Commit 1d989b7b authored by Blaise Li's avatar Blaise Li
Browse files

Added rmsk families to the alltypes tables.

This makes the DE results easier to compare with those from small
RNA-seq.
parent 17bfe0b6
......@@ -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:
......
......@@ -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:
......
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