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Blaise LI
bioinfo_utils
Commits
a26939b3
Commit
a26939b3
authored
Nov 04, 2019
by
Blaise Li
Browse files
Workaround check added in pyBigWig.
See
https://github.com/deeptools/pyBigWig/issues/97
parent
f6ff4000
Changes
5
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PRO-seq/PRO-seq.snakefile
View file @
a26939b3
...
...
@@ -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:
...
...
RNA_Seq_Cecere/RNA-seq.snakefile
View file @
a26939b3
...
...
@@ -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:
...
...
Ribo-seq/Ribo-seq.snakefile
View file @
a26939b3
...
...
@@ -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:
...
...
small_RNA-seq/requirements.txt
View file @
a26939b3
...
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@@ -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
...
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small_RNA-seq/small_RNA-seq.snakefile
View file @
a26939b3
...
...
@@ -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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