def importSplicingAnnotationDatabaseAndSequence(species, array_type, biotype):
array_ens_db = {}
if array_type == 'AltMouse':
filename = 'AltDatabase/' + species + '/' + array_type + '/' + array_type + '-Ensembl_relationships.txt'
update.verifyFile(filename,
array_type) ### Will force download if missing
fn = filepath(filename)
x = 0
for line in open(fn, 'r').xreadlines():
data, newline = string.split(line, '\n')
t = string.split(data, '\t')
if x == 0: x = 1
else:
array_gene, ens_gene = t
try:
array_ens_db[array_gene].append(ens_gene)
except KeyError:
array_ens_db[array_gene] = [ens_gene]
filename = 'AltDatabase/' + species + '/' + array_type + '/' + array_type + '_critical-junction-seq.txt'
fn = filepath(filename)
probeset_seq_db = {}
x = 0
for line in open(fn, 'r').xreadlines():
data, newline = string.split(line, '\n')
t = string.split(data, '\t')
if x == 0: x = 1
else:
probeset, probeset_seq, junction_seq = t
junction_seq = string.replace(junction_seq, '|', '')
probeset_seq_db[probeset] = probeset_seq, junction_seq
###Import reciprocol junctions, so we can compare these directly instead of hits to nulls and combine with sequence data
###This short-cuts what we did in two function in ExonSeqModule with exon level data
filename = 'AltDatabase/' + species + '/' + array_type + '/' + array_type + '_junction-comparisons.txt'
fn = filepath(filename)
probeset_gene_seq_db = {}
x = 0
for line in open(fn, 'r').xreadlines():
data, newline = string.split(line, '\n')
t = string.split(data, '\t')
if x == 0: x = 1
else:
array_gene, probeset1, probeset2, critical_exons = t #; critical_exons = string.split(critical_exons,'|')
probesets = [probeset1, probeset2]
if array_type == 'junction' or array_type == 'RNASeq':
array_ens_db[array_gene] = [array_gene]
if array_gene in array_ens_db:
ensembl_gene_ids = array_ens_db[array_gene]
for probeset_id in probesets:
if probeset_id in probeset_seq_db:
probeset_seq, junction_seq = probeset_seq_db[
probeset_id]
if biotype == 'gene':
for ensembl_gene_id in ensembl_gene_ids:
probe_data = ExonSeqModule.JunctionDataSimple(
probeset_id, ensembl_gene_id, array_gene,
probesets, critical_exons)
probe_data.SetExonSeq(probeset_seq)
probe_data.SetJunctionSeq(junction_seq)
try:
probeset_gene_seq_db[
ensembl_gene_id].append(probe_data)
except KeyError:
probeset_gene_seq_db[ensembl_gene_id] = [
probe_data
]
else: ### Used for probeset annotations downstream of sequence alignment in LinkEST, analagous to exon_db for exon analyses
probe_data = ExonSeqModule.JunctionDataSimple(
probeset_id, ensembl_gene_ids, array_gene,
probesets, critical_exons)
probe_data.SetExonSeq(probeset_seq)
probe_data.SetJunctionSeq(junction_seq)
probeset_gene_seq_db[probeset_id] = probe_data
print len(probeset_gene_seq_db), "genes with probeset sequence associated"
return probeset_gene_seq_db
