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app.py
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import os
import json
import fnmatch
import sys
import urllib2
import pandas as pd
import numpy as np
import clustergrammer as clustergrammer
from flask import Flask, make_response, send_from_directory, request, render_template, url_for, redirect
from Model.models import db
from Service.ilincsService import IlincsSearch
from Service.make_clustergrammer import LoadFile
from scipy import stats
def get_valid_pyc_files():
for import_path in sys.path:
for root, dir_names, file_names in os.walk(import_path):
for file_name in fnmatch.filter(file_names, '*.pyc'):
pyc_file_path = os.path.join(root, file_name)
py_file_path = pyc_file_path[:-1]
if os.path.isfile(py_file_path):
yield pyc_file_path
def ensure_root():
is_root = os.geteuid() == 0
if not is_root:
sys.exit('Must be run as root')
#def main():
def runserver():
ensure_root()
for pyc_file_path in get_valid_pyc_files():
print 'removing', pyc_file_path
os.remove(pyc_file_path)
port = int(os.environ.get('PORT', 4000))
app.run(host='0.0.0.0', port=port)
app = Flask(__name__)
# app.config['SQLALCHEMY_DATABASE_URI'] = 'postgresql://localhost/lincs2lincs'
# db.init_app(app)
app.secret_key = "development-key"
ilincsSearch = IlincsSearch()
loadFile = LoadFile()
# @app.route("/")
# @app.route("/home")
# @app.route("/about")
# @app.route("/clustergram")
# @app.route("/bootstrap")
# def basic_pages():
# return make_response(open('static/index.html').read())
@app.route("/api/clust/P100/")
def make_clustergram_p100():
petide2ptmAndGene = {
"IYQY[+80]IQSR": "Q13627[Y+80@321](DYRK1A)",
"TPKDS[+80]PGIPPSANAHQLFR": "P51812[S+80@369](RPS6KA3)",
"RNS[+80]SEASSGDFLDLK": "Q9UK76[S+80@87](JPT1)",
"LPLVPES[+80]PRR": "Q86WB0[S+80@321](ZC3HC1)",
"ANAS[+80]PQKPLDLK": "Q9Y618[S+80@956](NCOR2)",
"LENS[+80]PLGEALR": "Q9NX40[S+80@108](OCIAD1)",
"ANS[+80]FVGTAQYVSPELLTEK": "O15530[S+80@241](PDPK1)",
"TNPPTQKPPS[+80]PPMSGR": "Q8IZP0[S+80@183](ABI1)",
"SNS[+80]LPHSAVSNAGSK": "Q8TBZ3[S+80@434](WDR20)",
"VGS[+80]LDNVGHLPAGGAVK": "P27816[S+80@1073](MAP4)",
"AAPEAS[+80]SPPASPLQHLLPGK": "Q96TA1[S+80@691](FAM129B)",
"S[+122]DKPDM[+16]AEIEKFDK": "P62328[S+122@2][M+16@7](TMSB4X)",
"S[+122]DKPDMAEIEKFDK": "P62328[S+122@2](TMSB4X)",
"SLS[+80]LGDKEISR": "Q9UMZ2[S+80@1075](SYNRG)",
"DLVQPDKPAS[+80]PK": "Q6PJT7[S+80@515](ZC3H14)",
"SPS[+80]PAHLPDDPKVAEK": "Q92615[S+80@601](LARP4B)",
"S[+80]IQDLTVTGTEPGQVSSR": "O43318[S+80@439](MAP3K7)",
"IHS[+80]PIIR": "O60885[S+80@1117](BRD4)",
"TFS[+80]LTEVR": "O95239[S+80@801](KIF4A)",
"SLVGS[+80]WLK": "Q6ICG6[S+80@362](KIAA0930)",
"S[+80]PPAPGLQPMR": "P15408[S+80@200](FOSL2)",
"LAS[+80]PELER": "P17535[S+80@100](JUND)",
"IGPLGLS[+80]PK": "P30050[S+80@38](RPL12)",
"TPS[+80]IQPSLLPHAAPFAK": "P35658[S+80@1023](NUP214)",
"HAS[+80]PILPITEFSDIPR": "P42167[S+80@306](TMPO)",
"LIPGPLS[+80]PVAR": "P48634[S+80@1219](PRRC2A)",
"LGM[+16]LS[+80]PEGTC[+57]K": "P49327[S+80@207][M+16@205][C+57@212](FASN)",
"LGMLS[+80]PEGTC[+57]K": "P49327[S+80@207][C+57@212](FASN)",
"ISNLS[+80]PEEEQGLWK": "Q5HYJ3[S+80@193](FAM76B)",
"VSMPDVELNLKS[+80]PK": "Q09666[S+80@3426](AHNAK)",
"S[+122]DNGELEDKPPAPPVR": "Q13177[S+122@2](PAK2)",
"KAYS[+80]FC[+57]GTVEYM[+16]APEVVNR": "Q15418[S+80@221][M+16@229][C+57@223](RPS6KA1)",
"KAYS[+80]FC[+57]GTVEYMAPEVVNR": "Q15418[S+80@221][C+57@223](RPS6KA1)",
"NDS[+80]WGSFDLR": "Q7Z417[S+80@652](NUFIP2)",
"LEVTEIVKPS[+80]PK": "Q7Z6E9[S+80@1179](RBBP6)",
"YGS[+80]PPQRDPNWNGER": "O15234[S+80@265](CASC3)",
"QDDS[+80]PPRPIIGPALPPGFIK": "Q8IXQ4[S+80@105](GPALPP1)",
"SFS[+80]ADNFIGIQR": "Q8N7R7[S+80@344](CCNYL1)",
"VLS[+80]PLIIK": "Q8NCN4[S+80@403](RNF169)",
"AGS[+80]PDVLR": "Q8NDX6[S+80@44](ZNF740)",
"LGPGRPLPTFPTSEC[+57]TS[+80]DVEPDTR": "Q8TDD1[S+80@75][C+57@73](DDX54)",
"LAAPSVSHVS[+80]PR": "Q8WXE1[S+80@224](ATRIP)",
"VDDDS[+80]LGEFPVTNSR": "Q92785[S+80@142](DPF2)",
"NEEPVRS[+80]PERR": "Q92922[S+80@310](SMARCC1)",
"LFIIRGS[+80]PQQIDHAK": "Q92945[S+80@480](KHSRP)",
"S[+80]IEVENDFLPVEK": "Q96B97[S+80@230](SH3KBP1)",
"TAPTLS[+80]PEHWK": "Q96JM3[S+80@405](CHAMP1)",
"VLS[+80]PTAAKPSPFEGK": "Q96QC0[S+80@313](PPP1R10)",
"SSDQPLTVPVS[+80]PK": "Q9ULW0[S+80@738](TPX2)",
"FYETKEESYS[+80]PSKDR": "Q96T23[S+80@473](RSF1)",
"SDS[+80]PENKYSDSTGHSK": "Q9BTA9[S+80@64](WAC)",
"S[+80]IPLSIK": "Q9C0C9[S+80@515](UBE2O)",
"RLS[+80]QSDEDVIR": "Q9H7D7[S+80@121](WDR26)",
"ATS[+80]PVKSTTSITDAK": "Q9NQW6[S+80@295](ANLN)",
"ALGS[+80]PTKQLLPC[+57]EMAC[+57]NEK": "Q9NR45[S+80@275][C+57@283][C+57@287](NANS)",
"YLLGDAPVS[+80]PSSQK": "Q9NYB0[S+80@203](TERF2IP)",
"ANS[+80]PEKPPEAGAAHKPR": "Q9UFC0[S+80@212](LRWD1)",
"SEVQQPVHPKPLS[+80]PDSR": "Q9UHB6[S+80@362](LIMA1)",
"ETPHS[+80]PGVEDAPIAK": "Q9UHB6[S+80@490](LIMA1)",
"SQS[+80]PHYFR": "Q9UKJ3[S+80@1035](GPATCH8)",
"DRS[+80]SPPPGYIPDELHQVAR": "Q9Y2U5[S+80@163](MAP3K2)",
"SPALKS[+80]PLQSVVVR": "Q9Y2W1[S+80@253](THRAP3)",
"AFGSGIDIKPGT[+80]PPIAGR": "Q9Y520[T+80@2673](PRRC2C)",
"SFS[+80]SQRPVDR": "Q9Y520[S+80@1544](PRRC2C)",
"VYT[+80]HEVVTLWYR": "P06493[T+80@161](CDK1)",
"SST[+80]PLPTISSSAENTR": "P42167[T+80@160](TMPO)",
"QIT[+80]MEELVR": "Q15149[T+80@4030](PLEC)",
"TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q9BXP5[T+80@544](SRRT)",
"ALPQT[+80]PRPR": "Q9UQ35[T+80@1492](SRRM2)",
"SMS[+80]VDLSHIPLKDPLLFK": "A0JNW5[S+80@935](UHRF1BP1L)",
"S[+80]PTGPSNSFLANMGGTVAHK": "Q96I25[S+80@222](RBM17)",
"S[+80]LTAHSLLPLAEK": "Q86VI3[S+80@1424](IQGAP3)",
"S[+80]FAGNLNTYKR": "Q01813[S+80@386](PFKP)",
"HRPS[+80]PPATPPPK": "Q8IYB3[S+80@402](SRRM1)",
"LHS[+80]APNLSDLHVVRPK": "O75385[S+80@556](ULK1)",
