From 8214c5aa8d0a161f0c1ab3a75e52bf39c2dcc3d1 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 29 Jan 2020 11:40:44 +0100
Subject: [PATCH] No more numpy kwarg in pybigwig values().
---
PRO-seq/PRO-seq.snakefile | 2 +-
RNA_Seq_Cecere/RNA-seq.snakefile | 2 +-
Ribo-seq/Ribo-seq.snakefile | 6 +++---
small_RNA-seq/small_RNA-seq.snakefile | 6 +++---
4 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 7509054..7e1882b 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -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
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 51607f9..348b940 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -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
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index 2afb5d9..b33d2eb 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -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()
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 5725505..bd71de7 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -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()
--
GitLab