import os
import sys
import sfle
import pickle
import itertools
import re
import time
import sfle
g_iterCounter = itertools.count(0)
c_strID = arepa.cwd()
c_strPathRepo = arepa.name_repo()
c_strSufMap = ".map"
c_strMapped = "_mapped"
c_strDirData = sfle.d(arepa.path_repo(), sfle.c_strDirData)
c_strDirManMap = sfle.d(arepa.path_repo(), sfle.c_strDirEtc, "manual_mapping")
c_astrGeneTo = sfle.readcomment(
sfle.d(arepa.path_arepa(), sfle.c_strDirEtc, "geneid")
or [arepa.genemap_genename()])
c_strPathGeneMapper = sfle.d(arepa.path_arepa(), "GeneMapper")
c_strFileUnzipLog = sfle.d(c_strPathGeneMapper, sfle.c_strDirTmp, "unzip.log")
c_strFileCompileLog = sfle.d(c_strPathGeneMapper, sfle.c_strDirTmp,
"compile.log")
c_strPathTopMapping = sfle.d(c_strPathGeneMapper, sfle.c_strDirEtc,
"manual_mapping")
c_strPathUniprotKO = sfle.d(c_strPathGeneMapper, sfle.c_strDirEtc, "uniprotko")
c_fileProgMakeUnique = sfle.d(arepa.path_arepa(), sfle.c_strDirSrc,
"makeunique.py")
c_funcGeneMapper = sfle.d(c_strPathGeneMapper, sfle.c_strDirSrc,
"bridgemapper.py")
import sys
import metadata
import glob
def test(iLevel, strID, hashArgs):
return (iLevel == 1)
if "testing" in locals():
sys.exit()
pE = DefaultEnvironment()
c_strID = arepa.cwd()
c_fileInputC = sfle.d(pE, arepa.path_repo(), sfle.c_strDirTmp, "mpidbc")
c_fileIDPKL = sfle.d(pE, c_strID + ".pkl")
c_fileIDDAB = sfle.d(pE, c_strID + ".dab")
c_fileIDQUANT = sfle.d(c_strID + ".quant")
c_fileIDRawDAT = sfle.d(pE, c_strID + "_00raw.dat")
c_fileIDDAT = sfle.d(pE, c_strID + ".dat")
c_fileProgUnpickle = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"unpickle.py")
c_fileProgC2Metadata = sfle.d(pE, arepa.path_repo(), sfle.c_strDirSrc,
"c2metadata.py")
c_fileProgC2DAT = sfle.d(pE, arepa.path_repo(), sfle.c_strDirSrc, "c2dat.py")
c_fileInputManCurTXT = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc,
"manual_curation/", c_strID + sfle.c_strSufTXT)
c_fileInputSConscriptGM = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
annot2map.py:
parse mapping files
begins with !platform_table_begin
ends with !platform_table_end
"""
import sfle
import glob
import csv
import sys
import re
import arepa
import gzip
c_fileMapping = sfle.d(arepa.path_repo(), sfle.c_strDirEtc, "mapping")
c_hashHead = { k:v for (k, v) in [[y.strip() for y in x.split("%")] for x in sfle.readcomment( open( c_fileMapping))] } if sfle.readcomment(open(c_fileMapping))\
else {
"^ID .*? platform" : "Affy",
"Entrez Gene Symbol" : "HGNC",
"Uniprot .*? Symbol" : "Uniprot/TrEMBL",
"^(Entrez)? UniGene Symbol" : "UniGene",
"Entrez Unigene Identifier" : "UniGene_ID",
"GenBank Accession" : "GB_ACC",
"Entrez Gene identifier" : "Entrez Gene",
"GenBank Identifier" : "GenBank"
}
iArg = len(sys.argv)
strFileAnnotGZ = sys.argv[1] if iArg > 1 else None
strFileOut = sys.argv[2] if iArg > 2 else None
#!/usr/bin/env python
import arepa
import sys
def test(iLevel, strID, hashArgs):
return (iLevel == 2)
if "testing" in locals():
sys.exit()
#Import( "pE" )
#Import( "hashArgs" )
c_strID = arepa.cwd()
c_strInputIDSDRF = hashArgs["strFileIDSDRF"]
c_strInputIDIDF = hashArgs["strFileIDIDF"]
