OUT;
+
+# official ITAG2.3 gene models
+bin/flatfile-to-json.pl --compress \
+    --out $OUT \
+    --gff $IN/ITAG2.3_gene_models.gff3 \
+    --type mRNA \
+    --autocomplete all \
+    --trackLabel genes  \
+    --key 'Gene models' \
+    --getSubfeatures    \
+    --cssClass transcript \
+    --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' \
+    --arrowheadClass arrowhead \
+    --urltemplate "http://solgenomics.net/search/quick?term={name}" \
+    ;
+
+# SL2.40 assembly
+bin/flatfile-to-json.pl --compress  \
+    --out $OUT \
+    --trackLabel assembly \
+    --key 'Assembly' \
+    --gff $IN/ITAG2.3_assembly.gff3 \
+    --type supercontig,remark \
+    --autocomplete all \
+    --getSubfeatures \
+    --cssClass generic_parent \
+    --subfeatureClasses '{"contig": "feature3"}' \
+    --urltemplate "http://solgenomics.net/search/quick?term={name}" \
+    ;
+
+# SGN unigene alignments
+bin/flatfile-to-json.pl --compress  \
+    --out $OUT \
+    --trackLabel sgn_unigenes \
+    --key 'SGN unigenes' \
+    --gff $IN/ITAG2.3_sgn_data.gff3 \
+    --type match:ITAG_sgn_unigenes \
+    --autocomplete all \
+    --getSubfeatures \
+    --cssClass generic_parent \
+    --subfeatureClasses '{"match_part": "match_part"}' \
+    --arrowheadClass 'arrowhead' \
+    --urltemplate "http://solgenomics.net/search/quick?term={name}" \
+    ;
+
+# microtom cDNA alignments
+bin/flatfile-to-json.pl --compress  \
+    --out $OUT \
+    --trackLabel microtom_cdna \
+    --key 'MicroTom full-length cDNAs' \
+    --gff $IN/ITAG2.3_cdna_alignments.gff3 \
+    --type match:ITAG_microtom_flcdnas \
+    --autocomplete all \
+    --getSubfeatures \
+    --cssClass generic_parent \
+    --subfeatureClasses '{"match_part": "match_part"}' \
+    --arrowheadClass 'arrowhead' \
+    ;
+
+# SGN marker sequences
+bin/flatfile-to-json.pl --compress  \
+    --out $OUT \
+    --trackLabel sgn_markers \
+    --key 'SGN markers' \
+    --gff $IN/ITAG2.3_sgn_data.gff3 \
+    --type match:ITAG_sgn_markers \
+    --autocomplete all \
+    --getSubfeatures \
+    --cssClass transcript \
+    --subfeatureClasses '{"match_part": "match_part"}' \
+    --arrowheadClass 'arrowhead' \
+    --urltemplate "http://solgenomics.net/search/quick?term={name}" \
+    ;
+
+# index feature names
+bin/generate-names.pl --out $OUT;
+
+echo "To see the formatted ITAG2.3 tomato genome, point your browser at http://your.jbrowse.root/index.html?data=sample_data/json/tomato";