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Allow IGV.js to get genome reference #37

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Allow IGV.js to get genome reference #37

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33 changes: 33 additions & 0 deletions lib/galaxy/webapps/galaxy/api/genomes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,3 +43,36 @@ def show( self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ):
else:
rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low )
return rval

@web.expose_api_raw_anonymous
def indexes(self, trans, id, **kwd):
"""
GET /api/genomes/{id}/indexes?type={table name}

Returns all available indexes for a genome id for type={table name}
For instance, /api/genomes/hg19/indexes?type=fasta_indexes
"""
index_extensions = {'fasta_indexes': '.fai'}
id = get_id( id, kwd.get( 'format', None ) )
index_type = kwd.get('type', None)

tbl_entries = self.app.tool_data_tables.data_tables[index_type].data
index_file_name = [x[-1] for x in tbl_entries if id in x].pop()

if_open = open(index_file_name + index_extensions[index_type], mode='r')
return if_open.read()

@web.expose_api_raw_anonymous
def sequences(self, trans, id, num=None, chrom=None, low=None, high=None, **kwd ):
"""
GET /api/genomes/{id}/sequences

This is a wrapper for accepting sequence requests that
want a raw return, not json
"""
id = get_id( id, kwd.get( 'format', None ) )
reference = is_true( kwd.get( 'reference', False ) )
if reference:
region = self.app.genomes.reference( trans, dbkey=id, chrom=chrom, low=low, high=high )
rval = { 'dataset_type': 'refseq', 'data': region.sequence }
return rval['data']