"TLGRRDS[+80]SDDWEIPDGQITVGQR": "P15056[S+80@446](BRAF)",
"A[+42]TTATM[+16]ATSGS[+80]AR": "P38919[S+80@12][M+16@7][A+42@2](EIF4A3)",
"A[+42]TTATMATSGS[+80]AR": "P38919[S+80@12][A+42@2](EIF4A3)",
"IHVSRS[+80]PTRPR": "Q499Z4[S+80@189](ZNF672)",
"RPHS[+80]PEKAFSSNPVVR": "Q53F19[S+80@500](NCBP3)",
"KPNIFYSGPAS[+80]PARPR": "Q6PL18[S+80@327](ATAD2)",
"TEFLDLDNSPLSPPS[+80]PR": "Q8NCF5[S+80@204](NFATC2IP)",
"QGSGRES[+80]PSLASR": "Q8WWM7[S+80@339](ATXN2L)",
# "TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q8WWM7[S+80@339](SRRM2)",
"LQS[+80]EPESIR": "P09496[S+80@105](CLTA)",
"RLIS[+80]PYKK": "O14929[S+80@361](HAT1)",
"LLEDS[+80]EESSEETVSR": "O60231[S+80@103](DHX16)",
"S[+80]PPAPGLQPM[+16]R": "P15408[S+80@200][M+16@209](FOSL2)",
"RRLS[+80]SLR": "P62753[S+80@235](RPS6)",
"RLS[+80]ESQLSFRR": "Q96PK6[S+80@618](RBM14)",
"RLS[+80]LPGLLSQVSPR": "Q96Q42[S+80@483](ALS2)",
"SPDKPGGS[+80]PSASRR": "Q9Y3T9[S+80@56](NOC2L)",
"HLPS[+80]PPTLDSIITEYLR": "Q9Y4B6[S+80@1000](DCAF1)",
"ST[+80]FHAGQLR": "Q7KZI7[T+80@596](MARK2)",
"S[+80]LTNSHLEKK": "Q9H2H9[S+80@52](SLC38A1)",
"LQTPNT[+80]FPKR": "Q14978[T+80@610](NOLC1)",
"QIT[+80]M[+16]EELVR": "Q15149[M+16@4031][T+80@4030](PLEC)",
"T[+56]K[+56]QTAR": "P68431[me0K@5](HIST1H3A)",
"T[+56]K[+70]QTAR": "P68431[meK@5](HIST1H3A)",
"T[+56]K[+28]QTAR": "P68431[me2K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-me3K": "P68431[me3K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-aK": "P68431[aK@5](HIST1H3A)",
"K[+112.1]STGGK[+56]APR": "P68431[me0K@10][a0K@15](HIST1H3A)",
"K[+126.1]STGGK[+56]APR": "P68431[meK@10](HIST1H3A)",
"K[+84.1]STGGK[+56]APR": "P68431[me2K@10](HIST1H3A)",
"K[+98.1]STGGK[+56]APR": "P68431[me3K@10](HIST1H3A)",
"K[+98]STGGK[+56]APR": "P68431[aK@10](HIST1H3A)",
"K[+112.1]STGGK[+42]APR": "P68431[aK@15](HIST1H3A)",
"K[+126.1]STGGK[+42]APR": "P68431[meK@10][aK@15](HIST1H3A)",
"K[+84.1]STGGK[+42]APR": "P68431[me2K@10][aK@15](HIST1H3A)",
"K[+98.1]STGGK[+42]APR": "P68431[me3K@10][aK@15](HIST1H3A)",
"K[+98]STGGK[+42]APR": "P68431[aK@10][aK@15](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+56]APR": "P68431[pS@11](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+56]APR": "P68431[meK@10][pS@11](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+56]APR": "P68431[me2K@10][pS@11](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+56]APR": "P68431[me3K@10][pS@11](HIST1H3A)",
"K[+98]S[+80]TGGK[+56]APR": "P68431[aK@10][pS@11](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+42]APR": "P68431[pS@11][aK@15](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+42]APR": "P68431[meK@10][pS@11][aK@15](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+42]APR": "P68431[me2K@10][pS@11][aK@15](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+42]APR": "P68431[me3K@10][pS@11][aK@15](HIST1H3A)",
"K[+98]S[+80]TGGK[+42]APR": "P68431[aK@10][pS@11][aK@15](HIST1H3A)",
"K[+112.1]QLATK[+56]AAR": "P68431[a0K@19][a0K@24](HIST1H3A)",
"K[+98]QLATK[+56]AAR": "P68431[aK@19](HIST1H3A)",
"K[+112.1]QLATK[+42]AAR": "P68431[aK@24](HIST1H3A)",
"K[+98]QLATK[+42]AAR": "P68431[aK@19][aK@24](HIST1H3A)",
"K[+226.1]QLATK[+56]AAR": "P68431[ubK@19][a0K@24](HIST1H3A)",
"K[+112.1]QLATK[+170.1]AAR": "P68431[ubK@24](HIST1H3A)",
"K[+112.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me0K@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+56]K[+56]PHR": "P68431[meK@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+70]K[+56]PHR": "P68431[meK@28][meK@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+28]K[+56]PHR": "P68431[meK@28][me2K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+42]K[+56]PHR": "P68431[meK@28][me3K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me2K@28][me0K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me2K@28][meK@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me2K@28][me2K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me2K@28][me3K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me3K@28][me0K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me3K@28][meK@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me3K@28][me2K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me3K@28][me3K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+56]K[+56]PHR": "P68431[aK@28][me0K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+70]K[+56]PHR": "P68431[aK@28][meK@37](HIST1H3A)",
"K[+98]SAPATGGVK[+28]K[+56]PHR": "P68431[aK@28][me2K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+42]K[+56]PHR": "P68431[aK@28][me3K@37](HIST1H3A)",
"K[+112.1]SAPSTGGVK[+56]K[+56]PHR": "P84243[me0K@28][me0K@37](H3F3A)",
"Y[+56]RPGTVALR": "P68431-NORM(HIST1H3A)",
"Y[+56]QK[+56]STELLIR": "P68431[me0K@57](HIST1H3A)",
"E[+56]IAQDFK[+56]TDLR": "P68431[me0K@80](HIST1H3A)",
"E[+56]IAQDFK[+70]TDLR": "P68431[meK@80](HIST1H3A)",
"E[+56]IAQDFK[+28]TDLR": "P68431[me2K@80](HIST1H3A)",
"K[+112.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me0K@28][meK@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me0K@28][me2K@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me0K@28][me3K@37](HIST1H3A)",
"Y[+56]QK[+42]STELLIR": "P68431[aK@57](HIST1H3A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[a0K@6][a0K@13][a0K@17](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[aK@6](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+56]R": "P62805[aK@13](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+56]R": "P62805[aK@6][aK@9](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+42]R": "P62805[aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@6][aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@9][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@6][aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+70]R": "P62805[meK@17](HIST1H4A)",
