from django.http import HttpResponse
from django.shortcuts import render
from .forms import QueryForm
import os
import re
import logging
import pickle
# cmd = 'echo $LD_LIBRARY_PATH'
# r = os.popen(cmd).read()
# print('views.py library path=', r)
# import pandas as pd
log_level = 'DEBUG'
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
fn = os.path.join(BASE_DIR, 'all_protein_coding_gene_name.set.pkl')
hgnc_dict = pickle.load(open(fn, 'rb'))
fn = os.path.join(BASE_DIR, 'ddi_score_for_website.dict.pkl')
ddi = pickle.load(open(fn, 'rb'))
ddi_gn_set = set(ddi)
# print('\n'*4)
# print(f'using the ddi pdict using is {fn}')
# print(f'id for ddi dict = {id(ddi)}')
chrmap = {1: '1', 2: '2', 3: '3', 4: '4', 5: '5', 6: '6', 7: '7', 8: '8', 9: '9', 10: '10', 11: '11', 12: '12',
13: '13', 14: '14', 15: '15', 16: '16', 17: '17', 18: '18', 19: '19', 20: '20', 21: '21', 22: '22', 23: '23',
24: '24', 25: '25', 26: '26', '1': '1', '2': '2', '3': '3', '4': '4', '5': '5', '6': '6', '7': '7', '8': '8',
'9': '9', '10': '10', '11': '11', '12': '12', '13': '13', '14': '14', '15': '15', '16': '16', '17': '17',
'18': '18', '19': '19', '20': '20', '21': '21', '22': '22', '23': '23', '24': '24', '25': '25', '26': '26',
'chr1': '1', 'chr2': '2', 'chr3': '3', 'chr4': '4', 'chr5': '5', 'chr6': '6', 'chr7': '7', 'chr8': '8',
'chr9': '9', 'chr10': '10', 'chr11': '11', 'chr12': '12', 'chr13': '13', 'chr14': '14', 'chr15': '15',
'chr16': '16', 'chr17': '17', 'chr18': '18', 'chr19': '19', 'chr20': '20', 'chr21': '21', 'chr22': '22',
'chr23': '23', 'chr24': '24', 'chr25': '25', 'chr26': '26', 'chr01': '1', 'chr02': '2', 'chr03': '3',
'chr04': '4', 'chr05': '5', 'chr06': '6', 'chr07': '7', 'chr08': '8', 'chr09': '9', '01': '1', '02': '2',
'03': '3', '04': '4', '05': '5', '06': '6', '07': '7', '08': '8', '09': '9', 'x': '23', 'y': '24', 'xy': '25',
'mt': '26', '0x': '23', '0y': '24', 'X': '23', 'Y': '24', 'XY': '25', 'MT': '26', '0X': '23', '0Y': '24',
'chrx': '23', 'chry': '24', 'chrxy': '25', 'chrmt': '26', 'chr0x': '23', 'chr0y': '24', 'chrX': '23',
'chrY': '24', 'chrXY': '25', 'chrMT': '26', 'chr0X': '23', 'chr0Y': '24', 'chrM': '25', 'mito': '25', 'M':
'25', 'm': '25', 'chrm': '25', 'Mito': '25'}
map_ddi = {'gn': 0,
'dm': 1,
'DDI': 2,
'dmname': 3,
'dmfull': 4,
'DDI_rank': 5,
'len_dm': 6,
'len_cds': 7,
'mis_cds': 8,
'mis_dm': 9,
'enrichment': 10,
'path_count_dm': 11,
'path_count_gene': 12,
'or': 13,
'chr': 14,
'pos': 15,
'strand': 16}
selected_fields_ddi_dict = ['DDI', 'DDI_rank', 'gn', 'dmname', 'dmfull', 'dm', 'chr', 'pos', 'strand', 'or']
map_zresult = {'gn': 0,
'dm': 1,
'DDI': 2,
'dmname': 4,
'dmfull': 5,
'DDI_rank': 3,
'or': 9,
'chr': 6,
'pos': 7,
'strand': 8
}
def home_view(request):
igv_query = 'CACNA1A'
input_error = ''
input_error2 = ''
valid = 1
z_result = []
z_result_sorted = []
clinvar_gene = []
table_header = ['DDI',
'DDI rank',
'Gene',
'Domain Name',
'Domain Full Name',
'Pfam ID',
]
if request.method == 'POST':
form = QueryForm(request.POST)
if form.is_valid():
