""" import numpy as np import domainogram_diag2 import directional_indice import scn import ice_mirny3 import comp_short from pylab import * import gc_content import matplotlib.gridspec as gridspec BIN = 5000 data1 = loadtxt(sys.argv[1]) matscn1 = ice_mirny3.ice_func(data1, 100) matscn1 = scn.scn_func(matscn1, 0) #matscn1=data1; name = sys.argv[2] # PLOTTING MATRIX AND MULTI-SCALES DOMAINOGRAM: M = np.corrcoef(matscn1) #M = matscn1; n1 = M.shape[0] # Choice of scales: #v=10**(np.array(range(50,161)) *0.04) / BIN #v=v.astype(int); #v2=sorted(set(v)); #scales=v2; scales = range(0, 100) #---------------------------------------------------------------------------------
)
MATRICE2 = loadtxt(
"/home/axel/Bureau/data/vick/2014_05_HiSeq_Boccard/matrices_Vicky/ecoli_MM_deltaMatP/BC172_CGGT_fused7banks_ecoli_MM_deltaMatP/matrices_DeltaMatP/matrices_2kb/mat_temp.dat"
)
# Next seq data:
MATRICE1 = loadtxt(
"/run/media/axel/9e657c5d-6ac3-494e-81af-b25e389d59bd/vick_data_backup/exp5_dec2014_NextSeq/fastq/BC70_TACT_WT/matrices_BC70_TACT_WT/mat_temp.dat"
)
MATRICE2 = loadtxt(
"/run/media/axel/9e657c5d-6ac3-494e-81af-b25e389d59bd/vick_data_backup/exp5_dec2014_NextSeq/fastq/BC72_AGCT_MatP/matrices_BC72_AGCT_MatP/mat_temp.dat"
)
# Normalisations:
matscn1 = ice_mirny3.ice_func(MATRICE1, 100)
matscn1 = scn.scn_func(matscn1, 0)
matscn2 = ice_mirny3.ice_func(MATRICE2, 0)
matscn2 = scn.scn_func(matscn2, 0)
# Plots:
imshow(matscn1**0.2,
interpolation="none",
cmap=cm,
vmin=0.0,
vmax=matscn1.max()**0.2)
colorbar()
plot(mats / BIN, mats / BIN, "o", color="orange")
# Ratio:
r = matscn2 / matscn1
import distance_law
from scipy.stats.stats import pearsonr
import triangular_diag
import domainogram_diag2
import directional_indice
import gc_content
import scipy.ndimage
import scipy.io as sio
import sys
MAT_BIN = loadtxt(sys.argv[1])
name = sys.argv[2]
# Normalisation:
matscn1 = scn.scn_func(MAT_BIN, 0)
name = sys.argv[2]
# PLOTTING MATRIX:
matplotlib.rcParams.update({'font.size': 8})
subplots_adjust(hspace=0.5)
plt.figure(num=None, figsize=(8, 9), dpi=80, facecolor='w', edgecolor='k')
#gs = gridspec.GridSpec(1, 1,);
#ax0 = plt.subplot(gs[0]);
C2 = sio.loadmat(
'/home/axel/Bureau/bacteries_project/z-python_scripts/MyColormaps2.mat')
C = C2['mycmap2']
cm = mpl.colors.ListedColormap(C)
exponent = 0.2
import matplotlib.pyplot as plt
from matplotlib.legend_handler import HandlerLine2D
from scipy.integrate import simps, trapz
import statsmodels.api as sm
lowess = sm.nonparametric.lowess
from scipy.stats.stats import pearsonr
from scipy.stats.stats import spearmanr
import scn
#---------------------------------------------------------------------------------
data1 = loadtxt(
"/home/axel/Bureau/data/vick/2014_05_HiSeq_Boccard/matrices_Vicky/ecoli_MM_async/BC164_GTGT_fused7banks_Ecoli_MM_async/matrices_10kb/mat_temp.dat"
)
matscn1 = scn.scn_func(data1, 0)
length_genome = 4639675
bin_mat = 10000
bins = [
1055417, 3250851, 331520, 3841019, 4024867, 806540, 1379810, 2383627,
2470410
]
i = 0
for x_position in bins:
i = i + 1
print x_position
file = "/run/media/axel/9e657c5d-6ac3-494e-81af-b25e389d59bd1/ECOLI_PROJECT/CMP_3C_Recombination/boccard_DATA/" + str(