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Commit d34a6f77 authored by Blaise Li's avatar Blaise Li
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Using extra chromosomes (for transgenes).

This was missing, resulting in incomplete bigwig files.
parent e162df3d
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......@@ -14,6 +14,7 @@ from subprocess import CalledProcessError
from collections import defaultdict
from itertools import product
from cytoolz import valmap
import matplotlib as mpl
# To be able to run the script without a defined $DISPLAY
......@@ -41,6 +42,7 @@ aligner = config["aligner"]
genome_dict = config["genome_dict"]
genome = genome_dict["name"]
chrom_sizes = get_chrom_sizes(genome_dict["size"])
chrom_sizes.update(valmap(int, genome_dict.get("extra_chromosomes", {})))
genomelen = sum(chrom_sizes.values())
genome_db = genome_dict["db"][aligner]
# bed file binning the genome in 10nt bins
......
......@@ -18,6 +18,7 @@ import pandas as pd
from itertools import chain, repeat
from functools import reduce
from operator import or_ as union
from cytoolz import valmap
from smincludes import rules as irules
from smwrappers import wrappers_dir
......@@ -75,6 +76,7 @@ alignment_settings = {
genome_dict = config["genome_dict"]
genome = genome_dict["name"]
chrom_sizes = get_chrom_sizes(genome_dict["size"])
chrom_sizes.update(valmap(int, genome_dict.get("extra_chromosomes", {})))
genomelen = sum(chrom_sizes.values())
genome_db = genome_dict["db"][aligner]
# bed file binning the genome in 10nt bins
......
......@@ -34,6 +34,7 @@ warnings.formatwarning = formatwarning
# Useful for functional style
from itertools import product, starmap
from operator import eq
from cytoolz import valmap
# Useful data structures
from collections import OrderedDict
......@@ -182,6 +183,7 @@ genome_dict = config.get("genome_dict", None)
if genome_dict is not None:
genome = genome_dict["name"]
chrom_sizes = get_chrom_sizes(genome_dict["size"])
chrom_sizes.update(valmap(int, genome_dict.get("extra_chromosomes", {})))
genomelen = sum(chrom_sizes.values())
genome_db = genome_dict["db"][aligner]
# bed file binning the genome in 10nt bins
......
......@@ -55,7 +55,7 @@ def debug_wildcards(wildcards):
print(wildcards)
return []
from cytoolz import valmap
import matplotlib as mpl
# To be able to run the script without a defined $DISPLAY
mpl.use("PDF")
......@@ -242,6 +242,7 @@ aligner = config["aligner"]
genome_dict = config["genome_dict"]
genome = genome_dict["name"]
chrom_sizes = get_chrom_sizes(genome_dict["size"])
chrom_sizes.update(valmap(int, genome_dict.get("extra_chromosomes", {})))
genomelen = sum(chrom_sizes.values())
genome_db = genome_dict["db"][aligner]
# bed file binning the genome in 10nt bins
......
......@@ -71,7 +71,7 @@ from collections import defaultdict, Counter
from itertools import chain, combinations, product, repeat, starmap
from functools import reduce
from operator import or_ as union
from cytoolz import concat, merge_with, take_nth
from cytoolz import concat, merge_with, take_nth, valmap
def concat_lists(lists):
......@@ -281,6 +281,7 @@ aligner = config["aligner"]
genome_dict = config["genome_dict"]
genome = genome_dict["name"]
chrom_sizes = get_chrom_sizes(genome_dict["size"])
chrom_sizes.update(valmap(int, genome_dict.get("extra_chromosomes", {})))
genomelen = sum(chrom_sizes.values())
genome_db = genome_dict["db"][aligner]
# bed file binning the genome in 10nt bins
......
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