def get_20158_info(credentials, project_name_swe):
versions = {"01": ['Sample name Scilife', "Total reads per sample", "Sheet1","Passed=P/ not passed=NP*"],
"02": ["Sample name (SciLifeLab)", "Total number of reads (Millions)","Sheet1",
"Based on total number of reads after mapping and duplicate removal"],
"03": ["Sample name (SciLifeLab)", "Total number of reads (Millions)","Sheet1",
"Based on total number of reads after mapping and duplicate removal "],
"05": ["Sample name (from Project read counts)", "Total number","Sheet1",
"Based on total number of reads","Based on total number of reads after mapping and duplicate removal"],
"06": ["Sample name (from Project read counts)", "Total number","Sheet1",
"Based on total number of reads","Based on total number of reads after mapping and duplicate removal"]}
info = {}
client = SpreadSheet(credentials)
feed = client.get_spreadsheets_feed(project_name_swe + '_20158', False)
if len(feed.entry) != 0:
ssheet = feed.entry[0].title.text
version = ssheet.split(str('_20158_'))[1].split(' ')[0].split('_')[0]
client = SpreadSheet(credentials, ssheet)
content, ws_key, ss_key = get_google_document(ssheet, versions[version][2], client)
dummy, P_NP_colindex = get_column(content, versions[version][3])
dummy, No_reads_sequenced_colindex = get_column(content, versions[version][1])
row_ind, scilife_names_colindex = get_column(content, versions[version][0])
if (version=="05")| (version=="06"):
dummy, P_NP_duprem_colindex = get_column(content, versions[version][4]) ## [version][4] for dup rem
else:
P_NP_duprem_colindex=''
for j, row in enumerate(content):
if (j > row_ind):
try:
sci_name = str(row[scilife_names_colindex]).strip()
striped_name = strip_index(sci_name)
no_reads = str(row[No_reads_sequenced_colindex]).strip()
if (P_NP_duprem_colindex!='') and (str(row[P_NP_duprem_colindex]).strip()!=''):
status = str(row[P_NP_duprem_colindex]).strip()
else:
status = str(row[P_NP_colindex]).strip()
info[striped_name] = [status,no_reads]
except:
pass
else:
info=None
return info
def get_20158_info(credentials, project_name_swe):
versions = {
"01": [
'Sample name Scilife', "Total reads per sample", "Sheet1",
"Passed=P/ not passed=NP*"
],
"02": [
"Sample name (SciLifeLab)", "Total number of reads (Millions)",
"Sheet1",
"Based on total number of reads after mapping and duplicate removal"
],
"03": [
"Sample name (SciLifeLab)", "Total number of reads (Millions)",
"Sheet1",
"Based on total number of reads after mapping and duplicate removal "
],
"05": [
"Sample name (from Project read counts)", "Total number", "Sheet1",
"Based on total number of reads",
"Based on total number of reads after mapping and duplicate removal"
],
"06": [
"Sample name (from Project read counts)", "Total number", "Sheet1",
"Based on total number of reads",
"Based on total number of reads after mapping and duplicate removal"
]
}
info = {}
client = SpreadSheet(credentials)
feed = client.get_spreadsheets_feed(project_name_swe + '_20158', False)
if len(feed.entry) != 0:
ssheet = feed.entry[0].title.text
version = ssheet.split(str('_20158_'))[1].split(' ')[0].split('_')[0]
client = SpreadSheet(credentials, ssheet)
content, ws_key, ss_key = get_google_document(ssheet,
versions[version][2],
client)
dummy, P_NP_colindex = get_column(content, versions[version][3])
dummy, No_reads_sequenced_colindex = get_column(
content, versions[version][1])
row_ind, scilife_names_colindex = get_column(content,
versions[version][0])
if (version == "05") | (version == "06"):
dummy, P_NP_duprem_colindex = get_column(
content, versions[version][4]) ## [version][4] for dup rem
else:
P_NP_duprem_colindex = ''
for j, row in enumerate(content):
if (j > row_ind):
try:
sci_name = str(row[scilife_names_colindex]).strip()
striped_name = strip_index(sci_name)
no_reads = str(row[No_reads_sequenced_colindex]).strip()
if (P_NP_duprem_colindex != '') and (str(
row[P_NP_duprem_colindex]).strip() != ''):
status = str(row[P_NP_duprem_colindex]).strip()
else:
status = str(row[P_NP_colindex]).strip()
info[striped_name] = [status, no_reads]
except:
pass
else:
info = None
return info
