Uses TeX to create a pdf file with the visualization of an alignment.

draw_aln.py

#!/usr/bin/env python
"""
Creates a pdf alignment
"""

import sys
import os
import tempfile

input_filename = sys.argv[1]

tex_document = r"""\documentclass[12pt]{amsart}
\usepackage{geometry}
\geometry{a4paper}
\usepackage{texshade}

\begin{document}
\section*{%s}
\begin{texshade}{%s}
\end{texshade}

\end{document}
""" % (input_filename, input_filename)

temp_tex_file = tempfile.NamedTemporaryFile(delete=False)
temp_tex_filename = temp_tex_file.name

with open(temp_tex_filename, 'w') as fh:
        fh.write(tex_document)
        print('pdflatex %s' % temp_tex_filename)
os.system('pdflatex %s' % temp_tex_filename)