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Small bug fix to remove hard-coded directory paths #28

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Feb 4, 2017
Merged

Small bug fix to remove hard-coded directory paths #28

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4 changes: 2 additions & 2 deletions scripts/read_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -234,7 +234,7 @@ def download_puf(data_dir="../data/", all_columns=True , output_format="feather"
_download_data(url, data_dir=data_dir, data_name="puf.zip", zipped_data=True)

# read CSV into DataFrame
puf = pd.read_csv("../data/2010_PD_Profiles_PUF.csv")
puf = pd.read_csv(data_dir + "2010_PD_Profiles_PUF.csv")

# if we don't want to save all columns, drop those except for the three columns
# we're interested in.
Expand Down Expand Up @@ -293,7 +293,7 @@ def download_rxnorm(data_dir="../data/", output_format="feather"):
"SAUI", "SCUI", "SDUI", "SAB", "TTY", "CODE", "STR", "SRL", "SUPPRESS", "CVF"]

# we only want column 0 (the RXCUI identifier) and 14 (the commonly used name)
rxnorm = pd.read_csv("../data/rrf/RXNCONSO.RRF", sep="|", names=names, index_col=False,
rxnorm = pd.read_csv(data_dir + "rrf/RXNCONSO.RRF", sep="|", names=names, index_col=False,
usecols=[0,14])

# make all strings lowercase
Expand Down