update output plotting of chrom continuity
tforest
parent
8d4d36a1f9
commit
a7e78958b2
|
|
@ -153,7 +153,11 @@ def plot_matrix(mat, legend=None, color_scale_type="YlGn", cbarlabel = "qt", tit
|
|||
|
||||
def plot(x, y, outfile = None, outfolder = None, ylab=None, xlab=None,
|
||||
title=None, label = None, show=True, nb_subplots = None, subplot_init = False,
|
||||
subplot_id = None):
|
||||
subplot_id = None, output = None, dpi = 300, width = 15, height = 15, plot_init = True):
|
||||
|
||||
# before fig is generated, set its dimensions
|
||||
if plot_init:
|
||||
plt.figure(figsize=(width, height))
|
||||
if subplot_init:
|
||||
# define a certain amount of subplots
|
||||
fig, axs = plt.subplots(nb_subplots)
|
||||
|
|
@ -181,11 +185,11 @@ def plot(x, y, outfile = None, outfolder = None, ylab=None, xlab=None,
|
|||
if title:
|
||||
plt.title(title)
|
||||
if outfile:
|
||||
plt.savefig(outfile)
|
||||
else:
|
||||
plt.savefig(outfile, dpi = dpi)
|
||||
if show == True:
|
||||
plt.show()
|
||||
|
||||
|
||||
def scatter(x, y, ylab=None, xlab=None, title=None):
|
||||
plt.scatter(x, y)
|
||||
if ylab:
|
||||
|
|
@ -208,7 +212,7 @@ def barplot(x, y, ylab=None, xlab=None, title=None):
|
|||
|
||||
def plot_chrom_continuity(vcf_entries, chr_id, x=None, y=None, outfile = None,
|
||||
outfolder = None, returned=False, show=True, label=True, step=1, nb_subplots = None,
|
||||
subplot_init = False, subplot_id = None, title = None):
|
||||
subplot_init = False, subplot_id = None, title = None, plot_init = False):
|
||||
chr_name = list(vcf_entries.keys())[chr_id]
|
||||
if label:
|
||||
label = chr_name
|
||||
|
|
@ -226,10 +230,10 @@ def plot_chrom_continuity(vcf_entries, chr_id, x=None, y=None, outfile = None,
|
|||
xlab = "pos. in ref.",
|
||||
title = title,
|
||||
outfile = outfile, outfolder = outfolder, show=show, label=label,
|
||||
nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = subplot_id)
|
||||
nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = subplot_id, plot_init = plot_init)
|
||||
|
||||
def plot_whole_karyotype(recent_variants, mem_clean = False, step = 1, show = True, min_chr_id = 0,
|
||||
max_chr_id = None, stacked = False, title = None):
|
||||
max_chr_id = None, stacked = False, title = None, outfile = None):
|
||||
coords = []
|
||||
if max_chr_id :
|
||||
nb_iter = max_chr_id
|
||||
|
|
@ -246,7 +250,7 @@ def plot_whole_karyotype(recent_variants, mem_clean = False, step = 1, show = Tr
|
|||
nb_subplots = None
|
||||
subplot_init = False
|
||||
vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = min_chr_id, show = False, returned = False, step = step,
|
||||
nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = min_chr_id)
|
||||
nb_subplots = nb_subplots, subplot_init = subplot_init, subplot_id = min_chr_id, plot_init = True)
|
||||
else :
|
||||
iter_start = 0
|
||||
for chr in range(iter_start, nb_iter):
|
||||
|
|
@ -267,7 +271,9 @@ def plot_whole_karyotype(recent_variants, mem_clean = False, step = 1, show = Tr
|
|||
vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = chr, show = False, returned = False, step = step, subplot_id = chr)
|
||||
# last case
|
||||
if show == True:
|
||||
vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = nb_iter, show = True, returned = False, step = step, subplot_id = nb_iter, title = title)
|
||||
vcf_utils.customgraphics.plot_chrom_continuity(recent_variants, chr_id = nb_iter, show = True, returned = False, step = step, subplot_id = nb_iter,
|
||||
title = title,
|
||||
outfile = outfile, plot_init = False)
|
||||
# maybe add a clean of recent_variants in extreme cases, before building the plots
|
||||
if show == False:
|
||||
return coords
|
||||
|
|
|
|||
|
|
@ -100,7 +100,7 @@ def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, ver
|
|||
if verbose:
|
||||
print("SFS=", SFS_values)
|
||||
print("Pluriallelic sites =", count_pluriall)
|
||||
return SFS_values
|
||||
return SFS_values, count_pluriall
|
||||
|
||||
def barplot_sfs(sfs, folded=True, title = "Barplot"):
|
||||
sfs_val = []
|
||||
|
|
@ -117,7 +117,7 @@ def barplot_sfs(sfs, folded=True, title = "Barplot"):
|
|||
#build the plot
|
||||
title = title+" [folded="+str(folded)+"]"
|
||||
plt.title(title)
|
||||
plt.bar(sfs.keys(), sfs_val)
|
||||
plt.bar([i+1 for i in sfs.keys()], sfs_val)
|
||||
plt.show()
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
|
|
|||
110
vcf_to_sfs.py
110
vcf_to_sfs.py
|
|
@ -1,110 +0,0 @@
|
|||
#!/usr/bin/env python3
|
||||
|
||||
"""
|
||||
FOREST Thomas (thomas.forest@college-de-france.fr)
|
||||
|
||||
Caution : At the moment for gzipped files only.
