From 1d989b7becb446c1f37f8eda623f7d1799ccfee9 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 14 Dec 2017 18:06:13 +0100
Subject: [PATCH] Added rmsk families to the alltypes tables.
This makes the DE results easier to compare with those from small
RNA-seq.
---
PRO-seq/PRO-seq.snakefile | 5 +++--
RNA_Seq_Cecere/RNA-seq.snakefile | 8 ++++++--
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index de075fc..9766248 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -1011,9 +1011,10 @@ rule merge_bigwig_reps:
rule join_all_counts:
- """concat counts for base biotypes into all"""
+ """concat counts for all biotypes into all"""
input:
- counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in COUNT_BIOTYPES if bty[-9:] != "_families"]),
+ #counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in COUNT_BIOTYPES if bty[-9:] != "_families"]),
+ counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=COUNT_BIOTYPES),
output:
counts_table = OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"),
run:
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index d79a509..2cf6a1a 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -34,6 +34,9 @@ def formatwarning(message, category, filename, lineno, line):
warnings.formatwarning = formatwarning
import numpy as np
+import matplotlib as mpl
+# To be able to run the script without a defined $DISPLAY
+mpl.use("PDF")
import pandas as pd
# To catch errors when plotting KDE
from scipy.linalg import LinAlgError
@@ -733,9 +736,10 @@ rule merge_bigwig_reps:
rule join_all_counts:
- """concat counts for base biotypes into all"""
+ """concat counts for all biotypes into all"""
input:
- counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in BIOTYPES if bty[-9:] != "_families"]),
+ #counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in BIOTYPES if bty[-9:] != "_families"]),
+ counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=BIOTYPES),
output:
counts_table = OPJ(mapping_dir, aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"),
run:
--
GitLab