GeneBank文件绘图 超*初级

gb_plot.py

import matplotlib.pyplot as plt
import numpy as np
import sys

def get_features(gb):
    context=open(gb,"r").read().split("FEATURES")[1].split("ORIGIN")[0].splitlines()
    dc={}
    for line in context:
        if line[5]==' ':
            continue
        [item,ran]=line.split()
        ran=[int(i) for i in ran.split("..")]
        if item in dc.keys():
            dc[item].append(ran)
        else:
            dc[item]=[ran]
    return dc

level_color={1:'b',
             2:'r',
             3:'m',
             4:'y',
             5:'g',
             6:'k'}


def gb_plot(gb):
    features=get_features(gb)
    total=features['source'][0]
    fig=plt.figure()
    ax=fig.add_subplot(111)
    ax.plot(range(total[0],total[1]),[0]*(total[1]-total[0]),
             linewidth=10,color='c')
    ax.text(0,10,"source:"+str(total[0])+".."+str(total[1]),
            color='k')

    level=1
    for key in features.keys():
        if key=="source":
            continue
        sets=features[key]
        co=level_color[level]
        for se in sets:
            ax.axvline(x=se[0],color=co)
            ax.axvline(x=se[1],color=co)
            ax.plot(range(se[0]+1,se[1]-1),[level*50]*(se[1]-se[0]-2),linewidth=8,color=co)
        ax.text(0,level*50+10,key+":"+str(sets),color='k')
        level=level+1
        
    plt.axis([total[0],total[1],-30,300])
    plt.savefig(gb.replace(".gb",".png"))

if __name__=='__main__':
    gb_plot(sys.argv[1])