Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

Appendix A
# This is the main driver function in the CleansingPrep_6_23.py file which prepares the
ProbeFATE system for the BaFL filter cleansing
# tables parameter is a list of files to import or create
# example files are in the Supplementary Materials:
1) MissingQuantitation.csv quantitation types which I add to the system
2) Known.csv calculates or uses previously calculated deltaG (OligoArrayAux ) values
for probes with known sequences, flag meth[0] differentiates
3) SampleMask.csv a file which describes the data (abbrev. sample sd, orig sample id,
the associated .cel file, disease class, and the file source for this information
4) SNP_by_pos.csv a file created w/ Sunita.py, which parses the information from
AffyMAPSDetector output
5) probe_mapping.csv file is created through ENSEMBL mappings or probes, flag[1]
indicates whether the latest ENSEMBL build is used otherwise the build needs to be
provided
def prepareCleansing(db, usr, pswd, fpath, logfile, tables, meth):
# tables = [added_qts, sample_info, snp_info, xhybrid_info]
# add new qts
i=0
CreateNew_QTs(db, usr, pswd, tables[0], logfile)
i+=1
# map known chip sequence info
if lower(meth[0])=='copy':
Copy_deltaG(db, usr, pswd, tables[1], logfile)
i+=1
elif lower(meth[0][:4])=='calc':
Calc_deltaG(db, usr, pswd, fpath, logfile)
else:
print 'Method:', meth[0], 'does not exist.'
return -1
# set sample mask
Sample_mask(db, usr, pswd, logfile, tables[i])
i+=1
# map SNP info
SNP_mask(db, usr, pswd, tables[i], logfile)
i+=1
# map xhybridization info
if lower(meth[1])=='new':
new_Xhybrid(db, usr, pswd, tables[i], logfile)
else:
version_Xhybrid(db, usr, pswd, tables[i], logfile, meth[1])
Mod_wk_registry(db, usr, pswd)
print '\nXHYBRID INFO MAPPED\n'
print '\n\tALMOST READY TO PROBE CLEANSE\n'
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