"K[+112.1]VLR": "P62805[me0K@21](HIST1H4A)",
"K[+126.1]VLR": "P62805[meK@21](HIST1H4A)",
"K[+84.1]VLR": "P62805[me2K@21](HIST1H4A)",
"K[+98.1]VLR": "P62805[me3K@21](HIST1H4A)",
"D[+56]AVTYTEHAK[+56]R": "P62805-NORM(HIST1H4A)",
"Y[+56]QK[+28]STELLIR": "P68431[me2K@57](HIST1H3A)"
}
P100_data = pd.read_csv('static/data/P100-all-plates-Level4.2018_08_07.processed.csv', sep=',', header=None)
print P100_data.shape
# print P100_data[0]
print P100_data[0][5]
print P100_data[12][5]
col_cell_line = []
col_pert_name = []
col_pert_dose = []
col_pert_time = []
col_pert_type = []
row_peptide = []
row_protein = []
row_gene = []
row_shorthand = []
for i in range(0, 96):
row_peptide.append('Peptide: ' + str(P100_data[6][29 + i]))
shorthand = petide2ptmAndGene[str(P100_data[6][29 + i])]
row_shorthand.append('PTM Proteins: ' + shorthand)
row_protein.append('Protein: ' + str(P100_data[11][29 + i]))
row_gene.append('Gene: ' + str(P100_data[2][29 + i]))
for column in range(21, P100_data.shape[1]):
col_cell_line.append('Cell Line: ' + str(P100_data[column][1]))
col_pert_dose.append('Dose: ' + str(P100_data[column][11]) + str(P100_data[column][12]))
col_pert_time.append('Time: ' + str(P100_data[column][15]))
col_pert_name.append('Perturnations: ' + str(P100_data[column][14]))
if "_sg01" not in str(P100_data[column][14]) and "_sg02" not in str(P100_data[column][14]):
col_pert_type.append('Type: Small Molecule')
else:
col_pert_type.append('Type: CRISPR')
arrays_rows2 = [np.array(row_shorthand),np.array(row_peptide),np.array(row_protein),np.array(row_gene)]
arrays_columns2 = [np.array(col_cell_line), np.array(col_pert_type), np.array(col_pert_name), np.array(col_pert_dose), np.array(col_pert_time)]
tuples_rows2 = list(zip(*arrays_rows2))
#print tuples_rows2
tuples_columns2 = list(zip(*arrays_columns2))
#print tuples_columns2
rows_labels2 = pd.MultiIndex.from_tuples(tuples_rows2)
columns_labels2 = pd.MultiIndex.from_tuples(tuples_columns2)
a2 = np.matrix(P100_data.iloc[29:29+96, 21:P100_data.shape[1]].fillna(0))
aa = a2.astype(np.float)
print a2
print a2.shape
print columns_labels2.shape
print rows_labels2.shape
# {'nop': row1, 'o0p': row2, 'zaz': row3, 'zax': row4, 'oof': row5, 'oye': row6}
# df = pd.DataFrame(a, index=rows_labels, columns=columns_labels)
df2 = pd.DataFrame(aa, index=rows_labels2, columns=columns_labels2)
#print df2
P100_all_json = loadFile.make_json_from_txt(df2)
json.dump(P100_all_json, open("static/data/P100_all_clustergram.json", 'w'))
return P100_all_json
@app.route("/api/clust/GCP/aggregatedd/depricated/")
def make_clustergram_GCP_aggregated_depricated():
petide2ptmAndGene = {
"IYQY[+80]IQSR": "Q13627[Y+80@321](DYRK1A)",
"TPKDS[+80]PGIPPSANAHQLFR": "P51812[S+80@369](RPS6KA3)",
"RNS[+80]SEASSGDFLDLK": "Q9UK76[S+80@87](JPT1)",
"LPLVPES[+80]PRR": "Q86WB0[S+80@321](ZC3HC1)",
"ANAS[+80]PQKPLDLK": "Q9Y618[S+80@956](NCOR2)",
"LENS[+80]PLGEALR": "Q9NX40[S+80@108](OCIAD1)",
"ANS[+80]FVGTAQYVSPELLTEK": "O15530[S+80@241](PDPK1)",
"TNPPTQKPPS[+80]PPMSGR": "Q8IZP0[S+80@183](ABI1)",
"SNS[+80]LPHSAVSNAGSK": "Q8TBZ3[S+80@434](WDR20)",
"VGS[+80]LDNVGHLPAGGAVK": "P27816[S+80@1073](MAP4)",
"AAPEAS[+80]SPPASPLQHLLPGK": "Q96TA1[S+80@691](FAM129B)",
"S[+122]DKPDM[+16]AEIEKFDK": "P62328[S+122@2][M+16@7](TMSB4X)",
"S[+122]DKPDMAEIEKFDK": "P62328[S+122@2](TMSB4X)",
"SLS[+80]LGDKEISR": "Q9UMZ2[S+80@1075](SYNRG)",
"DLVQPDKPAS[+80]PK": "Q6PJT7[S+80@515](ZC3H14)",
"SPS[+80]PAHLPDDPKVAEK": "Q92615[S+80@601](LARP4B)",
"S[+80]IQDLTVTGTEPGQVSSR": "O43318[S+80@439](MAP3K7)",
"IHS[+80]PIIR": "O60885[S+80@1117](BRD4)",
"TFS[+80]LTEVR": "O95239[S+80@801](KIF4A)",
"SLVGS[+80]WLK": "Q6ICG6[S+80@362](KIAA0930)",
"S[+80]PPAPGLQPMR": "P15408[S+80@200](FOSL2)",
"LAS[+80]PELER": "P17535[S+80@100](JUND)",
"IGPLGLS[+80]PK": "P30050[S+80@38](RPL12)",
"TPS[+80]IQPSLLPHAAPFAK": "P35658[S+80@1023](NUP214)",
"HAS[+80]PILPITEFSDIPR": "P42167[S+80@306](TMPO)",
"LIPGPLS[+80]PVAR": "P48634[S+80@1219](PRRC2A)",
"LGM[+16]LS[+80]PEGTC[+57]K": "P49327[S+80@207][M+16@205][C+57@212](FASN)",
"LGMLS[+80]PEGTC[+57]K": "P49327[S+80@207][C+57@212](FASN)",
"ISNLS[+80]PEEEQGLWK": "Q5HYJ3[S+80@193](FAM76B)",
"VSMPDVELNLKS[+80]PK": "Q09666[S+80@3426](AHNAK)",
"S[+122]DNGELEDKPPAPPVR": "Q13177[S+122@2](PAK2)",
"KAYS[+80]FC[+57]GTVEYM[+16]APEVVNR": "Q15418[S+80@221][M+16@229][C+57@223](RPS6KA1)",
"KAYS[+80]FC[+57]GTVEYMAPEVVNR": "Q15418[S+80@221][C+57@223](RPS6KA1)",
"NDS[+80]WGSFDLR": "Q7Z417[S+80@652](NUFIP2)",
"LEVTEIVKPS[+80]PK": "Q7Z6E9[S+80@1179](RBBP6)",
"YGS[+80]PPQRDPNWNGER": "O15234[S+80@265](CASC3)",
"QDDS[+80]PPRPIIGPALPPGFIK": "Q8IXQ4[S+80@105](GPALPP1)",
"SFS[+80]ADNFIGIQR": "Q8N7R7[S+80@344](CCNYL1)",
"VLS[+80]PLIIK": "Q8NCN4[S+80@403](RNF169)",
"AGS[+80]PDVLR": "Q8NDX6[S+80@44](ZNF740)",
"LGPGRPLPTFPTSEC[+57]TS[+80]DVEPDTR": "Q8TDD1[S+80@75][C+57@73](DDX54)",
"LAAPSVSHVS[+80]PR": "Q8WXE1[S+80@224](ATRIP)",
"VDDDS[+80]LGEFPVTNSR": "Q92785[S+80@142](DPF2)",
"NEEPVRS[+80]PERR": "Q92922[S+80@310](SMARCC1)",
"LFIIRGS[+80]PQQIDHAK": "Q92945[S+80@480](KHSRP)",
"S[+80]IEVENDFLPVEK": "Q96B97[S+80@230](SH3KBP1)",
"TAPTLS[+80]PEHWK": "Q96JM3[S+80@405](CHAMP1)",
"VLS[+80]PTAAKPSPFEGK": "Q96QC0[S+80@313](PPP1R10)",
"SSDQPLTVPVS[+80]PK": "Q9ULW0[S+80@738](TPX2)",
"FYETKEESYS[+80]PSKDR": "Q96T23[S+80@473](RSF1)",
"SDS[+80]PENKYSDSTGHSK": "Q9BTA9[S+80@64](WAC)",
"S[+80]IPLSIK": "Q9C0C9[S+80@515](UBE2O)",
"RLS[+80]QSDEDVIR": "Q9H7D7[S+80@121](WDR26)",
"ATS[+80]PVKSTTSITDAK": "Q9NQW6[S+80@295](ANLN)",
