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Two bugs about data type #182

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Two bugs about data type #182

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5 changes: 2 additions & 3 deletions make_annot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def make_annot_files(args, bed_for_annot):
print('making annot file')
df_bim = pd.read_csv(args.bimfile,
delim_whitespace=True, usecols = [0,1,2,3], names = ['CHR','SNP','CM','BP'])
iter_bim = [['chr'+str(x1), x2, x2] for (x1, x2) in np.array(df_bim[['CHR', 'BP']])]
iter_bim = [['chr'+str(x1), int(x2), int(x2)] for (x1, x2) in np.array(df_bim[['CHR', 'BP']])]
bimbed = BedTool(iter_bim)
annotbed = bimbed.intersect(bed_for_annot)
bp = [x.start for x in annotbed]
Expand All @@ -29,8 +29,7 @@ def make_annot_files(args, bed_for_annot):
df_annot.fillna(0, inplace=True)
df_annot = df_annot[['ANNOT']].astype(int)
if args.annot_file.endswith('.gz'):
with gzip.open(args.annot_file, 'wb') as f:
df_annot.to_csv(f, sep = "\t", index = False)
df_annot.to_csv(args.annot_file, sep = "\t", index = False, compression='\gzip')
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@tpoterba tpoterba Nov 21, 2019

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Can we get rid of the backslash on \gzip?

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@tpoterba tpoterba Nov 21, 2019

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also, pandas 0.24 can infer compression based on extension, but not in 0.20 which we're pinned to (bummer)

else:
df_annot.to_csv(args.annot_file, sep="\t", index=False)

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