annotate ramachandran_auto_protein.py @ 5:dfda5e713926 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"

#!/usr/bin/env python

import argparse
import base64
import importlib
import sys

import MDAnalysis as mda
from MDAnalysis.analysis.dihedrals import Ramachandran

import h5py

from jinja2 import Environment, FileSystemLoader

import matplotlib
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker

import numpy as np
import numpy.linalg

import seaborn as sns


matplotlib.use('Agg')  # noqa


def parse_command_line(argv):
    parser = argparse.ArgumentParser()
    parser.add_argument('--itraj', help='input traj')
    parser.add_argument('--istr', help='input str')
    parser.add_argument('--itrajext', help='input traj ext')
    parser.add_argument('--istrext', help='input str ext')
    parser.add_argument('--isegid1', help='segid 1')
    parser.add_argument('--iresid1', help='resid start')
    parser.add_argument('--iresid2', help='resid end')
    parser.add_argument('--iresname', help='resname e.g. ALA')
    parser.add_argument('--igroupby', help='groupby names or ids')
    parser.add_argument('--itemplatepath', help='template path')
    parser.add_argument('--o_plot1', help='MDA Ramachandran plot')
    parser.add_argument('--o_plot2', help='Seaborn Ramachandran plot')
    parser.add_argument('--o_data1', help='Timeseries in HDF5 format')
    parser.add_argument('--o_html1', help='Html overview output of all plots')
    return parser.parse_args()


args = parse_command_line(sys.argv)

currentpath = "."
if args.itemplatepath is not None:
    currentpath = args.itemplatepath


u = mda.Universe(args.istr, args.itraj,
                 topology_format=args.istrext, format=args.itrajext)
selection = "(segid %s)" % \
    (args.isegid1)

if args.iresname is not None:
    selection = "(segid %s and resname %s)" % \
        (args.isegid1, args.iresname)

if args.iresid1 is not None and args.iresid2 is not None:
    assert(int(args.iresid1) > 0), "ResID numbering starts at 1 for this tool."
    assert(int(args.iresid2) > 0), "ResID numbering starts at 1 for this tool."
    assert(int(args.iresid2) > int(args.iresid1)
           ), "ResID2 must be at least ResID1+1"
    selection = "(segid %s and resid %s-%s)" % \
        (args.isegid1, int(args.iresid1), int(args.iresid2))
    if args.iresname is not None:
        selection = "(segid %s and resid %s-%s and resname %s)" % \
            (args.isegid1, int(args.iresid1), int(args.iresid2), args.iresname)

r = u.select_atoms(selection)

assert(r != u.select_atoms('name thiscannotpossiblyexist')
       ), \
               """The selection you specified returns an empty result.
               Check segment names and residue ID's. Also check the
                structure and trajectory file selected are the correct ones"""

if args.igroupby is not None:
    group_selections = {}  # dictionary of selections
    if args.igroupby == 'name':
        groupby = sorted(list(set(r.resnames)))
        for e in groupby:
            s = r & u.select_atoms("resname %s" % e)
            this_sel = "%s and resname %s" % (selection, e)
            group_selections[this_sel] = s
    elif args.igroupby == 'id':
        groupby = sorted(list(set(r.resids)))
        for e in groupby:
            s = r & u.select_atoms("resid %s" % e)
            this_sel = "%s and resid %s" % (selection, e)
            group_selections[this_sel] = s
    else:
        assert False, ("Invalid argument for igroupby. "
                       "Only name and id are valid options.")


def ramachandran_plot(atomgroup, selection, outputfile1, outputfile2,
                      image_format='png'):
    # plot standard mdanalysis and seaborn 2D with kde
    R = Ramachandran(atomgroup).run()
    fig, ax = plt.subplots(figsize=plt.figaspect(1))
    R.plot(ax=ax, color='k', marker='.', ref=True)

    a = R.angles.reshape(np.prod(R.angles.shape[:2]), 2)
    # open hdf file
    with h5py.File(args.o_data1, 'a') as f:
        setname = "%s" % (selection)
        f["/" + setname + "/ramachandran/phi"] = a[:, 0]
        f["/" + setname + "/ramachandran/psi"] = a[:, 1]
    plt.tight_layout()
    # svg is better but sticking with png for now
    plt.savefig(outputfile1, format=image_format)

    sns.reset_defaults()
    importlib.reload(plt)
    importlib.reload(sns)
    with sns.axes_style("white"):
        h = sns.jointplot(x=a[:, 0], y=a[:, 1],
                          kind="kde", space=0)
        h.set_axis_labels(r'$\phi$ (deg)', r'$\psi$ (deg)')
        h.ax_joint.set_xlim(-180, 180)
        h.ax_joint.set_ylim(-180, 180)
        h.ax_joint.xaxis.set_major_locator(ticker.MultipleLocator(60))
        h.ax_joint.yaxis.set_major_locator(ticker.MultipleLocator(60))
        plt.savefig(outputfile2, format=image_format, bbox_inches='tight')


def get_base64_encoded_image(image_path):
    """  encode image to string for use in html later"""
    with open(image_path, "rb") as img_file:
        return base64.b64encode(img_file.read()).decode('utf-8')


plots = []
if args.igroupby is not None:
    for k, v in group_selections.items():
        print(k, v)
        try:
            ramachandran_plot(v, str(k), "ramachandran1" +
                              str(k), "ramachandran2" + str(k))
            plots.append({'Name': "%s" % (k), 'plot1':
                         get_base64_encoded_image("ramachandran1" + str(k)),
                         'plot2': get_base64_encoded_image("ramachandran2"
                          + str(k))})
        except Exception as einstance:
            print(type(einstance))
            print(einstance.args)
            print(einstance)

ramachandran_plot(r, selection, args.o_plot1, args.o_plot2)
plots.insert(0, {'Name': selection, 'plot1': get_base64_encoded_image(
    args.o_plot1), 'plot2': get_base64_encoded_image(args.o_plot2)})

template_environment = Environment(loader=FileSystemLoader(
    currentpath), lstrip_blocks=True, trim_blocks=True)
template = template_environment.get_template(
    'ramachandran_auto_protein_html.j2')
with open(args.o_html1, 'w+') as f:
    f.write(template.render(title="Ramachandran Plots", plots=plots))