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Enabling support for other filetypes, i.e. tsv and txt #6

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Enabling support for other filetypes, i.e. tsv and txt #6

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33 changes: 25 additions & 8 deletions ukbb_parser/scripts/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,14 @@ def check(incsv, datafield, category):

Please see https://github.com/USC-IGC/ukbb_parser for additional documentation.
'''
if incsv.endswith(".csv"):
delimiter = ','
elif incsv.endswith(".txt") or incsv.endswith(".tsv"):
delimiter = '\t'

with open(incsv, 'r') as f:
first_line = f.readline()
columns = first_line.strip().split(",")
columns = first_line.strip().split(delimiter)
datafields = set([col.split("-")[0] for col in columns])
datafields = list(datafields)
if datafields[0].startswith('"'):
Expand Down Expand Up @@ -96,9 +101,9 @@ def update(previous, new, outcsv):
Please see https://github.com/USC-IGC/ukbb_parser for additional documentation.
'''
click.echo("Loading "+previous)
pc = read_spreadsheet(previous, 'csv')
pc = read_spreadsheet(previous, 'unknown')
click.echo("Loading "+new)
nc = read_spreadsheet(new, 'csv')
nc = read_spreadsheet(new, 'unknown')

keep = ['eid']
for col in pc.columns:
Expand Down Expand Up @@ -189,7 +194,12 @@ def parse(incsv, out, incon, excon, insr, exsr, incat, excat, inhdr, exhdr, subj

arglist = ' '.join(sys.argv)
pd.set_option("display.max_colwidth", 500)


if incsv.endswith(".csv"):
delimiter = ','
elif incsv.endswith(".txt") or incsv.endswith(".tsv"):
delimiter = '\t'

### Functions... We like functions

time_between_online_cognitive_test_and_imaging = {
Expand All @@ -213,7 +223,7 @@ def delta_t_days(datafield, dataframe):
### Filter data columns, Part I ###
####################################

all_columns = pd.read_csv(incsv, encoding='ISO-8859-1', nrows=2)
all_columns = pd.read_csv(incsv, encoding='ISO-8859-1', nrows=2, delimiter=delimiter)
all_columns = list(all_columns.columns)
defcols = ["eid"]
covariate_columns = ['eid']
Expand Down Expand Up @@ -506,7 +516,8 @@ def delta_t_days(datafield, dataframe):

# df.dropna(axis=1, how="all", inplace=True)

for i, df in enumerate(pd.read_csv(incsv, encoding='ISO-8859-1', chunksize=chunksize, usecols=defcols)):
for i, df in enumerate(pd.read_csv(incsv, encoding='ISO-8859-1', chunksize=chunksize, usecols=defcols,
delimiter=delimiter)):

if rcols:
df.rename(columns=revert_names, inplace=True)
Expand Down Expand Up @@ -710,8 +721,13 @@ def inventory(incsv, outcsv, subjects, rcols, datatype, code, level, all_codes,
click.echo("Number of --level and --code flags used should match. Please double check your inputs before trying again.")
sys.exit(1)

if incsv.endswith(".csv"):
delimiter = ','
elif incsv.endswith(".txt") or incsv.endswith(".tsv"):
delimiter = '\t'

# Load Datafields from Column Headers
all_columns = pd.read_csv(incsv, encoding='ISO-8859-1', nrows=2)
all_columns = pd.read_csv(incsv, encoding='ISO-8859-1', nrows=2, delimiter=delimiter)
all_columns = list(all_columns.columns)

# R columns
Expand Down Expand Up @@ -781,7 +797,8 @@ def inventory(incsv, outcsv, subjects, rcols, datatype, code, level, all_codes,
# df = read_spreadsheet(incsv)
reldfs = list(defcols)
reldfs.remove('eid')
for i, df in enumerate(pd.read_csv(incsv, encoding='ISO-8859-1', chunksize=chunksize, usecols=defcols)):
for i, df in enumerate(pd.read_csv(incsv, encoding='ISO-8859-1', chunksize=chunksize, usecols=defcols,
delimiter=delimiter)):

# Filter Subjects
if len(sublist) > 0:
Expand Down