def returnGeneDescLs(cls, gene_annotation, gene_id_ls=[]):
"""
2009-6-22
fix a bug. db_user and other variables are now accessible from config['app_conf'], not model.xxx
"""
DrawSNPRegion_ins = DrawSNPRegion(
db_user=config["app_conf"]["db_user"],
db_passwd=config["app_conf"]["db_passwd"],
hostname=config["app_conf"]["hostname"],
database=config["app_conf"]["dbname"],
input_fname="/tmp/dumb",
output_dir="/tmp",
debug=0,
)
matrix_of_gene_descriptions = []
for gene_id in gene_id_ls:
gene_model = gene_annotation.gene_id2model.get(gene_id)
if gene_model:
if len(gene_model.gene_commentaries) == 0:
gene_commentaries = [gene_model] # fake one here
else:
gene_commentaries = gene_model.gene_commentaries
for gene_commentary in gene_commentaries:
gene_desc_ls = DrawSNPRegion_ins.returnGeneDescLs(
DrawSNPRegion_ins.gene_desc_names, gene_model, gene_commentary
)
matrix_of_gene_descriptions.append(gene_desc_ls)
return matrix_of_gene_descriptions
def dealWithGeneAnnotation():
gene_annotation_picklef = "/Network/Data/250k/tmp-yh/at_gene_model_pickelf"
DrawSNPRegion_ins = DrawSNPRegion(
db_user=db_user,
db_passwd=db_passwd,
hostname=hostname,
database=dbname,
input_fname="/tmp/dumb",
output_dir="/tmp",
debug=0,
)
gene_annotation = DrawSNPRegion_ins.dealWithGeneAnnotation(
gene_annotation_picklef, cls_with_db_args=DrawSNPRegion_ins
)
return gene_annotation
def getPlot(self):
"""
2010-1-22
add argument call_method_id when calling DrawSNPRegion.drawRegionAroundThisSNP()
2009-4-30
"""
chromosome = int(request.params.get('chromosome', 1))
start = int(request.params.get('start', 1))
stop = int(request.params.get('stop', 10))
if start>stop:
start, stop = stop, start
snps_id = '%s_%s'%(chromosome, start)
call_method_id = int(request.params.getone('call_method_id'))
phenotype_method_id = int(request.params.getone('phenotype_method_id'))
list_type_id = int(request.params.get('list_type_id', None))
plot_key = (chromosome, start, stop, call_method_id, phenotype_method_id, list_type_id)
if not hasattr(model, "plot_key2png_data"):
model.plot_key2png_data = {}
png_data = model.plot_key2png_data.get(plot_key)
if png_data is not None:
if hasattr(png_data, 'getvalue'): # png_data is StringIO
response.headers['Content-type'] = 'image/png'
return png_data.getvalue()
else:
return png_data
if not getattr(model, 'phenotype_id2analysis_method_id2gwr', None):
model.phenotype_id2analysis_method_id2gwr = {}
analysis_method_id2gwr = model.phenotype_id2analysis_method_id2gwr.get(phenotype_method_id)
if not analysis_method_id2gwr:
analysis_method_id2gwr = DrawSNPRegion.getSimilarGWResultsGivenResultsByGene(phenotype_method_id, call_method_id)
model.phenotype_id2analysis_method_id2gwr[phenotype_method_id] = analysis_method_id2gwr
if list_type_id>0: #2009-2-22
candidate_gene_set = GeneListRankTest.dealWithCandidateGeneList(list_type_id, return_set=True)
else:
candidate_gene_set = set()
gene_annotation = model.gene_annotation
snpData = hc.getSNPDataGivenCallMethodID(call_method_id)
pheno_data = hc.getPhenotypeDataInSNPDataOrder(snpData)
if h.ecotype_info is None: #2009-3-6 not used right now
h.ecotype_info = getEcotypeInfo(model.db)
snp_info = getattr(model, 'snp_info', None)
if snp_info is None:
snp_info = DrawSNPRegion.getSNPInfo(model.db)
model.snp_info = snp_info
LD_info = None
output_dir = '/tmp/' #not used at all, place holder
which_LD_statistic = 1
this_snp = SNPPassingData(chromosome=chromosome, position=start, stop=stop, snps_id='%s_%s'%(chromosome, start))
DrawSNPRegion.construct_chr_pos2index_forSNPData(snpData) #prerequisite
after_plot_data = DrawSNPRegion.drawRegionAroundThisSNP(phenotype_method_id, this_snp, candidate_gene_set, \
gene_annotation, snp_info, \
analysis_method_id2gwr, LD_info, output_dir, which_LD_statistic, \
min_distance=20000, list_type_id=list_type_id,
label_gene=True, \
draw_LD_relative_to_center_SNP=False,\
commit=True, snpData=snpData, phenData=pheno_data, \
ecotype_info=h.ecotype_info, snpData_before_impute=None,\
snp_matrix_data_type=1, call_method_id=call_method_id)
if getattr(after_plot_data, 'png_data', None):
response.headers['Content-type'] = 'image/png'
model.plot_key2png_data[plot_key] = after_plot_data.png_data
return after_plot_data.png_data.getvalue()
else:
model.plot_key2png_data[plot_key] = "No Plot"
return model.plot_key2png_data[plot_key]
#!/usr/bin/env python
"""
2008-10-01
example to call DrawSNPRegion as an API
"""
import sys, os, math
sys.path.insert(0, os.path.expanduser('~/lib/python'))
sys.path.insert(0, os.path.join(os.path.expanduser('~/script')))
from variation.src.DrawSNPRegion import DrawSNPRegion
instance = DrawSNPRegion(db_user='******', db_passwd='', hostname='papaya.usc.edu', database='stock_250k', input_fname='/tmp/dumb', output_dir='/tmp', debug=0)
gene_annotation_picklef = '/Network/Data/250k/tmp-yh/at_gene_model_pickelf'
LD_info_picklef = '/Network/Data/250k/tmp-yh/call_method_17_LD_m0.2_n0.1_m40000'
#LD_info_picklef = None
LD_fname = '/Network/Data/250k/tmp-yh/call_method_17_LD_m0.2.tsv' #optional
phenotype_method_id = 1
chromosome, start, stop = 2, 9588685-40000, 9588685+40000
output_fname = '/tmp/SNP_2_9588685'
center_snp_position = 9588685
instance.drawSNPRegion(gene_annotation_picklef, LD_info_picklef, phenotype_method_id, chromosome, start, stop, \
output_fname, center_snp_position=center_snp_position, LD_fname=LD_fname,\
which_LD_statistic=2, call_method_id=17, min_MAF=0.1)
