From 00f3e4197b5f5c9d4ae8016af57663b4a6c3433c Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 4 Jun 2018 11:56:38 +0200
Subject: [PATCH] Library function to make empty bigwig files.
---
libhts/__init__.py | 4 +++-
libhts/libhts.py | 9 +++++++++
2 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/libhts/__init__.py b/libhts/__init__.py
index c342524..5a45ee3 100644
--- a/libhts/__init__.py
+++ b/libhts/__init__.py
@@ -1,5 +1,7 @@
from .libhts import (
- do_deseq2, gtf_2_genes_exon_lengths, median_ratio_to_pseudo_ref_size_factors,
+ do_deseq2, gtf_2_genes_exon_lengths,
+ make_empty_bigwig,
+ median_ratio_to_pseudo_ref_size_factors,
plot_boxplots, plot_counts_distribution, plot_histo,
plot_lfc_distribution, plot_MA,
plot_norm_correlations, plot_paired_scatters, plot_scatter,
diff --git a/libhts/libhts.py b/libhts/libhts.py
index 2597cf3..b377576 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -39,6 +39,7 @@ from rpy2.rinterface import RRuntimeError
from rpy2.robjects.packages import importr
deseq2 = importr("DESeq2")
from pybedtools import BedTool
+import pyBigWig
import networkx as nx
@@ -175,6 +176,14 @@ def spikein_gtf_2_lengths(spikein_gtf):
name=("union_exon_len")).rename_axis("gene"))
+def make_empty_bigwig(filename, chrom_sizes):
+ bw_out = pyBigWig.open(filename, "w")
+ bw_out.addHeader(list(chrom_sizes.items()))
+ for (chrom, chrom_len) in bw_out.chroms().items():
+ bw_out.addEntries(chrom, 0, values=np.nan_to_num(np.zeros(chrom_len)[0::10]), span=10, step=10)
+ bw_out.close()
+
+
def do_deseq2(cond_names, conditions, counts_data,
formula=None, contrast=None, deseq2_args=None):
"""Runs a DESeq2 differential expression analysis."""
--
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