c_astrInputADFs = hashArgs["astrFileADFs"]
c_strFileIDTXT = c_strID + ".txt"
c_strProgIDF2Metadata = arepa.d(arepa.path_repo(), arepa.c_strDirSrc,
"idf2metadata.py")
arepa.pipe(pE, c_strInputIDIDF, c_strProgIDF2Metadata, c_strFileIDTXT,
[[True, s] for s in ([c_strInputIDSDRF] + c_astrInputADFs)])
Default(c_strFileIDTXT)
if "testing" in locals():
sys.exit()
pE = DefaultEnvironment()
c_strID = arepa.cwd()
c_strGDS, c_strGPL = c_strID.split("-")[:2]
c_fileInputSConscript = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"SConscript_pcl-dab.py")
c_fileRSConscript = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"SConscript_rpackage.py")
c_fileInputSOFTGZ = sfle.d(pE, "../" + c_strGDS + ".soft.gz")
c_fileInputManCurTXT = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc,
"manual_curation/", c_strID + ".txt")
c_filePPfun = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc, "preprocess")
c_strPPfun = sfle.readcomment(c_filePPfun)[0]
c_fileTaxa = sfle.d(pE, "taxa.txt")
c_fileStatus = sfle.d(pE, "status.txt")
c_filePlatform = sfle.d(pE, "platform.txt")
c_fileIDMap = sfle.d(pE, c_strID + ".map")
c_fileIDMapRaw = sfle.d(pE, c_strID + "_raw.map")
c_fileIDPKL = sfle.d(pE, c_strID + ".pkl")
c_fileGPLTXTGZ = sfle.d(pE, c_strGPL + ".annot.gz")
c_fileIDRawPCL = sfle.d(pE, c_strID + "_00raw.pcl")
c_fileLogPackage = sfle.d(pE, "package")
c_fileConfigPacakge = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc,
"rpackage")
import metadata
import re
def test(iLevel, strID, hashArgs):
return (iLevel == 2) and (strID.find("GSE") == 0)
if "testing" in locals():
sys.exit()
pE = DefaultEnvironment()
c_strID = arepa.cwd()
c_strSufRPackage = "_rpackage"
c_fileGPL = sfle.d(pE, arepa.path_repo(), sfle.c_strDirTmp, "gpl.txt")
c_fileAnnot = sfle.d(pE, arepa.path_repo(), sfle.c_strDirTmp, "annot.txt")
c_fileInputSConscript = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"SConscript_pcl-dab.py")
c_fileRSConscript = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"SConscript_rpackage.py")
c_fileProgUnpickle = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"unpickle.py")
c_fileInputGSER = sfle.d(pE, arepa.path_repo(), sfle.c_strDirSrc, "gse.R")
c_fileInputManCurTXT = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc,
"manual_curation/", c_strID + ".txt")
c_filePPfun = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc, "preprocess")
c_fileRunRaw = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc, "raw")
c_fileIDPKL = sfle.d(pE, c_strID + ".pkl")
if "testing" in locals():
sys.exit()
#Import( "pE" )
#Import( "hashArgs" )
c_strID = arepa.cwd()
c_strPrefix, c_strSuffix = c_strID.split("_")
c_strType = c_strID[2:6]
c_strInputIDSDRF = hashArgs["strFileIDSDRF"]
c_astrInputADFs = hashArgs["astrFileADFs"]
c_strInputSConscript = arepa.d(arepa.path_arepa(), arepa.c_strDirSrc,
"SConscript_pcl-dab.py")
c_strFileIDRawPCL = c_strID + "_00raw.pcl"
c_strFileIDNormPCL = c_strID + "_01norm.pcl"
c_strProgSamples2PCL = arepa.d(arepa.path_repo(), arepa.c_strDirSrc,
"samples2pcl.py")
c_fileInputData = Glob("../" + c_strPrefix + "*processed-data*" + c_strSuffix +
"*")[0]
