From a26939b3d66e94be4e01c223be14d6e75fba62f0 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 4 Nov 2019 11:24:49 +0100
Subject: [PATCH] Workaround check added in pyBigWig.
See https://github.com/deeptools/pyBigWig/issues/97
---
PRO-seq/PRO-seq.snakefile | 2 +-
RNA_Seq_Cecere/RNA-seq.snakefile | 2 +-
Ribo-seq/Ribo-seq.snakefile | 2 +-
small_RNA-seq/requirements.txt | 1 -
small_RNA-seq/small_RNA-seq.snakefile | 2 +-
5 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 8e12e5b..bca5c25 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -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:
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 6f9b419..9263c50 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -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:
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index 8d45d15..fe47b8b 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -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:
diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt
index 7d1c244..6e99775 100644
--- a/small_RNA-seq/requirements.txt
+++ b/small_RNA-seq/requirements.txt
@@ -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
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 8e8c88c..889c3c8 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -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:
--
GitLab