# get the value from the client-end input !
normal = 1 # status , if some abormal occure, would not proceed the following steps
query_item = form.cleaned_data['gene'].strip().upper()
# the query is a range
reg_range = re.compile(r'^(?:chr)?([\dxymt]+)[:\-]([\d ,]+)\-([\d ,]+)$')
reg_range_single_positon = re.compile(r'^(?:chr)?([\dxymt]+)[:\-]([\d ,]+)\S*$')
m_range1 = re.match(reg_range, query_item.lower())
m_range2 = re.match(reg_range_single_positon, query_item.lower())
if m_range1 or m_range2:
# chrx:9991000-9992000
try:
chr_, pos_s, pos_e = m_range1.groups()
except:
chr_, pos_s = m_range2.groups()
pos_e = pos_s
pos_s = re.sub("[, ]", '', pos_s)
pos_e = re.sub("[, ]", '', pos_e)
chr_ = chrmap[chr_]
try:
pos_s = int(pos_s)+1
pos_e = int(pos_e)
except:
normal = 0
# the intersect
if normal:
# print(f'chr_={chr_}, pos_s={pos_s}, pos_e={pos_e}')
igv_query = f'{chr_}:{pos_s}-{pos_e}'
cmd = f"""/var/www/html/miniconda/bin/bedtools intersect -a stdin -b {BASE_DIR}/static/files/range_dm.bed -wb <<<$'{chr_}\t{pos_s-1}\t{pos_e}'|cut -f 2,3,7,8 2>/dev/null"""
res = os.popen(cmd).read().strip().split('\n')
print('res=',res)
query_tmp = {} # store the max and min value for the start and end
for ires in res:
try:
q_s, q_e, ign, idm_raw = ires.split('\t')
q_s = int(q_s)
q_e = int(q_e)
except:
print(f'error spliting bedtools result {ires}')
normal = 0
continue
try:
if query_tmp[idm_raw][0] > q_s:
query_tmp[idm_raw][0] = q_s
except:
query_tmp[idm_raw] = [q_s, q_e, ign]
if query_tmp[idm_raw][1] < q_e:
query_tmp[idm_raw][1] = q_e
# get each domain
# if normal:
check_dup = set()
for idm_raw, v in query_tmp.items():
idm, idm_sn = idm_raw.split('#')
q_s, q_e, ign = v
k = f'{ign}_{idm}'
if k not in check_dup:
check_dup.add(k)
else:
continue
try:
ddi_res = [ddi[ign][idm][map_ddi[_]] for _ in selected_fields_ddi_dict]
except:
print(f' this domain is not included in the DDI result : gn= {ign}, dm = {idm}')
continue
ddi_res.extend([q_s, q_e, chr_])
z_result.append(ddi_res)
## sort the result, to enable the domains in the table are the same as the lollipop
# must consider the strand issue
# ['DDI', 'DDI_rank', 'gn', 'dmname', 'dmfull', 'dm', 'chr', 'pos', 'strand', 'or']
if z_result:
reverse_tag = {'+': False, '-': True}[list(z_result)[0][-5]] # strand = -5
z_result_sorted = sorted(z_result, key=lambda _: _[-6], reverse=reverse_tag) # pos= -6
# -1 = domain sn
z_result_sorted = [[i[_] for _ in [0, 1, -1, -3, -2, 2, 3, 4, 5]] for i in z_result_sorted]
table_header.insert(2, 'Query_Match_End')
table_header.insert(2, 'Query_Match_Start')
table_header.insert(2, 'Chrom')
clinvar_gene.extend([_[2] for _ in z_result if _[-4] != 'NA']) # or = -4
else:
# check if this request is in other gene elements
cmd = f"""/var/www/html/miniconda/bin/bedtools intersect -a stdin -b {BASE_DIR}/static/files/range_cds_and_intron.bed -wb <<<$'{chr_}\t{pos_s-1}\t{pos_e}'|cut -f 2,3,5,6,7,8 2>/dev/null"""
res = os.popen(cmd).read().strip()
if not res:
input_error = 'The query range is outside of gene
'
else:
res = res.split('\n')
print(res)
tmp = res[0].split('\t')
ign = tmp[-2]
region = tmp[-1]
input_error2 = f'The query range is the {region} region of gene {ign}, but outside of Pfam domain region
'
# valid gene name
elif query_item in hgnc_dict:
igv_query = query_item
table_header.insert(2, 'Chrom')
if query_item not in ddi_gn_set:
# print('pos1')
valid = 0
input_error = 'Gene not found
'
else:
#z_result = ddi.loc[ddi['gn'] == query_item].transpose().to_dict().values()
# print('pos1')
tmp = list(ddi[query_item].values())
# print(f'tmp={tmp}')
for dm_tmp in tmp:
chr_ = dm_tmp[map_ddi['chr']]
ddi_res = [dm_tmp[map_ddi[_]] for _ in selected_fields_ddi_dict]
ddi_res.append(chr_)
z_result.append(ddi_res)
# sort the result, to enable the domains in the table are the same as the lollipop
# must consider the strand issue
# ['DDI', 'DDI_rank', 'gn', 'dmname', 'dmfull', 'dm', 'chr', 'pos', 'strand', 'or']
reverse_tag = {'+': False, '-': True}[list(z_result)[0][-3]] # strand = -2
z_result_sorted = sorted(z_result, key=lambda _: _[-3], reverse=reverse_tag)
z_result_sorted = [[i[_] for _ in [0, 1, -1, 2, 3, 4, 5]] for i in z_result_sorted]
# _[2] = ign
# _[-1] = odds ratio
clinvar_gene.extend([_[2] for _ in z_result if _[-1] != 'NA'])
else:
valid = 0
input_error = 'not a protein coding gene or invalid input
'
igv_query = query_item
else:
# print(f'is_bound {switch_toggle.is_bound}')
valid = 0
query_item = 'CACNA1A'
igv_query = 'CACNA1A'
input_error = 'Invalid Input
'
# the unbounded request
else:
valid = 0
query_item = 'CACNA1A'
form = QueryForm()
# print(f'error={input_error}, query_item={query_item}')
return render(
request, 't.html',
{
'form': form,
'igv_query': igv_query,
'query_item': query_item,
'input_error': input_error,
'input_error2': input_error2,
'valid': valid,
'z_result': z_result_sorted,
'clinvar_gene': set(clinvar_gene),
'table_header': table_header,
})
def test_view(request, *args, **kwargs):
for i in dir(request):
res = eval(f'request.{i}')
print(f'{i} = {res}\n**************\n')
return HttpResponse(f' this is the test page
')