"ALGS[+80]PTKQLLPC[+57]EMAC[+57]NEK": "Q9NR45[S+80@275][C+57@283][C+57@287](NANS)",
"YLLGDAPVS[+80]PSSQK": "Q9NYB0[S+80@203](TERF2IP)",
"ANS[+80]PEKPPEAGAAHKPR": "Q9UFC0[S+80@212](LRWD1)",
"SEVQQPVHPKPLS[+80]PDSR": "Q9UHB6[S+80@362](LIMA1)",
"ETPHS[+80]PGVEDAPIAK": "Q9UHB6[S+80@490](LIMA1)",
"SQS[+80]PHYFR": "Q9UKJ3[S+80@1035](GPATCH8)",
"DRS[+80]SPPPGYIPDELHQVAR": "Q9Y2U5[S+80@163](MAP3K2)",
"SPALKS[+80]PLQSVVVR": "Q9Y2W1[S+80@253](THRAP3)",
"AFGSGIDIKPGT[+80]PPIAGR": "Q9Y520[T+80@2673](PRRC2C)",
"SFS[+80]SQRPVDR": "Q9Y520[S+80@1544](PRRC2C)",
"VYT[+80]HEVVTLWYR": "P06493[T+80@161](CDK1)",
"SST[+80]PLPTISSSAENTR": "P42167[T+80@160](TMPO)",
"QIT[+80]MEELVR": "Q15149[T+80@4030](PLEC)",
"TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q9BXP5[T+80@544](SRRT)",
"ALPQT[+80]PRPR": "Q9UQ35[T+80@1492](SRRM2)",
"SMS[+80]VDLSHIPLKDPLLFK": "A0JNW5[S+80@935](UHRF1BP1L)",
"S[+80]PTGPSNSFLANMGGTVAHK": "Q96I25[S+80@222](RBM17)",
"S[+80]LTAHSLLPLAEK": "Q86VI3[S+80@1424](IQGAP3)",
"S[+80]FAGNLNTYKR": "Q01813[S+80@386](PFKP)",
"HRPS[+80]PPATPPPK": "Q8IYB3[S+80@402](SRRM1)",
"LHS[+80]APNLSDLHVVRPK": "O75385[S+80@556](ULK1)",
"TLGRRDS[+80]SDDWEIPDGQITVGQR": "P15056[S+80@446](BRAF)",
"A[+42]TTATM[+16]ATSGS[+80]AR": "P38919[S+80@12][M+16@7][A+42@2](EIF4A3)",
"A[+42]TTATMATSGS[+80]AR": "P38919[S+80@12][A+42@2](EIF4A3)",
"IHVSRS[+80]PTRPR": "Q499Z4[S+80@189](ZNF672)",
"RPHS[+80]PEKAFSSNPVVR": "Q53F19[S+80@500](NCBP3)",
"KPNIFYSGPAS[+80]PARPR": "Q6PL18[S+80@327](ATAD2)",
"TEFLDLDNSPLSPPS[+80]PR": "Q8NCF5[S+80@204](NFATC2IP)",
"QGSGRES[+80]PSLASR": "Q8WWM7[S+80@339](ATXN2L)",
# "TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q8WWM7[S+80@339](SRRM2)",
"LQS[+80]EPESIR": "P09496[S+80@105](CLTA)",
"RLIS[+80]PYKK": "O14929[S+80@361](HAT1)",
"LLEDS[+80]EESSEETVSR": "O60231[S+80@103](DHX16)",
"S[+80]PPAPGLQPM[+16]R": "P15408[S+80@200][M+16@209](FOSL2)",
"RRLS[+80]SLR": "P62753[S+80@235](RPS6)",
"RLS[+80]ESQLSFRR": "Q96PK6[S+80@618](RBM14)",
"RLS[+80]LPGLLSQVSPR": "Q96Q42[S+80@483](ALS2)",
"SPDKPGGS[+80]PSASRR": "Q9Y3T9[S+80@56](NOC2L)",
"HLPS[+80]PPTLDSIITEYLR": "Q9Y4B6[S+80@1000](DCAF1)",
"ST[+80]FHAGQLR": "Q7KZI7[T+80@596](MARK2)",
"S[+80]LTNSHLEKK": "Q9H2H9[S+80@52](SLC38A1)",
"LQTPNT[+80]FPKR": "Q14978[T+80@610](NOLC1)",
"QIT[+80]M[+16]EELVR": "Q15149[M+16@4031][T+80@4030](PLEC)",
"T[+56]K[+56]QTAR": "P68431[me0K@5](HIST1H3A)",
"T[+56]K[+70]QTAR": "P68431[meK@5](HIST1H3A)",
"T[+56]K[+28]QTAR": "P68431[me2K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-me3K": "P68431[me3K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-aK": "P68431[aK@5](HIST1H3A)",
"K[+112.1]STGGK[+56]APR": "P68431[me0K@10][a0K@15](HIST1H3A)",
"K[+126.1]STGGK[+56]APR": "P68431[meK@10](HIST1H3A)",
"K[+84.1]STGGK[+56]APR": "P68431[me2K@10](HIST1H3A)",
"K[+98.1]STGGK[+56]APR": "P68431[me3K@10](HIST1H3A)",
"K[+98]STGGK[+56]APR": "P68431[aK@10](HIST1H3A)",
"K[+112.1]STGGK[+42]APR": "P68431[aK@15](HIST1H3A)",
"K[+126.1]STGGK[+42]APR": "P68431[meK@10][aK@15](HIST1H3A)",
"K[+84.1]STGGK[+42]APR": "P68431[me2K@10][aK@15](HIST1H3A)",
"K[+98.1]STGGK[+42]APR": "P68431[me3K@10][aK@15](HIST1H3A)",
"K[+98]STGGK[+42]APR": "P68431[aK@10][aK@15](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+56]APR": "P68431[pS@11](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+56]APR": "P68431[meK@10][pS@11](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+56]APR": "P68431[me2K@10][pS@11](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+56]APR": "P68431[me3K@10][pS@11](HIST1H3A)",
"K[+98]S[+80]TGGK[+56]APR": "P68431[aK@10][pS@11](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+42]APR": "P68431[pS@11][aK@15](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+42]APR": "P68431[meK@10][pS@11][aK@15](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+42]APR": "P68431[me2K@10][pS@11][aK@15](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+42]APR": "P68431[me3K@10][pS@11][aK@15](HIST1H3A)",
"K[+98]S[+80]TGGK[+42]APR": "P68431[aK@10][pS@11][aK@15](HIST1H3A)",
"K[+112.1]QLATK[+56]AAR": "P68431[a0K@19][a0K@24](HIST1H3A)",
"K[+98]QLATK[+56]AAR": "P68431[aK@19](HIST1H3A)",
"K[+112.1]QLATK[+42]AAR": "P68431[aK@24](HIST1H3A)",
"K[+98]QLATK[+42]AAR": "P68431[aK@19][aK@24](HIST1H3A)",
"K[+226.1]QLATK[+56]AAR": "P68431[ubK@19][a0K@24](HIST1H3A)",
"K[+112.1]QLATK[+170.1]AAR": "P68431[ubK@24](HIST1H3A)",
"K[+112.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me0K@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+56]K[+56]PHR": "P68431[meK@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+70]K[+56]PHR": "P68431[meK@28][meK@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+28]K[+56]PHR": "P68431[meK@28][me2K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+42]K[+56]PHR": "P68431[meK@28][me3K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me2K@28][me0K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me2K@28][meK@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me2K@28][me2K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me2K@28][me3K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me3K@28][me0K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me3K@28][meK@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me3K@28][me2K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me3K@28][me3K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+56]K[+56]PHR": "P68431[aK@28][me0K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+70]K[+56]PHR": "P68431[aK@28][meK@37](HIST1H3A)",
"K[+98]SAPATGGVK[+28]K[+56]PHR": "P68431[aK@28][me2K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+42]K[+56]PHR": "P68431[aK@28][me3K@37](HIST1H3A)",