#===============================================================================
# Calculate the final PCL + DAB
#===============================================================================
#- Map probe IDs and add PCL formatting
arepa.pipe(pE, c_fileInputData, c_strProgSamples2PCL, c_strFileIDRawPCL,
[[True, s] for s in ([c_strInputIDSDRF] + c_astrInputADFs)])
exec(compile(open(c_strInputSConscript).read(), c_strInputSConscript, 'exec'))
if "testing" in locals():
sys.exit()
pE = DefaultEnvironment()
c_strID = arepa.cwd().replace("-RAW", "")
c_strURLGEO = 'ftp.ncbi.nih.gov'
c_strURLGEOsupp = 'pub/geo/DATA/supplementary/samples/'
c_strURLSupp = 'ftp://' + c_strURLGEO + '/' + c_strURLGEOsupp
c_strFileGSM = "../GSM.txt"
c_strFilePCL = "../" + c_strID + ".pcl"
c_listTs = sfle.readcomment(c_strFileGSM)
c_fileProgReadCel = sfle.d(pE, arepa.path_repo(), sfle.c_strDirSrc,
"readCel.R")
c_fileProgProcessRaw = sfle.d(pE, arepa.path_repo(), sfle.c_strDirSrc,
"preprocessRaw.R")
c_strInputRData = arepa.cwd() + ".RData"
c_strOutputRData = c_strInputRData.replace("-RAW", "")
c_filePPfun = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc, "preprocess")
c_strPPfun = sfle.readcomment( c_filePPfun )[0] if \
sfle.readcomment( c_filePPfun ) else "affy::rma"
c_fileExpTable = sfle.d(pE, "../" + c_strID + "_exp_metadata.txt")
c_fileCondTable = sfle.d(pE, "../" + c_strID + "_cond_metadata.txt")
Import("hashArgs")
import metadata
import glob
from subprocess import call as ex
c_aiCOL = [0]
c_iSkip = 2
c_iCOL = len(c_aiCOL)
c_fileIDNormPCL = sfle.d(pE, c_strID + "_01norm.pcl")
c_fileIDPCL = sfle.d(pE, c_strID + ".pcl")
c_fileIDDAB = sfle.d(pE, c_strID + ".dab")
c_fileIDQUANT = sfle.d(pE, c_strID + ".quant")
c_fileIDPKL = sfle.d(pE, c_strID + ".pkl")
c_fileStatus = sfle.d(pE, "status.txt")
c_fileIDMap = sfle.d(pE, c_strID + ".map")
c_fileIDMapRaw = sfle.d(pE, c_strID + "_raw.map")
c_strDirManMap = sfle.d(arepa.path_repo(), sfle.c_strDirEtc, "manual_mapping")
c_fileIDMappedPCL = sfle.d(pE, c_strID + "_00mapped.pcl")
c_fileIDMappedPCL2 = sfle.d(pE, c_strID + "_01mapped.pcl")
c_fileFlagSleipnir = sfle.d(pE, arepa.path_repo(), sfle.c_strDirEtc,
"sleipnir")
#Load GeneMapper SConscript
exec(compile(open(arepa.genemapper()).read(), arepa.genemapper(), 'exec'))
#- Normalize
def funcIDNormPCL(target, source, env, iMaxLines=100000):
strT, astrSs = sfle.ts(target, source)
strS = astrSs[1] if (
substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE
OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import arepa
import os
import sfle
import sys
c_afileSConscripts = sorted(
Glob(sfle.d(arepa.path_repo(), sfle.c_strDirSrc, "SConscript*")))
if os.path.isfile("SConscript"):
exec(compile(open("SConscript").read(), "SConscript", 'exec'))
else:
hashArgs = {}
# I tried very hard to do this using import, but I can't find a way to prematurely
# halt an import without sys.exit, which kills the entire process.
for fileSConscript in c_afileSConscripts:
strSConscript = fileSConscript.get_abspath()
hashEnv = {"test": lambda *a: False, "testing": True}
try:
exec(compile(open(strSConscript).read(), strSConscript, 'exec'),
hashEnv)
except SystemExit:
