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