"K[+112.1]SAPSTGGVK[+56]K[+56]PHR": "P84243[me0K@28][me0K@37](H3F3A)",
"Y[+56]RPGTVALR": "P68431-NORM(HIST1H3A)",
"Y[+56]QK[+56]STELLIR": "P68431[me0K@57](HIST1H3A)",
"E[+56]IAQDFK[+56]TDLR": "P68431[me0K@80](HIST1H3A)",
"E[+56]IAQDFK[+70]TDLR": "P68431[meK@80](HIST1H3A)",
"E[+56]IAQDFK[+28]TDLR": "P68431[me2K@80](HIST1H3A)",
"K[+112.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me0K@28][meK@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me0K@28][me2K@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me0K@28][me3K@37](HIST1H3A)",
"Y[+56]QK[+42]STELLIR": "P68431[aK@57](HIST1H3A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[a0K@6][a0K@13][a0K@17](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[aK@6](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+56]R": "P62805[aK@13](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+56]R": "P62805[aK@6][aK@9](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+42]R": "P62805[aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@6][aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@9][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@6][aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+70]R": "P62805[meK@17](HIST1H4A)",
"K[+112.1]VLR": "P62805[me0K@21](HIST1H4A)",
"K[+126.1]VLR": "P62805[meK@21](HIST1H4A)",
"K[+84.1]VLR": "P62805[me2K@21](HIST1H4A)",
"K[+98.1]VLR": "P62805[me3K@21](HIST1H4A)",
"D[+56]AVTYTEHAK[+56]R": "P62805-NORM(HIST1H4A)",
"Y[+56]QK[+28]STELLIR": "P68431[me2K@57](HIST1H3A)"
}
GCP_data = pd.read_csv('static/data/GCP-all-plates-Level4.2018_08_07.processed.csv', sep=',', header=None)
GCP_unique_complete = {}
for column in range(25, GCP_data.shape[1]):
# print (column)
# identifier = str(GCP_data[column][10]) +"++"+str(GCP_data[column][3]) +"++"+ str(GCP_data[column][7]) +"++"+ str(GCP_data[column][11])
GCP_identifier_complete = str(GCP_data[column][1]) + "++" + str(GCP_data[column][5]) + "++" + str(
GCP_data[column][7]) + "++" + str(GCP_data[column][8]) + "++" + str(GCP_data[column][9]) + "++" + \
str(GCP_data[column][11]) + "++" + str(GCP_data[column][12]) + "++" + \
str(GCP_data[column][13]) + "++" + str(GCP_data[column][14]) + "++" \
+ str(GCP_data[column][15]) + "++" + \
str(GCP_data[column][16]) + "++" + str(GCP_data[column][17]) + "++" + \
str(GCP_data[column][18]) + "++" + str(GCP_data[column][19]) + "++" + \
str(GCP_data[column][20]) + "++" + str(GCP_data[column][21]) + "++" + \
str(GCP_data[column][22]) + "++" + str(GCP_data[column][23]) + "++" + \
str(GCP_data[column][24]) + "++" + str(GCP_data[column][25]) + "++" + \
str(GCP_data[column][26]) + "++" + str(GCP_data[column][27])
if GCP_identifier_complete not in GCP_unique_complete.keys():
# print identifier_complete
GCP_unique_complete[GCP_identifier_complete] = []
GCP_unique_complete.get(GCP_identifier_complete).append(column)
else:
GCP_unique_complete.get(GCP_identifier_complete).append(column)
iterator = 0
for key in GCP_unique_complete:
val = GCP_unique_complete.get(key)
value = list(val)
# print key
for item in value:
iterator += 1
# print item
# print "------------------------"
print iterator
#print unique_complete_modified
total = 0
total_complete = 0
print "size of unique_complete keys"
print len(GCP_unique_complete.keys())
print "size of unique_complete"
print len(GCP_unique_complete)
unique_sum = {}
# unique_sum_modified = {}
unique_pvalue = {}
col_cell_line = []
col_pert_name = []
col_pert_dose = []
col_pert_time = []
col_pert_type = []
my_data_con = []
keyIter = 0
first_loop = True
for key in GCP_unique_complete:
initial = [0.0]*79
initial2 = [0.0] * 79
initial_not_na = [0.0] * 79
unique_sum[key] = initial
unique_pvalue[key] = initial2
val = GCP_unique_complete.get(key)
key_splitted = key.split("++")
print key_splitted
col_cell_line.append('Cell Line: ' + key_splitted[0])
col_pert_dose.append('Dose: ' + key_splitted[5] + key_splitted[6])
col_pert_time.append('Time: ' + key_splitted[9] + key_splitted[10])
col_pert_name.append('Perturnations: ' + key_splitted[8])
if "_sg01" not in key_splitted[8] and "_sg02" not in key_splitted[8]:
col_pert_type.append('Type: Small Molecule')
else:
col_pert_type.append('Type: CRISPR')
item = list(val)
# if len(item) == 1:
# print '111111 %d =========== %s %s' % (keyIter, key, val)
keyIter += 1
value_list = 0
for item_iter in range(0, 79):
aux_list = []
for col in item:
aux_list.append(float(GCP_data[col][item_iter + 28]))
if GCP_data[col][item_iter + 28] != "NA":
unique_sum.get(key)[item_iter] += float(GCP_data[col][item_iter + 28])
initial_not_na[item_iter] += 1
if initial_not_na[item_iter] > 0:
unique_sum.get(key)[item_iter] /= initial_not_na[item_iter]
meanValue = np.mean(aux_list)
average = sum(aux_list) / len(aux_list)
# print "++++++++++++++++++"
# print average
# print meanValue
# print unique_sum.get(key)[item_iter]
if len(aux_list) > 1:
variance2 = sum((average - value) ** 2 for value in aux_list) / (len(aux_list)-1)
print "end of loop"
x1 = np.array(unique_sum.get(key))
print "end of loop1"
x2 = x1[:, np.newaxis]
print "end of loop2"
my_data_final = np.asarray(x2)
print "end of loop3"
if first_loop:
my_data_con = my_data_final
first_loop = False
else:
my_data_con = np.hstack((my_data_con, my_data_final))
print "end of loop4"
print "======================"
print "======================"
print "======================"
print my_data_con.shape
row_peptide = []
row_protein = []
row_gene = []
row_shorthand = []
for i in range(0, 79):
print str(GCP_data[4][28 + i])
peptide = str(GCP_data[4][28 + i])
if(peptide == 'T[+56]K[+42]QTAR'):
