methylSimulateSpectrum.py

#!/usr/bin/env python
"""
Read in a sparky peaklist file, and output a scatterplot showing
peak positions, with the area of each marker proportional to the
height of the peak.
"""
import sys
import pylab
from math import sqrt

def main():
    if len(sys.argv) != 3:
        print "Usage:"
        print "methylSimulateSpectrum.py spectrum.list chart.pdf"
        return

    infile = sys.argv[1]
    outfile = sys.argv[2]
    openfile = open(infile,'r')
    listDict = {}
    heights = True
    for line in openfile.readlines():
        if '-' in line:
            columns = line.split()
            res = columns[0].split('-')[0]
            Cppm = float(columns[1])
            Hppm = float(columns[2])
            try:
                height = float(columns[3])
            except IndexError, e:
                heights = False
            if heights:
                listDict[res]=(Cppm,Hppm,height)
            else:
                listDict[res]=(Cppm,Hppm)
    openfile.close()
    residues = listDict.keys()
    Clist = [listDict[res][0] for res in residues]
    Hlist = [listDict[res][1] for res in residues]
    if heights:
        sizes = [listDict[res][2] for res in residues]
        maxsize = max(sizes)
        scaledsizes = [100*x/maxsize for x in sizes]
        pylab.figure()
        pylab.scatter(Hlist,Clist,marker='o',s=scaledsizes)
    else:
        pylab.figure()
        pylab.scatter(Hlist,Clist,marker='o')
    pylab.xlabel("$\omega$ H (ppm)")
    pylab.ylabel("$\omega$ C (ppm)")
    axes = pylab.gca()
    axes.invert_xaxis()
    axes.invert_yaxis()
    for label, x, y in zip(residues, Hlist, Clist):
        pylab.annotate(
            label, 
            xy = (x, y), xytext = (-2, 3),
            textcoords = 'offset points', ha = 'right', va = 'bottom',
            size=5,
            arrowprops = dict(arrowstyle = '->', connectionstyle = 'arc3,rad=0'))

    pylab.savefig(outfile)
    

main()