python graph

src/graphical_seq_consensus_analysis.py

+#!/usr/bin/env python3
+import sys,csv
+import matplotlib.pyplot as plt
+from pylab import *
+plt.style.use('seaborn-whitegrid')
+import numpy as np
+def recovered_threshold(file):
+  path=file.split("_")[-1].split(".")[0][1:]
+  return path
+
+attribute=sys.argv[1]
+dir_out=sys.argv[2]
+files=[sys.argv[3]]#,sys.argv[4]]
+data={}
+attribute_max=""
+
+for file in files:
+  threshold=recovered_threshold(file)
+  with open(file, newline='') as csvfile:
+    data[threshold]={}
+    spamreader=csv.reader(csvfile)
+    titles={}
+    for row in spamreader:
+      if row[0]== "MSA":
+        for i in range(len(row)):
+          titles[row[i]]=i
+      else:
+        msa=row[titles["MSA"]]
+        region_size=row[titles["region_size"]]
+        depth=row[titles["depth"]]
+        if msa not in data[threshold]:
+          data[threshold][msa]={}
+        if region_size not in data[threshold][msa]:
+          data[threshold][msa][region_size]={}
+          data[threshold][msa][region_size]["depth"]=[]
+          data[threshold][msa][region_size]["attribute"]=[]
+        if depth not in data[threshold][msa][region_size]:
+          data[threshold][msa][region_size]["depth"].append(int(depth))
+          
+        val=row[titles[attribute]]
+        if val > attribute_max:
+          attribute_max=val
+        data[threshold][msa][region_size]["attribute"].append(float(val))
+
+print(data)
+print(attribute_max)
+color=["b","r","g","p","y"]
+for threshold in data:
+  for msa in data[threshold]:
+    fig = plt.figure()
+    ax = plt.axes()
+    ax = ax.set(xlabel='Depth', ylabel=attribute)
+    plt.title(attribute + " for " + msa)
+    i=0
+    plt.axis([0, 50,0, float(attribute_max)+10]);
+    for region_size in data[threshold][msa]:
+      x = np.array(data[threshold][msa][region_size]["depth"])
+      y = np.array(data[threshold][msa][region_size]["attribute"])
+      plt.plot(x, y, color=color[i], linestyle='solid', label=" Region size: " + region_size)
+      i+=1
+    plt.legend(loc='lower left');
+  
+fig = plt.figure()
+ax = plt.axes()
+x = np.array([10,20,50])
+y = np.array([10,20,50])
+plt.plot(x, y, color='blue', linestyle='solid', label='bleu')
+show()
+