Commit a26939b3 authored by Blaise Li's avatar Blaise Li
Browse files

Workaround check added in pyBigWig.

See https://github.com/deeptools/pyBigWig/issues/97
parent f6ff4000
......@@ -1179,7 +1179,7 @@ rule merge_bigwig_reps:
else:
bw_out = pyBigWig.open(output.bw, "w")
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
for (chrom, chrom_len) in chrom_sizes.items():
try:
assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
except KeyError as e:
......
......@@ -1486,7 +1486,7 @@ rule merge_bigwig_reps:
else:
bw_out = pyBigWig.open(output.bw, "w")
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
for (chrom, chrom_len) in chrom_sizes.items():
try:
assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
except KeyError as e:
......
......@@ -1850,7 +1850,7 @@ rule merge_bigwig_reps:
else:
bw_out = pyBigWig.open(output.bw, "w")
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
for (chrom, chrom_len) in chrom_sizes.items():
try:
assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
except KeyError as e:
......
......@@ -14,7 +14,6 @@ libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/li
libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
rpy2
# extra dependencies for the sRNA-seq annotation script small_RNA_seq_annotate.py
pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
pysam
......
......@@ -2772,7 +2772,7 @@ rule merge_bigwig_reps:
else:
bw_out = pyBigWig.open(output.bw, "w")
bw_out.addHeader(list(chrom_sizes.items()))
for (chrom, chrom_len) in bw_out.chroms().items():
for (chrom, chrom_len) in chrom_sizes.items():
try:
assert all([bw.chroms()[chrom] == chrom_len for bw in bws])
except KeyError as e:
......
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