def tiers2xls(tier_dirs, output_dir):
# make new excel output worksheet
wb = xlwt.Workbook()
for dir in tier_dirs:
dirname = general_utils.get_file_or_dir_name(dir)
sheetname = dirname
sheet = wb.add_sheet(sheetname)
rowNum = 0 # number of row to write to within excel sheet
tier0file = os.path.join(dir, 'tiering_allvars.tier0.txt')
tier1file = os.path.join(dir, 'tiering_allvars.tier1.txt')
tier2file = os.path.join(dir, 'tiering_allvars.tier2.txt')
tier3file = os.path.join(dir, 'tiering_allvars.tier3.txt')
tier4file = os.path.join(dir, 'tiering_allvars.tier4.txt')
tierFiles = [tier0file, tier1file, tier2file, tier3file, tier4file]
for idx,tierFile in enumerate(tierFiles):
tierh = open(tierFile, 'r')
if(idx != 0): # skip header for all files except the first one
tierh.readline()
for line in tierh:
lineContents = line.rstrip("\n").split("\t")
for col,value in enumerate(lineContents):
sheet.write(rowNum, col, value)
rowNum += 1
#save the excel file
out_path = os.path.join(output_dir, 'tiered_output.xls')
wb.save(out_path)
return out_path
def tiers2xls(tier_dirs, output_dir, yaml_commands):
print 'Saving tiered variants to Excel worksheet'
# make new excel output worksheet
wb = xlwt.Workbook(
encoding='latin-1'
) # needed since our SQLite database gives results using latin-1 encoding (so we'd otherwise get UnicodeDecode errors when attempting to decode certain characters if we specified nothing (default is probably ascii) or (probably) UTF-8 as the encoding for the workbook).
for dir in tier_dirs:
dirname = general_utils.get_file_or_dir_name(dir)
sheetname = dirname
sheet = wb.add_sheet(sheetname)
rowNum = 0 # number of row to write to within excel sheet
tier0file = os.path.join(dir, 'tiering_allvars.tier0.txt')
tier1file = os.path.join(dir, 'tiering_allvars.tier1.txt')
tier2file = os.path.join(dir, 'tiering_allvars.tier2.txt')
tier3file = os.path.join(dir, 'tiering_allvars.tier3.txt')
tier4file = os.path.join(dir, 'tiering_allvars.tier4.txt')
tierFiles = [tier0file, tier1file, tier2file, tier3file, tier4file]
for idx, tierFile in enumerate(tierFiles):
tierh = open(tierFile, 'r')
if (idx != 0): # skip header for all files except the first one
tierh.readline()
warned_of_tier_variants_exceeded = False
for lineNum, line in enumerate(tierh):
lineContents = line.rstrip("\n").split("\t")
for col, value in enumerate(lineContents):
if (len(value) > 32767):
print 'warning: tierFile ' + str(
tierFile) + ' line ' + str(
lineNum) + ' col ' + str(
col) + ' has length ' + str(
len(value)
) + ' longer than 32767 chars. Truncating.'
sheet.write(rowNum, col, value[:32767])
elif (lineNum >
yaml_commands[yaml_keys.kModules][yaml_keys.kTiering]
[yaml_keys.kTMaxNumVariantsPerTier]):
if (not warned_of_tier_variants_exceeded):
print 'warning: number of variants exceeded for ' + str(
tierFile
) + '. Omitting remaining variants in this tier from XLS file. Current max variants per tier: ' + str(
yaml_commands[yaml_keys.kModules][
yaml_keys.kTiering][
yaml_keys.kTMaxNumVariantsPerTier]
) + '. To output more variants per tier, modify this value in modules.yml.'
warned_of_tier_variants_exceeded = True
continue # don't increment the rowNum since we didn't write anything
else:
sheet.write(rowNum, col, value)
rowNum += 1
#save the excel file
out_path = os.path.join(output_dir, 'tiered_output.xls')
wb.save(out_path)
return out_path
def tiers2xls(tier_dirs, output_dir, yaml_commands):
print 'Saving tiered variants to Excel worksheet'
# make new excel output worksheet
wb = xlwt.Workbook(encoding='latin-1') # needed since our SQLite database gives results using latin-1 encoding (so we'd otherwise get UnicodeDecode errors when attempting to decode certain characters if we specified nothing (default is probably ascii) or (probably) UTF-8 as the encoding for the workbook).
for dir in tier_dirs:
dirname = general_utils.get_file_or_dir_name(dir)
sheetname = dirname
sheet = wb.add_sheet(sheetname)
rowNum = 0 # number of row to write to within excel sheet
tier0file = os.path.join(dir, 'tiering_allvars.tier0.txt')
tier1file = os.path.join(dir, 'tiering_allvars.tier1.txt')
tier2file = os.path.join(dir, 'tiering_allvars.tier2.txt')
tier3file = os.path.join(dir, 'tiering_allvars.tier3.txt')
tier4file = os.path.join(dir, 'tiering_allvars.tier4.txt')
tierFiles = [tier0file, tier1file, tier2file, tier3file, tier4file]
for idx,tierFile in enumerate(tierFiles):
tierh = open(tierFile, 'r')
if(idx != 0): # skip header for all files except the first one
tierh.readline()
warned_of_tier_variants_exceeded = False
for lineNum,line in enumerate(tierh):
lineContents = line.rstrip("\n").split("\t")
for col,value in enumerate(lineContents):
if(len(value) > 32767):
print 'warning: tierFile ' + str(tierFile) + ' line ' + str(lineNum) + ' col ' + str(col) + ' has length ' + str(len(value)) + ' longer than 32767 chars. Truncating.'
sheet.write(rowNum, col, value[:32767])
elif(lineNum > yaml_commands[yaml_keys.kModules][yaml_keys.kTiering][yaml_keys.kTMaxNumVariantsPerTier]):
if(not warned_of_tier_variants_exceeded):
print 'warning: number of variants exceeded for ' + str(tierFile) + '. Omitting remaining variants in this tier from XLS file. Current max variants per tier: ' + str(yaml_commands[yaml_keys.kModules][yaml_keys.kTiering][yaml_keys.kTMaxNumVariantsPerTier]) + '. To output more variants per tier, modify this value in modules.yml.'
warned_of_tier_variants_exceeded = True
continue # don't increment the rowNum since we didn't write anything
else:
sheet.write(rowNum, col, value)
rowNum += 1
#save the excel file
out_path = os.path.join(output_dir, 'tiered_output.xls')
wb.save(out_path)
return out_path
