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Fix globbing bug in splitp #221

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merged 4 commits into from
Jul 24, 2020
Merged

Fix globbing bug in splitp #221

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a251b09
Fix globbing bug in splitp
emschorsch Jun 19, 2020
9bdd737
infer compression from first chromosome present
emschorsch Jun 19, 2020
bf2df25
undo _split change
emschorsch Jun 19, 2020
85ad283
undo moving function location
emschorsch Jun 19, 2020
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infer compression from first chromosome present
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@emschorsch
emschorsch authored Jun 19, 2020
commit 9bdd73745eea9d112fa8826b6a8fa2a2f49790ab
9 changes: 5 additions & 4 deletions ldscore/parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,9 +118,9 @@ def ldscore(fh, num=None):
'''Parse .l2.ldscore files, split across num chromosomes. See docs/file_formats_ld.txt.'''
suffix = '.l2.ldscore'
if num is not None: # num files, e.g., one per chromosome
first_fh = sub_chr(fh, 1) + suffix
s, compression = which_compression(first_fh)
chrs = get_present_chrs(fh, num+1)
first_fh = sub_chr(fh, chrs[0]) + suffix
s, compression = which_compression(first_fh)
chr_ld = [l2_parser(sub_chr(fh, i) + suffix + s, compression) for i in chrs]
x = pd.concat(chr_ld) # automatically sorted by chromosome
else: # just one file
Expand Down Expand Up @@ -187,8 +187,9 @@ def annot(fh_list, num=None, frqfile=None):
annot_suffix = ['.annot' for fh in fh_list]
annot_compression = []
if num is not None: # 22 files, one for each chromosome
chrs = get_present_chrs(fh, num+1)
for i, fh in enumerate(fh_list):
first_fh = sub_chr(fh, 1) + annot_suffix[i]
first_fh = sub_chr(fh, chrs[0]) + annot_suffix[i]
annot_s, annot_comp_single = which_compression(first_fh)
annot_suffix[i] += annot_s
annot_compression.append(annot_comp_single)
Expand All @@ -201,7 +202,7 @@ def annot(fh_list, num=None, frqfile=None):

y = []
M_tot = 0
for chrom in get_present_chrs(fh, num+1):
for chrom in chrs:
if frqfile is not None:
df_annot_chr_list = [annot_parser(sub_chr(fh, chrom) + annot_suffix[i], annot_compression[i],
sub_chr(frqfile, chrom) + frq_suffix, frq_compression)
Expand Down