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Add functionality to write pdf

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HarshitGupta11 2019-06-12 17:52:20 +05:30 committed by GitHub
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commit f3ca3a5870
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1 changed files with 62 additions and 15 deletions
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77
open_synteny_matrices.py
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@ -1,38 +1,74 @@
import numpy as np
import os
import json
import gc
from read_data import read_data_homology
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib.backends.backend_pdf import PdfPages
a_h,_=read_data_homology("data_homology")
a_h,d_h=read_data_homology("data_homology")
d_h=list(d_h.keys())
ndir="processed/synteny_matrices/"
nf1="synteny_matrices_global_"
nf2="synteny_matrices_local_"
nf3="indexes_"
nf1="_synteny_matrices_global"
nf2="_synteny_matrices_local"
nf3="_indexes"
lsy={}
with open("processed/neighbor_genes.json","r") as file:
lsy=dict(json.load(file))
synteny_matrices_global=np.load(ndir+nf1+"11"+".npy")
synteny_matrices_local=np.load(ndir+nf2+"11"+".npy")
indexes=np.load(ndir+nf3+"11"+".npy")
for i in range(len(d_h)):
print("{}.{}".format(i+1,d_h[i]))
df=a_h[0].loc[indexes]
while(1):
try:
ch=int(input("Enter your choice:"))
synteny_matrices_global=np.load(ndir+str(d_h[ch-1])+nf1+".npy")
synteny_matrices_local=np.load(ndir+str(d_h[ch-1])+nf2+".npy")
indexes=np.load(ndir+str(d_h[ch-1])+nf3+".npy")
break
except:
print("Choice invalid or incomplete files!!!!!. Try Another Index.")
df=a_h[ch-1].loc[indexes]
a_h=[]
gc.collect()
inddict={}
for i in range(len(indexes)):
inddict[indexes[i]]=i
ng=["Levenshtein Distance","Levenshtein Distance Reverse"]
nl=["Local Alignment Score","Local Alignment Score Reverse"]
print(indexes)
while(1):
i=int(input("Enter the index"))
try:
i=int(input("Enter the index:"))
except:
break
if i in inddict:
font = {'family': 'sans-serif',
'color': 'darkturquoise',
'weight': 'heavy',
'size': 20,
}
pdf=PdfPages(str(i)+".pdf")
print("Species",df.loc[i].species)
print("Homology Species",df.loc[i].homology_species)
print("Gene Stable Id:",df.loc[i].gene_stable_id)
print("Homology Gene Stable Id:",df.loc[i].homology_gene_stable_id)
text="Species:"+df.loc[i].species
text+="\n"+"Gene Stable Id:"+df.loc[i].gene_stable_id
text+="\n"+"Homology Species:"+df.loc[i].homology_species
text+="\n"+"Homology Gene Stable Id:"+df.loc[i].homology_gene_stable_id
text+="\n"+"Homology Type:"+df.loc[i].homology_type
fp=plt.figure(figsize=(10,10))
fp.text(0.5,0.5,text,ha="center",fontdict=font)
pdf.savefig()
plt.close()
print("Global aligned matrix:")
g1=df.loc[i].gene_stable_id
@ -56,19 +92,30 @@ while(1):
sl=synteny_matrices_local[loc]
for m in range(sg.shape[-1]):
matrix=sg[:,:,m]
print(matrix)
hmap=sns.heatmap(matrix,xticklabels=y, yticklabels=x,annot=True)
print(matrix)
fig,ax=plt.subplots(figsize=(8,8))
ax.set_xlabel(str(df.loc[i].homology_species),fontsize=10)
ax.set_ylabel(str(df.loc[i].species),fontsize=10)
hmap=sns.heatmap(matrix,xticklabels=y, yticklabels=x,annot=True,ax=ax,linewidths=.5,cmap="YlGnBu",annot_kws={"size": 10})
hmap.figure.subplots_adjust(left=0.33,bottom=0.33,right=0.79,top=0.79)
ax.set_title(ng[m])
#plt.text(1,0.5,text,size=10)
pdf.savefig()
plt.show()
print("Local Alignment Matrix")
for m in range(sg.shape[-1]):
matrix=sl[:,:,m]
print(matrix)
hmap=sns.heatmap(matrix,xticklabels=y, yticklabels=x,annot=True)
fig,ax=plt.subplots(figsize=(8,8))
ax.set_xlabel(df.loc[i].homology_species)
ax.set_ylabel(df.loc[i].species)
hmap=sns.heatmap(matrix,xticklabels=y, yticklabels=x,annot=True,ax=ax,linewidths=.5,cmap="YlGnBu",annot_kws={"size": 10})
hmap.figure.subplots_adjust(left=0.27,bottom=0.29,right=0.92)
ax.set_title(nl[m])
pdf.savefig()
plt.show()
pdf.close()
else:
print("Index not found")