Commit 17bfe0b6 authored by Blaise Li's avatar Blaise Li
Browse files

Folder rearrangement.

For RNA-seq and GRO-seq, log and data directories are now subdirectories
of output directories. local_annot_dir also moves as subdirectory of
GRO-seq output.
parent 4280ef4c
......@@ -117,8 +117,6 @@ ANNOT_BIOTYPES = config["annot_biotypes"]
#METAGENE_BIOTYPES=["protein_coding", "DNA_transposons_rmsk", "RNA_transposons_rmsk"]
METAGENE_BIOTYPES=["protein_coding"]
ID_LISTS = ["lfc_statuses", "germline_specific", "histone", "spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014"]
log_dir = config["log_dir"]
data_dir = config["data_dir"]
annot_dir = config["annot_dir"]
gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
avail_id_lists = set(glob(OPJ(gene_lists_dir, "*_ids.txt")))
......@@ -126,11 +124,14 @@ chrom_sizes = get_chrom_sizes(config["genome_size"])
genomelen = sum(chrom_sizes.values())
genome_binned = "/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/genome_binned_10.bed"
#gene_lists_dir = config["gene_lists_dir"]
local_annot_dir = config["local_annot_dir"]
#local_annot_dir = config["local_annot_dir"]
aligner = config["aligner"]
index = config["index"]
convert_dir = config["convert_dir"]
output_dir = config["output_dir"]
log_dir = OPJ(output_dir, "logs")
data_dir = OPJ(output_dir, "data")
local_annot_dir = OPJ(output_dir, "annotations")
# Used to skip some genotype x treatment x replicate number combinations
# when some of them were not sequenced
forbidden = {frozenset(wc_comb.items()) for wc_comb in config["missing"]}
......
......@@ -106,8 +106,6 @@ COND_COLUMNS = pd.DataFrame(CONDITIONS).assign(
BIOTYPES = config["biotypes"]
ID_LISTS = ["lfc_statuses", "germline_specific", "histone", "spermatogenic_Ortiz_2014", "oogenic_Ortiz_2014"]
log_dir = config["log_dir"]
data_dir = config["data_dir"]
annot_dir = config["annot_dir"]
gene_lists_dir = "/pasteur/entites/Mhe/bli/Gene_lists"
avail_id_lists = set(glob(OPJ(gene_lists_dir, "*_ids.txt")))
......@@ -124,6 +122,8 @@ aligner = config["aligner"]
COUNTERS = ["feature_count"]
convert_dir = config["convert_dir"]
output_dir = config["output_dir"]
log_dir = OPJ(output_dir, "logs")
data_dir = OPJ(output_dir, "data")
SIZE_FACTORS = ["protein_coding", "miRNA", "median_ratio_to_pseudo_ref"]
assert set(SIZE_FACTORS).issubset(set(BIOTYPES) | {"median_ratio_to_pseudo_ref"})
......
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