mmds_rs = np.zeros(n)
cmds_rs = np.zeros(n)
minimds_rs = np.zeros(n)
mogen_rs = np.zeros(n)
for i, chrom in enumerate(chroms):
bedpath = "hic_data/GM12878_combined_{}_10kb.bed".format(chrom)
mmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_mmds_coords.tsv".format(chrom))
contactMat = dt.matFromBed(bedpath, mmds_structure)
mmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(mmds_true_mat)
for j in range(len(mmds_true_mat)): #remove diagonal
mmds_true_mat[j, j] = 0
mmds_distMat = misc.distMat(mmds_structure)
mmds_rs[i] = misc.pearson(mmds_true_mat, mmds_distMat)
cmds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_cmds_coords.tsv".format(chrom))
contactMat = dt.matFromBed(bedpath, cmds_structure)
cmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(cmds_true_mat)
for j in range(len(cmds_true_mat)): #remove diagonal
cmds_true_mat[j, j] = 0
cmds_distMat = misc.distMat(cmds_structure)
cmds_rs[i] = misc.pearson(cmds_true_mat, cmds_distMat)
minimds_structure = dt.structure_from_file(
"hic_data/GM12878_combined_{}_10kb_minimds_coords.tsv".format(chrom))
contactMat = dt.matFromBed(bedpath, minimds_structure)
import sys
sys.path.append("..")
import data_tools as dt
import array_tools as at
import misc
bedpath = "hic_data/GM12878_combined_22_100kb.bed"
mmds_cluster = dt.clusterFromFile(
"hic_data/GM12878_combined_22_100kb_mmds_coords.tsv")
contactMat = dt.matFromBed(bedpath, mmds_cluster)
mmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(mmds_true_mat)
for j in range(len(mmds_true_mat)): #remove diagonal
mmds_true_mat[j, j] = 0
mmds_distMat = misc.distMat(mmds_cluster)
mmds_r = misc.pearson(mmds_true_mat, mmds_distMat)
cmds_cluster = dt.clusterFromFile(
"hic_data/GM12878_combined_22_100kb_cmds_coords.tsv")
contactMat = dt.matFromBed(bedpath, cmds_cluster)
cmds_true_mat = at.contactToDist(contactMat)
at.makeSymmetric(cmds_true_mat)
for j in range(len(cmds_true_mat)): #remove diagonal
cmds_true_mat[j, j] = 0
cmds_distMat = misc.distMat(cmds_cluster)
cmds_r = misc.pearson(cmds_true_mat, cmds_distMat)
minimds_cluster = dt.clusterFromFile(
"hic_data/GM12878_combined_22_100kb_minimds_coords.tsv")
contactMat = dt.matFromBed(bedpath, minimds_cluster)