def load_genecluster_info(seq_record, options, searchtype="general"):
#Gather and store data on each gene cluster
smcogdict, smcogdescriptions = utils.get_smcog_annotations(seq_record)
gtrcoglist = ['SMCOG1045', 'SMCOG1062', 'SMCOG1102']
transportercoglist = [
'SMCOG1000', 'SMCOG1005', 'SMCOG1011', 'SMCOG1020', 'SMCOG1029',
'SMCOG1033', 'SMCOG1035', 'SMCOG1044', 'SMCOG1065', 'SMCOG1067',
'SMCOG1069', 'SMCOG1074', 'SMCOG1085', 'SMCOG1096', 'SMCOG1106',
'SMCOG1118', 'SMCOG1131', 'SMCOG1166', 'SMCOG1169', 'SMCOG1184',
'SMCOG1202', 'SMCOG1205', 'SMCOG1214', 'SMCOG1234', 'SMCOG1243',
'SMCOG1245', 'SMCOG1252', 'SMCOG1254', 'SMCOG1288'
]
seq_record.qgeneclusterdata = {}
geneclusters = utils.get_sorted_cluster_features(seq_record)
for genecluster in geneclusters:
geneclusternr = utils.get_cluster_number(genecluster)
clustergenes, clustertype, annotations, colors, starts, ends, strands, pksnrpsprots, gtrs, transporters, clustersize = retrieve_gene_cluster_annotations(
seq_record, smcogdict, gtrcoglist, transportercoglist,
geneclusternr)
if options.clusterblast:
hitgeneclusterdata = retrieve_clusterblast_info(
seq_record, geneclusternr, searchtype=searchtype)
else:
hitgeneclusterdata = {}
pksnrpsprotsnames, pksnrpsdomains, domlist, domsdetails, substrspecnrpspredictordict, substrspecminowadict, substrspecpkssigdict, substrspecconsensusdict, krpredictionsdict, structpred = retrieve_pksnrps_info(
seq_record, geneclusternr, pksnrpsprots)
seq_record.qgeneclusterdata[geneclusternr] = [
clustertype, clustersize, clustergenes, annotations, starts, ends,
strands, pksnrpsprots, pksnrpsprotsnames, pksnrpsdomains,
substrspecnrpspredictordict, substrspecminowadict,
substrspecpkssigdict, substrspecconsensusdict, gtrs, transporters,
colors, hitgeneclusterdata, structpred, krpredictionsdict
]
def generate_searchgtr_htmls(seq_records, options):
#Generate lists of COGs that are glycosyltransferases or transporters
gtrcoglist = ['SMCOG1045', 'SMCOG1062', 'SMCOG1102']
searchgtrformtemplateparts = load_searchgtr_search_form_template()
options.searchgtr_links = {}
for seq_record in seq_records:
smcogdict, _ = utils.get_smcog_annotations(seq_record)
for feature in utils.get_cds_features(seq_record):
gene_id = utils.get_gene_id(feature)
if smcogdict.has_key(gene_id):
smcog = smcogdict[gene_id]
if smcog in gtrcoglist:
if not os.path.exists(options.full_outputfolder_path +
os.sep + "html"):
os.mkdir(options.full_outputfolder_path + os.sep +
"html")
formfileloc = options.full_outputfolder_path + os.sep + "html" + os.sep + utils.get_gene_id(
feature) + "_searchgtr.html"
link_loc = "html" + os.sep + utils.get_gene_id(
feature) + "_searchgtr.html"
options.searchgtr_links[seq_record.id + "_" +
gene_id] = link_loc
formfile = open(formfileloc, "w")
specificformtemplate = searchgtrformtemplateparts[
0].replace("GlycTr", gene_id)
formfile.write(specificformtemplate)
formfile.write("%s\n%s" %
(gene_id, utils.get_aa_sequence(feature)))
formfile.write(searchgtrformtemplateparts[1])
formfile.close()
def test_get_smcog_annotations(self):
"Test utils.get_smcog_annotations()"
expected_dict = {
'orf0001': 'SMCOG0001',
'orf0003': 'SMCOG0003',
'orf0006': 'SMCOG0006',
}
expected_desc = {
'SMCOG0001': 'FAKE0001 ',
'SMCOG0003': 'FAKE0003 ',
'SMCOG0006': 'FAKE0006 ',
}
smcogdict, smcog_desc = utils.get_smcog_annotations(self.rec)
self.assertEqual(expected_dict, smcogdict)
self.assertEqual(expected_desc, smcog_desc)