print str(GCP_data[2][28 + i])
if(str(GCP_data[2][28 + i]) == 'BI10006'):
peptide = "T[+56]K[+42]QTAR-me3K"
else:
peptide = "T[+56]K[+42]QTAR-aK"
print peptide
row_peptide.append('Peptide: ' + peptide)
shorthand = petide2ptmAndGene[peptide]
print shorthand
row_shorthand.append('PTM Proteins: ' + shorthand)
row_protein.append('Protein: ' + str(GCP_data[9][28 + i]))
row_gene.append('Gene: ' + str(GCP_data[6][28 + i]))
arrays_rows2 = [np.array(row_shorthand),np.array(row_peptide),np.array(row_protein),np.array(row_gene)]
arrays_columns2 = [np.array(col_pert_name), np.array(col_pert_time), np.array(col_pert_dose), np.array(col_pert_type),np.array(col_cell_line)]
tuples_rows2 = list(zip(*arrays_rows2))
#print tuples_rows2
tuples_columns2 = list(zip(*arrays_columns2))
#print tuples_columns2
rows_labels2 = pd.MultiIndex.from_tuples(tuples_rows2)
columns_labels2 = pd.MultiIndex.from_tuples(tuples_columns2)
#my_data_con = my_data_con.fillna(0)
print "after na to zero"
a2 = np.nan_to_num(my_data_con)
#a2 = my_data_con
aa = a2.astype(np.float)
print a2
print a2.shape
print columns_labels2.shape
print rows_labels2.shape
# {'nop': row1, 'o0p': row2, 'zaz': row3, 'zax': row4, 'oof': row5, 'oye': row6}
#df = pd.DataFrame(a, index=rows_labels, columns=columns_labels)
df2 = pd.DataFrame(aa, index=rows_labels2, columns=columns_labels2)
#print df2
GCP_all_json = loadFile.make_json_from_txt(df2)
json.dump(GCP_all_json, open("static/data/GCP_aggregated_clustergram.json", 'w'))
return GCP_all_json
@app.route("/api/test/<vars>")
def doSomething(vars):
for var in vars.split(","):
print var
@app.route("/api/clust/GCP/aggregated/")
def make_clustergram_GCP_aggregated():
petide2ptmAndGene = {
"IYQY[+80]IQSR": "Q13627[Y+80@321](DYRK1A)",
"TPKDS[+80]PGIPPSANAHQLFR": "P51812[S+80@369](RPS6KA3)",
"RNS[+80]SEASSGDFLDLK": "Q9UK76[S+80@87](JPT1)",
"LPLVPES[+80]PRR": "Q86WB0[S+80@321](ZC3HC1)",
"ANAS[+80]PQKPLDLK": "Q9Y618[S+80@956](NCOR2)",
"LENS[+80]PLGEALR": "Q9NX40[S+80@108](OCIAD1)",
"ANS[+80]FVGTAQYVSPELLTEK": "O15530[S+80@241](PDPK1)",
"TNPPTQKPPS[+80]PPMSGR": "Q8IZP0[S+80@183](ABI1)",
"SNS[+80]LPHSAVSNAGSK": "Q8TBZ3[S+80@434](WDR20)",
"VGS[+80]LDNVGHLPAGGAVK": "P27816[S+80@1073](MAP4)",
"AAPEAS[+80]SPPASPLQHLLPGK": "Q96TA1[S+80@691](FAM129B)",
"S[+122]DKPDM[+16]AEIEKFDK": "P62328[S+122@2][M+16@7](TMSB4X)",
"S[+122]DKPDMAEIEKFDK": "P62328[S+122@2](TMSB4X)",
"SLS[+80]LGDKEISR": "Q9UMZ2[S+80@1075](SYNRG)",
"DLVQPDKPAS[+80]PK": "Q6PJT7[S+80@515](ZC3H14)",
"SPS[+80]PAHLPDDPKVAEK": "Q92615[S+80@601](LARP4B)",
"S[+80]IQDLTVTGTEPGQVSSR": "O43318[S+80@439](MAP3K7)",
"IHS[+80]PIIR": "O60885[S+80@1117](BRD4)",
"TFS[+80]LTEVR": "O95239[S+80@801](KIF4A)",
"SLVGS[+80]WLK": "Q6ICG6[S+80@362](KIAA0930)",
"S[+80]PPAPGLQPMR": "P15408[S+80@200](FOSL2)",
"LAS[+80]PELER": "P17535[S+80@100](JUND)",
"IGPLGLS[+80]PK": "P30050[S+80@38](RPL12)",
"TPS[+80]IQPSLLPHAAPFAK": "P35658[S+80@1023](NUP214)",
"HAS[+80]PILPITEFSDIPR": "P42167[S+80@306](TMPO)",
"LIPGPLS[+80]PVAR": "P48634[S+80@1219](PRRC2A)",
"LGM[+16]LS[+80]PEGTC[+57]K": "P49327[S+80@207][M+16@205][C+57@212](FASN)",
"LGMLS[+80]PEGTC[+57]K": "P49327[S+80@207][C+57@212](FASN)",
"ISNLS[+80]PEEEQGLWK": "Q5HYJ3[S+80@193](FAM76B)",
"VSMPDVELNLKS[+80]PK": "Q09666[S+80@3426](AHNAK)",
"S[+122]DNGELEDKPPAPPVR": "Q13177[S+122@2](PAK2)",
"KAYS[+80]FC[+57]GTVEYM[+16]APEVVNR": "Q15418[S+80@221][M+16@229][C+57@223](RPS6KA1)",
"KAYS[+80]FC[+57]GTVEYMAPEVVNR": "Q15418[S+80@221][C+57@223](RPS6KA1)",
"NDS[+80]WGSFDLR": "Q7Z417[S+80@652](NUFIP2)",
"LEVTEIVKPS[+80]PK": "Q7Z6E9[S+80@1179](RBBP6)",
"YGS[+80]PPQRDPNWNGER": "O15234[S+80@265](CASC3)",
"QDDS[+80]PPRPIIGPALPPGFIK": "Q8IXQ4[S+80@105](GPALPP1)",
"SFS[+80]ADNFIGIQR": "Q8N7R7[S+80@344](CCNYL1)",
"VLS[+80]PLIIK": "Q8NCN4[S+80@403](RNF169)",
"AGS[+80]PDVLR": "Q8NDX6[S+80@44](ZNF740)",
"LGPGRPLPTFPTSEC[+57]TS[+80]DVEPDTR": "Q8TDD1[S+80@75][C+57@73](DDX54)",
"LAAPSVSHVS[+80]PR": "Q8WXE1[S+80@224](ATRIP)",
"VDDDS[+80]LGEFPVTNSR": "Q92785[S+80@142](DPF2)",
"NEEPVRS[+80]PERR": "Q92922[S+80@310](SMARCC1)",
"LFIIRGS[+80]PQQIDHAK": "Q92945[S+80@480](KHSRP)",
"S[+80]IEVENDFLPVEK": "Q96B97[S+80@230](SH3KBP1)",
"TAPTLS[+80]PEHWK": "Q96JM3[S+80@405](CHAMP1)",
"VLS[+80]PTAAKPSPFEGK": "Q96QC0[S+80@313](PPP1R10)",
"SSDQPLTVPVS[+80]PK": "Q9ULW0[S+80@738](TPX2)",
"FYETKEESYS[+80]PSKDR": "Q96T23[S+80@473](RSF1)",
"SDS[+80]PENKYSDSTGHSK": "Q9BTA9[S+80@64](WAC)",
"S[+80]IPLSIK": "Q9C0C9[S+80@515](UBE2O)",
"RLS[+80]QSDEDVIR": "Q9H7D7[S+80@121](WDR26)",
"ATS[+80]PVKSTTSITDAK": "Q9NQW6[S+80@295](ANLN)",
"ALGS[+80]PTKQLLPC[+57]EMAC[+57]NEK": "Q9NR45[S+80@275][C+57@283][C+57@287](NANS)",
"YLLGDAPVS[+80]PSSQK": "Q9NYB0[S+80@203](TERF2IP)",
"ANS[+80]PEKPPEAGAAHKPR": "Q9UFC0[S+80@212](LRWD1)",
"SEVQQPVHPKPLS[+80]PDSR": "Q9UHB6[S+80@362](LIMA1)",
"ETPHS[+80]PGVEDAPIAK": "Q9UHB6[S+80@490](LIMA1)",
"SQS[+80]PHYFR": "Q9UKJ3[S+80@1035](GPATCH8)",
"DRS[+80]SPPPGYIPDELHQVAR": "Q9Y2U5[S+80@163](MAP3K2)",
"SPALKS[+80]PLQSVVVR": "Q9Y2W1[S+80@253](THRAP3)",
"AFGSGIDIKPGT[+80]PPIAGR": "Q9Y520[T+80@2673](PRRC2C)",
"SFS[+80]SQRPVDR": "Q9Y520[S+80@1544](PRRC2C)",
"VYT[+80]HEVVTLWYR": "P06493[T+80@161](CDK1)",
"SST[+80]PLPTISSSAENTR": "P42167[T+80@160](TMPO)",
"QIT[+80]MEELVR": "Q15149[T+80@4030](PLEC)",
"TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q9BXP5[T+80@544](SRRT)",
"ALPQT[+80]PRPR": "Q9UQ35[T+80@1492](SRRM2)",
"SMS[+80]VDLSHIPLKDPLLFK": "A0JNW5[S+80@935](UHRF1BP1L)",
"S[+80]PTGPSNSFLANMGGTVAHK": "Q96I25[S+80@222](RBM17)",
"S[+80]LTAHSLLPLAEK": "Q86VI3[S+80@1424](IQGAP3)",
"S[+80]FAGNLNTYKR": "Q01813[S+80@386](PFKP)",
"HRPS[+80]PPATPPPK": "Q8IYB3[S+80@402](SRRM1)",
