Commit 5e09e511 authored by Blaise Li's avatar Blaise Li
Browse files

Fix source functions and errors.

parent 36cf4b8c
......@@ -134,7 +134,7 @@ from libdeseq import do_deseq2
from libhts import status_setter
from libhts import median_ratio_to_pseudo_ref_size_factors, size_factor_correlations
from libhts import plot_paired_scatters, plot_norm_correlations, plot_counts_distribution, plot_boxplots, plot_histo
from libworkflows import texscape, ensure_relative, cleanup_and_backup
from libworkflows import texscape, wc_applied, ensure_relative, cleanup_and_backup
from libworkflows import get_chrom_sizes, column_converter, make_id_list_getter
from libworkflows import read_int_from_file, strip_split, file_len, last_lines, save_plot, SHELL_FUNCTIONS
from libworkflows import sum_by_family, read_feature_counts, sum_feature_counts, sum_htseq_counts, warn_context
......@@ -194,7 +194,7 @@ EFF_LIBS = list(config["transcriptome_TPM"].keys())
series_dict = config["series"]
SERIES_TYPES = list(series_dict.keys())
genotype_series = series_dict["genotype_series"]
dt_series = series_dict["dt_series"]
dt_series = series_dict.get("dt_series", {})
merged_series = merge_with(concat_lists, *series_dict.values())
ALL_SERIES = list(merged_series.keys())
#all_libs_in series = concat_lists(merge_with(concat_lists, *series_dict.values()).values())
......@@ -711,6 +711,7 @@ rule select_size_range:
"""
@wc_applied
def source_fastq(wildcards):
"""Determine the fastq file corresponding to a given read type."""
read_type = wildcards.read_type
......@@ -940,6 +941,7 @@ rule count_RPF:
nb_RPF_file.write(f"{nb_RPF}\n")
@wc_applied
def source_counts(wildcards):
"""Determines from which rule the gathered counts should be sourced."""
if wildcards.biotype == "alltypes":
......@@ -1737,6 +1739,7 @@ def bamcoverage_filter(wildcards):
return ""
@wc_applied
def source_norm_file(wildcards):
return rules.make_read_counts_summary.output.summary
......@@ -2840,7 +2843,7 @@ rule plot_size_distribution:
input:
rules.compute_size_distribution.output
output:
OPJ("figures", "{lib}_{{rep}}", "{read_type}_size_distribution.pdf"),
OPJ("figures", "{lib}_{rep}", "{read_type}_size_distribution.pdf"),
message:
"Plotting size distribution for {wildcards.lib}_{wildcards.rep}_{wildcards.read_type}."
run:
......
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