import gzip
def test(iLevel, strID, hashArgs):
return (iLevel == 2) and (strID.find("GDS") == 0)
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")
Maintainer: $arepa_maintainer
Description: Automatically generated R package by arepa
Depends: R (>= 2.10.0), affy
Suggests: survival
License: MIT
URL: http://huttenhower.sph.harvard.edu/arepa
"""
import sfle
import arepa
import sys
import pickle
c_strNAMESPACE = r"'exportPattern("'"^[[:alpha:]]+"'")'"
c_fileProgUnpickle = sfle.d( pE, arepa.path_arepa(), sfle.c_strDirSrc, "unpickle.py" )
def funcCheckRStructure( pE, strDatasetName, filePKL, fileNAMESPACE, fileDESCRIPTION, fileManMaster, strNAMESPACE = c_strNAMESPACE ):
'''
Completes necessary components for R package building
Assumes that data/ and man/ directories have the corresponding data and manual files per dataset
Input:
fileNAMESPACE = pointer to NAMESPACE file to be tracked
fileManMaster = pointer to the master manual file in man/
'''
def _makeDescription( target, source, env ):
strT, astrSs = sfle.ts( target, source )
pHash = pickle.load(open(astrSs[0]))
pHashDescription = { "Package": strDatasetName.replace("-", "."), "Type": "Package", "Title": pHash.get("title"),
if strName.find("processed-data") >= 0:
return True
return False
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)])
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.
SConscript_dat-dab.py:
shared code across modules
handles all behavior pertaining to
mapping dat to dab and generating quant files
"""
import sfle
import arepa
c_fileFlagSleipnir = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirEtc,
"sleipnir")
def funcDAB(pE, fileOutDAB, afileInDAT):
astrSleipnir = sfle.readcomment(c_fileFlagSleipnir)
bSleipnir = (astrSleipnir[0] == "True")
print("sleipnir", ("On" if bSleipnir else "Off"))
def _funcDAB(target, source, env):
strT, astrSs = sfle.ts(target, source)
strOut, strMap = astrSs[:2]
return sfle.ex(("Dat2Dab", "-o", strT, "-i",
(strOut if sfle.isempty(strMap) else strMap)))
for strName in pZIP.namelist():
if strName.find("sample_table") >= 0:
return True
return False
if "testing" in locals():
sys.exit()
#Import( "pE" )
#Import( "hashArgs" )
c_strID = arepa.cwd()
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_strFileIDRawTXT = c_strID + "_00raw.txt"
c_strFileIDRawPCL = c_strID + "_01raw.pcl"
c_strFileIDNormPCL = c_strID + "_02norm.pcl"
c_strFileIDPCL = c_strID + ".pcl"
c_strFileIDDAB = c_strID + ".dab"
c_strProgMergeTables = arepa.d(arepa.path_arepa(), arepa.c_strDirSrc,
"merge_tables.py")
c_strProgSamples2PCL = arepa.d(arepa.path_repo(), arepa.c_strDirSrc,
"samples2pcl.py")
c_afileInputSamples = Glob("../*sample_table*")
#===============================================================================
# Clip sample tables to first two columns
#===============================================================================
if "testing" in locals():
sys.exit()
pE = DefaultEnvironment()
c_strID = arepa.cwd()
c_fileInputC = sfle.d(pE, arepa.path_repo(), sfle.c_strDirTmp, "stringc")
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,
"SConscript_genemapping.py")
c_fileInputSConscriptDAB = sfle.d(pE, arepa.path_arepa(), sfle.c_strDirSrc,
"SConscript_dat-dab.py")
c_fileStatus = sfle.d(pE, "status.txt")
c_strGeneFrom = None # we do not know a priori what the gene identifiers are going to be