"LHS[+80]APNLSDLHVVRPK": "O75385[S+80@556](ULK1)",
"TLGRRDS[+80]SDDWEIPDGQITVGQR": "P15056[S+80@446](BRAF)",
"A[+42]TTATM[+16]ATSGS[+80]AR": "P38919[S+80@12][M+16@7][A+42@2](EIF4A3)",
"A[+42]TTATMATSGS[+80]AR": "P38919[S+80@12][A+42@2](EIF4A3)",
"IHVSRS[+80]PTRPR": "Q499Z4[S+80@189](ZNF672)",
"RPHS[+80]PEKAFSSNPVVR": "Q53F19[S+80@500](NCBP3)",
"KPNIFYSGPAS[+80]PARPR": "Q6PL18[S+80@327](ATAD2)",
"TEFLDLDNSPLSPPS[+80]PR": "Q8NCF5[S+80@204](NFATC2IP)",
"QGSGRES[+80]PSLASR": "Q8WWM7[S+80@339](ATXN2L)",
# "TQLWASEPGT[+80]PPLPTSLPSQNPILK": "Q8WWM7[S+80@339](SRRM2)",
"LQS[+80]EPESIR": "P09496[S+80@105](CLTA)",
"RLIS[+80]PYKK": "O14929[S+80@361](HAT1)",
"LLEDS[+80]EESSEETVSR": "O60231[S+80@103](DHX16)",
"S[+80]PPAPGLQPM[+16]R": "P15408[S+80@200][M+16@209](FOSL2)",
"RRLS[+80]SLR": "P62753[S+80@235](RPS6)",
"RLS[+80]ESQLSFRR": "Q96PK6[S+80@618](RBM14)",
"RLS[+80]LPGLLSQVSPR": "Q96Q42[S+80@483](ALS2)",
"SPDKPGGS[+80]PSASRR": "Q9Y3T9[S+80@56](NOC2L)",
"HLPS[+80]PPTLDSIITEYLR": "Q9Y4B6[S+80@1000](DCAF1)",
"ST[+80]FHAGQLR": "Q7KZI7[T+80@596](MARK2)",
"S[+80]LTNSHLEKK": "Q9H2H9[S+80@52](SLC38A1)",
"LQTPNT[+80]FPKR": "Q14978[T+80@610](NOLC1)",
"QIT[+80]M[+16]EELVR": "Q15149[M+16@4031][T+80@4030](PLEC)",
"T[+56]K[+56]QTAR": "P68431[me0K@5](HIST1H3A)",
"T[+56]K[+70]QTAR": "P68431[meK@5](HIST1H3A)",
"T[+56]K[+28]QTAR": "P68431[me2K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-me3K": "P68431[me3K@5](HIST1H3A)",
"T[+56]K[+42]QTAR-aK": "P68431[aK@5](HIST1H3A)",
"K[+112.1]STGGK[+56]APR": "P68431[me0K@10][a0K@15](HIST1H3A)",
"K[+126.1]STGGK[+56]APR": "P68431[meK@10](HIST1H3A)",
"K[+84.1]STGGK[+56]APR": "P68431[me2K@10](HIST1H3A)",
"K[+98.1]STGGK[+56]APR": "P68431[me3K@10](HIST1H3A)",
"K[+98]STGGK[+56]APR": "P68431[aK@10](HIST1H3A)",
"K[+112.1]STGGK[+42]APR": "P68431[aK@15](HIST1H3A)",
"K[+126.1]STGGK[+42]APR": "P68431[meK@10][aK@15](HIST1H3A)",
"K[+84.1]STGGK[+42]APR": "P68431[me2K@10][aK@15](HIST1H3A)",
"K[+98.1]STGGK[+42]APR": "P68431[me3K@10][aK@15](HIST1H3A)",
"K[+98]STGGK[+42]APR": "P68431[aK@10][aK@15](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+56]APR": "P68431[pS@11](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+56]APR": "P68431[meK@10][pS@11](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+56]APR": "P68431[me2K@10][pS@11](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+56]APR": "P68431[me3K@10][pS@11](HIST1H3A)",
"K[+98]S[+80]TGGK[+56]APR": "P68431[aK@10][pS@11](HIST1H3A)",
"K[+112.1]S[+80]TGGK[+42]APR": "P68431[pS@11][aK@15](HIST1H3A)",
"K[+126.1]S[+80]TGGK[+42]APR": "P68431[meK@10][pS@11][aK@15](HIST1H3A)",
"K[+84.1]S[+80]TGGK[+42]APR": "P68431[me2K@10][pS@11][aK@15](HIST1H3A)",
"K[+98.1]S[+80]TGGK[+42]APR": "P68431[me3K@10][pS@11][aK@15](HIST1H3A)",
"K[+98]S[+80]TGGK[+42]APR": "P68431[aK@10][pS@11][aK@15](HIST1H3A)",
"K[+112.1]QLATK[+56]AAR": "P68431[a0K@19][a0K@24](HIST1H3A)",
"K[+98]QLATK[+56]AAR": "P68431[aK@19](HIST1H3A)",
"K[+112.1]QLATK[+42]AAR": "P68431[aK@24](HIST1H3A)",
"K[+98]QLATK[+42]AAR": "P68431[aK@19][aK@24](HIST1H3A)",
"K[+226.1]QLATK[+56]AAR": "P68431[ubK@19][a0K@24](HIST1H3A)",
"K[+112.1]QLATK[+170.1]AAR": "P68431[ubK@24](HIST1H3A)",
"K[+112.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me0K@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+56]K[+56]PHR": "P68431[meK@28][me0K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+70]K[+56]PHR": "P68431[meK@28][meK@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+28]K[+56]PHR": "P68431[meK@28][me2K@37](HIST1H3A)",
"K[+126.1]SAPATGGVK[+42]K[+56]PHR": "P68431[meK@28][me3K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me2K@28][me0K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me2K@28][meK@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me2K@28][me2K@37](HIST1H3A)",
"K[+84.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me2K@28][me3K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+56]K[+56]PHR": "P68431[me3K@28][me0K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me3K@28][meK@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me3K@28][me2K@37](HIST1H3A)",
"K[+98.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me3K@28][me3K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+56]K[+56]PHR": "P68431[aK@28][me0K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+70]K[+56]PHR": "P68431[aK@28][meK@37](HIST1H3A)",
"K[+98]SAPATGGVK[+28]K[+56]PHR": "P68431[aK@28][me2K@37](HIST1H3A)",
"K[+98]SAPATGGVK[+42]K[+56]PHR": "P68431[aK@28][me3K@37](HIST1H3A)",
"K[+112.1]SAPSTGGVK[+56]K[+56]PHR": "P84243[me0K@28][me0K@37](H3F3A)",
"Y[+56]RPGTVALR": "P68431-NORM(HIST1H3A)",
"Y[+56]QK[+56]STELLIR": "P68431[me0K@57](HIST1H3A)",
"E[+56]IAQDFK[+56]TDLR": "P68431[me0K@80](HIST1H3A)",
"E[+56]IAQDFK[+70]TDLR": "P68431[meK@80](HIST1H3A)",
"E[+56]IAQDFK[+28]TDLR": "P68431[me2K@80](HIST1H3A)",
"K[+112.1]SAPATGGVK[+70]K[+56]PHR": "P68431[me0K@28][meK@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+28]K[+56]PHR": "P68431[me0K@28][me2K@37](HIST1H3A)",
"K[+112.1]SAPATGGVK[+42]K[+56]PHR": "P68431[me0K@28][me3K@37](HIST1H3A)",
"Y[+56]QK[+42]STELLIR": "P68431[aK@57](HIST1H3A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[a0K@6][a0K@13][a0K@17](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+56]R": "P62805[aK@6](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+56]R": "P62805[aK@13](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+56]R": "P62805[aK@6][aK@9](HIST1H4A)",
"G[+56]K[+42]GGK[+56]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+42]GGAK[+42]R": "P62805[aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+56]R": "P62805[aK@6][aK@9][aK@13](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+56]GGAK[+42]R": "P62805[aK@6][aK@9][aK@17](HIST1H4A)",