|
||||
|
||||
ARGS
|
||||
--------
|
||||
|
||||
standalone usage : vcf_to_sfs.py VCF.gz nb_indiv
|
||||
|
||||
"""
|
||||
|
||||
import gzip
|
||||
import sys
|
||||
|
||||
def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, verbose = False):
|
||||
|
||||
""" Returns an SFS from a VCF file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
n : int
|
||||
Nb of individuals in sample.
|
||||
vcf_file : str
|
||||
SNPs in VCF file format.
|
||||
|
||||
Used to generate a Site Frequency Spectrum (SFS) from a VCF.
|
||||
|
||||
Returns
|
||||
-------
|
||||
dict
|
||||
Site Frequency Spectrum (SFS)
|
||||
|
||||
|
||||
"""
|
||||
|
||||
if diploid and not folded:
|
||||
n *= 2
|
||||
# initiate SFS_values with a zeros dict
|
||||
SFS_values = dict.fromkeys(range(n),0)
|
||||
# store nb polyallellic sites
|
||||
polyall = 0
|
||||
with gzip.open(vcf_file, "rb") as inputgz:
|
||||
line = inputgz.readline()
|
||||
genotypes = []
|
||||
print("Parsing VCF", vcf_file, "... Please wait...")
|
||||
while line:
|
||||
# decode gzipped binary lines
|
||||
line = line.decode('utf-8').strip()
|
||||
# every snp line, not comment or header
|
||||
if not line.startswith("##") and not line.startswith("#"):
|
||||
FIELDS = line.split("\t")
|
||||
# REF is col 4 of VCF
|
||||
REF = FIELDS[3].split(",")
|
||||
# ALT is col 5 of VCF
|
||||
ALT = FIELDS[4].split(",")
|
||||
FORMAT = line.split("\t")[8:9]
|
||||
SAMPLES = line.split("\t")[9:]
|
||||
snp_genotypes = []
|
||||
allele_counts = {}
|
||||
allele_counts_list = []
|
||||
# SKIP the SNP if :
|
||||
# 1 : missing
|
||||
# 2 : deletion among REF
|
||||
# 3 : deletion among ALT
|
||||
if "./.:." in line \
|
||||
or len(ALT[0]) > 1 \
|
||||
or len(REF[0]) > 1:
|
||||
line = inputgz.readline()
|
||||
continue
|
||||
for sample in SAMPLES:
|
||||
if not phased:
|
||||
# for UNPHASED data
|
||||
smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']
|
||||
else:
|
||||
# for PHASED
|
||||
smpl_genotype = [int(a) for a in sample.split(':')[0].split('|') if a != '.']
|
||||
nb_alleles = set(smpl_genotype)
|
||||
snp_genotypes += smpl_genotype
|
||||
# skip if all individuals have the same genotype
|
||||
if len(set(snp_genotypes)) == 1:
|
||||
line = inputgz.readline()
|
||||
continue
|
||||
for k in set(snp_genotypes):
|
||||
allele_counts[snp_genotypes.count(k)] = k
|
||||
allele_counts_list.append(snp_genotypes.count(k))
|
||||
if folded and len(ALT) >= 2:
|
||||
polyall += 1
|
||||
else:
|
||||
SFS_values[min(allele_counts_list)-1] += 1
|
||||
line = inputgz.readline()
|
||||
if verbose:
|
||||
print(SFS_values)
|
||||
return SFS_values, polyall
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
if len(sys.argv) != 3:
|
||||
print("Need 2 args")
|
||||
exit(0)
|
||||
|
||||
# PARAM : vcf_file
|
||||
vcf_file = sys.argv[1]
|
||||
# PARAM : Nb of indiv
|
||||
n = int(sys.argv[2])
|
||||
|
||||
sfs, nb_polyall = sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False)
|
||||
print(sfs)
|
||||
|
|
@ -185,9 +185,6 @@ def genotyping_continuity_plot(vcf_entries,
|
|||
progress = round(k/int(last_pos))*100
|
||||
if progress % 10 == 0:
|
||||
print(progress, "%")
|
||||
# if pos is genotyped
|
||||
# if k in vcf_entries:
|
||||
# y=k*step
|
||||
y+=1*step
|
||||
x=pos
|
||||
coords[0].append(x)
|
||||
|
|
|
|||
Loading…
Reference in New Issue