Commit 8214c5aa authored by Blaise Li's avatar Blaise Li
Browse files

No more numpy kwarg in pybigwig values().

parent 9a7b7d98
......@@ -1194,7 +1194,7 @@ rule merge_bigwig_reps:
warn(f"The bigwig files without {chrom} will be skipped.\n")
to_use = [bw for bw in bws if chrom in bw.chroms()]
if to_use:
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
else:
means = np.zeros(chrom_len)
# bin size is 10
......
......@@ -1510,7 +1510,7 @@ rule merge_bigwig_reps:
warn(f"The bigwig files without {chrom} will be skipped.\n")
to_use = [bw for bw in bws if chrom in bw.chroms()]
if to_use:
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
else:
means = np.zeros(chrom_len)
# bin size is 10
......
......@@ -1868,7 +1868,7 @@ rule merge_bigwig_reps:
warn(f"The bigwig files without {chrom} will be skipped.\n")
to_use = [bw for bw in bws if chrom in bw.chroms()]
if to_use:
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
else:
means = np.zeros(chrom_len)
# bin size is 10
......@@ -1905,8 +1905,8 @@ rule make_bigwig_ratios:
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
assert cond_bw.chroms()[chrom] == chrom_len
#ratios = np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True))
ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True)))
#ratios = np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len))
ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len)))
# bin size is 10
bw_out.addEntries(chrom, 0, values=np.nan_to_num(ratios[0::10]), span=10, step=10)
bw_out.close()
......
......@@ -2841,7 +2841,7 @@ rule merge_bigwig_reps:
raise
to_use = [bw for bw in bws if chrom in bw.chroms()]
if to_use:
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len, numpy=True) for bw in to_use]), axis=0)
means = np.nanmean(np.vstack([bw.values(chrom, 0, chrom_len) for bw in to_use]), axis=0)
else:
means = np.zeros(chrom_len)
# bin size is 10
......@@ -2881,8 +2881,8 @@ rule make_bigwig_ratios:
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
assert cond_bw.chroms()[chrom] == chrom_len
#ratios = np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True))
ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len, numpy=True), ref_bw.values(chrom, 0, chrom_len, numpy=True)))
#ratios = np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len))
ratios = np.log2(np.divide(cond_bw.values(chrom, 0, chrom_len), ref_bw.values(chrom, 0, chrom_len)))
# bin size is 10
bw_out.addEntries(chrom, 0, values=np.nan_to_num(ratios[0::10]), span=10, step=10)
bw_out.close()
......
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