"G[+56]K[+42]GGK[+42]GLGK[+42]GGAK[+42]R": "P62805[aK@6][aK@9][aK@13][aK@17](HIST1H4A)",
"G[+56]K[+56]GGK[+56]GLGK[+56]GGAK[+70]R": "P62805[meK@17](HIST1H4A)",
"K[+112.1]VLR": "P62805[me0K@21](HIST1H4A)",
"K[+126.1]VLR": "P62805[meK@21](HIST1H4A)",
"K[+84.1]VLR": "P62805[me2K@21](HIST1H4A)",
"K[+98.1]VLR": "P62805[me3K@21](HIST1H4A)",
"D[+56]AVTYTEHAK[+56]R": "P62805-NORM(HIST1H4A)",
"Y[+56]QK[+28]STELLIR": "P68431[me2K@57](HIST1H3A)"
}
GCP_data = pd.read_csv('static/data/GCP-all-plates-Level4.2018_08_07.processed.csv', sep=',', header=None)
GCP_unique_complete = {}
print GCP_data.shape
print "inside /api/clust/GCP/aggregated/"
for column in range(25, GCP_data.shape[1]):
print (column)
# identifier = str(GCP_data[column][10]) +"++"+str(GCP_data[column][3]) +"++"+ str(GCP_data[column][7]) +"++"+ str(GCP_data[column][11])
GCP_identifier_complete = str(GCP_data[column][1]) + "++" + str(GCP_data[column][5]) \
+ "++" + str(GCP_data[column][7]) + "++" + str(GCP_data[column][8]) + "++" + \
str(GCP_data[column][11]) + "++" + str(GCP_data[column][12]) + "++" + \
str(GCP_data[column][13]) + "++" + str(GCP_data[column][14]) + "++" \
+ str(GCP_data[column][15]) + "++" + \
str(GCP_data[column][16]) + "++" + str(GCP_data[column][17]) + "++" + \
str(GCP_data[column][18]) + "++" + str(GCP_data[column][19]) + "++" + \
str(GCP_data[column][20]) + "++" + str(GCP_data[column][21]) + "++" + \
str(GCP_data[column][22]) + "++" + str(GCP_data[column][23]) + "++" + \
str(GCP_data[column][24]) + "++" + str(GCP_data[column][25]) + "++" + \
str(GCP_data[column][26]) + "++" + str(GCP_data[column][27])
if GCP_identifier_complete not in GCP_unique_complete.keys():
# print identifier_complete
GCP_unique_complete[GCP_identifier_complete] = []
GCP_unique_complete.get(GCP_identifier_complete).append(column)
else:
GCP_unique_complete.get(GCP_identifier_complete).append(column)
iterator = 0
for key in GCP_unique_complete:
val = GCP_unique_complete.get(key)
value = list(val)
# print key
for item in value:
iterator += 1
# print item
# print "------------------------"
print iterator
# print unique_complete_modified
total = 0
total_complete = 0
print "size of unique_complete keys"
print len(GCP_unique_complete.keys())
print "size of unique_complete"
print len(GCP_unique_complete)
unique_sum = {}
# unique_sum_modified = {}
unique_pvalue = {}
col_cell_line = []
col_pert_name = []
col_pert_dose = []
col_pert_time = []
col_pert_type = []
col_pert_signature = []
my_data_con = []
keyIter = 0
first_loop = True
# {"pertAnnotation": [{"LINCS_UNIQUE": "LINCSTP_0094", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "A375",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P1", "lsmId": "LSM-42750"},
# {"LINCS_UNIQUE": "LINCSTP_0236", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "MCF7",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P2", "lsmId": "LSM-42750"},
# {"LINCS_UNIQUE": "LINCSTP_0259", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "NPC",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P3", "lsmId": "LSM-42750"},
# {"LINCS_UNIQUE": "LINCSTP_0116", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "A549",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P4", "lsmId": "LSM-42750"},
# {"LINCS_UNIQUE": "LINCSTP_0275", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "PC3",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P5", "lsmId": "LSM-42750"},
# {"LINCS_UNIQUE": "LINCSTP_0441", "pertVehicle": "DMSO", "pertName": "CPI-169", "cellId": "YAPC",
# "pubchemCid": "71712226", "pertId": "BRD-A48881734", "pertType": "trt_cp", "pertTime": "3",
# "pertDose": "1", "id": "P6", "lsmId": "LSM-42750"}]}, "LINCSTP_0002":
pertAnnotation = {}
# this is for slicing the clustergrammer
pertAnnotation_for_slicing = {}
pertJson = {}
unique_iterator = 10000
keylist = GCP_unique_complete.keys()
keylist.sort()
for key in keylist:
initial = [0.0] * 79
initial2 = [0.0] * 79
initial_not_na = [0.0] * 79
signature_id = "LINCS_TP" + str(unique_iterator)
unique_iterator += 1
unique_sum[key] = initial
unique_pvalue[key] = initial2
val = GCP_unique_complete.get(key)
key_splitted = key.split("++")
print key_splitted
col_cell_line.append('Cell Line: ' + key_splitted[0])
col_pert_dose.append('Dose: ' + key_splitted[4] + key_splitted[5])
col_pert_time.append('Time: ' + key_splitted[8] + key_splitted[9])
col_pert_name.append(
'Perturbations: ' + key_splitted[7] + "/" + key_splitted[4] + key_splitted[5] + "/" + key_splitted[8] +
key_splitted[9])
col_pert_signature.append('Signature ID: ' + signature_id)
if "_sg01" not in key_splitted[7] and "_sg02" not in key_splitted[7]:
cpType = 'Small Molecule'
else:
cpType = 'CRISPR'
col_pert_type.append('Type: ' + cpType)
compound_name = str(key_splitted[7]).upper()
cp_metaData = {}
cp_metaData_for_data_slicing = {}
cp_metaData["Cell_line"] = key_splitted[0]
cp_metaData["Dose"] = key_splitted[4] + " " + key_splitted[5]
cp_metaData["Time"] = key_splitted[8] + " " + key_splitted[9]
cp_metaData["Perturbations"] = compound_name
cp_metaData["Type"] = cpType
cp_metaData["Sig_id"] = signature_id
cp_metaData_for_data_slicing["Cell_line"] = key_splitted[0]
cp_metaData_for_data_slicing["Dose"] = key_splitted[4] + " " + key_splitted[5]
cp_metaData_for_data_slicing["Time"] = key_splitted[8] + " " + key_splitted[9]
cp_metaData_for_data_slicing["Perturbations"] = compound_name
cp_metaData_for_data_slicing["Type"] = cpType
cp_metaData_for_data_slicing["Sig_id"] = signature_id