From 519923a06c5866acae2afbe1012de138e3f33e10 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 9 Jul 2019 15:21:03 +0200
Subject: [PATCH] Unset use of LaTeX, fix read type examination.
---
libhts/libhts.py | 38 +++++++++++++++++++++++++-------------
1 file changed, 25 insertions(+), 13 deletions(-)
diff --git a/libhts/libhts.py b/libhts/libhts.py
index 07b5698..6631039 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -20,18 +20,19 @@ from scipy.stats.stats import pearsonr, linregress
from scipy.stats.mstats import gmean
import matplotlib as mpl
import matplotlib.pyplot as plt
+# TODO: set this at the "correct" place
# https://stackoverflow.com/a/42768093/1878788
-from matplotlib.backends.backend_pgf import FigureCanvasPgf
-mpl.backend_bases.register_backend('pdf', FigureCanvasPgf)
-TEX_PARAMS = {
- "text.usetex": True, # use LaTeX to write all text
- "pgf.rcfonts": False, # Ignore Matplotlibrc
- "pgf.texsystem": "lualatex", # hoping to avoid memory issues
- "pgf.preamble": [
- r'\usepackage{color}' # xcolor for colours
- ]
-}
-mpl.rcParams.update(TEX_PARAMS)
+#from matplotlib.backends.backend_pgf import FigureCanvasPgf
+#mpl.backend_bases.register_backend('pdf', FigureCanvasPgf)
+#TEX_PARAMS = {
+# "text.usetex": True, # use LaTeX to write all text
+# "pgf.rcfonts": False, # Ignore Matplotlibrc
+# "pgf.texsystem": "lualatex", # hoping to avoid memory issues
+# "pgf.preamble": [
+# r'\usepackage{color}' # xcolor for colours
+# ]
+#}
+#mpl.rcParams.update(TEX_PARAMS)
import seaborn as sns
# from rpy2.robjects import r, pandas2ri, Formula, StrVector
# as_df = r("as.data.frame")
@@ -275,11 +276,22 @@ def aligner2min_mapq(aligner, wildcards):
What minimal MAPQ value should a read have to be considered uniquely mapped?
See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
"""
+ mapping_type = None
try:
mapping_type = wildcards.mapping_type
except AttributeError:
- mapping_type = wildcards.mapped_type
- if mapping_type.startswith("unique_"):
+ pass
+ if mapping_type is None:
+ try:
+ mapping_type = wildcards.mapped_type
+ except AttributeError:
+ pass
+ if mapping_type is None:
+ try:
+ mapping_type = wildcards.read_type
+ except AttributeError:
+ pass
+ if mapping_type is None or mapping_type.startswith("unique_"):
if aligner == "hisat2":
return "-Q 60"
elif aligner == "bowtie2":
--
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