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I have a script that converts a text file to html. The text file is an output of a program (needle). The function takes the text file as an input. I am aware the script is awful. I use this function in Django. I would like to improve it. Can you help me with it?. Here is the result file from the script.

def write_html(result):
    sequence_1 = ''
    sequence_2 = ''
    identity = ''
    similarity = ''
    gaps = ''
    html_string = ''
    with open("/Users/catuf/Desktop/needle_align.txt", "w") as e:
        e.write('{% extends "database/base_table.html" %}' + "\n")
        e.write('\n')
        e.write("{% block content %}"+"\n")
        table1 = '''
        <!DOCTYPE html>
        <html>
        <head>
        <style>
        table, th, td {
          border: 1px solid black;
        }
        </style>
        </head>
        <body>

        <table>
          <tr>
            <th>Query Sequence </th>
            <th>Matched Sequence </th>
            <th>Identity </th>
            <th>Similarity </th>
            <th>Gaps </th>
          </tr>
          <tr>
        '''

        table2 = """
          </tr>
        </table>

        </body>
        </html>
        """
        for line in result.splitlines():
            #s = html.unescape(lines)
            #print(line)
            if line.startswith('# 1:'):
                line = line.split()
                sequence_1 = line[2]
            elif line.startswith('# 2:'):
                line = line.split()
                #print(line)
                sequence_2 = line[2]

            elif line.startswith('# Identity:'):
                identity = re.search(r"\d{1,3}\.\d*\%", line)
                identity = identity.group()
                identity = identity.replace('%', '')
                #identity = float(identity)* 100
                #identity = str(identity)

            elif line.startswith('# Similarity:'):
                similarity = re.search(r"\d{1,3}\.\d*\%", line)
                similarity = similarity.group()
                similarity = similarity.replace('%', '')

            elif line.startswith('# Gaps:'):
                line = line.split()
                gaps = line[2]

            elif line.startswith('#'):
                pass
            else:
                s = "<pre>" + line + "</pre>"
                html_string += s

        e.write(table1)
        e.write("<td>" + sequence_1 + '</td>' + '\n')
        e.write("<td>" + sequence_2 + '</td>'+ '\n')
        e.write("<td>"+ identity + "%" + '</td>'+ '\n')
        e.write("<td>"+ similarity+ "%" +'</td>'+ '\n')
        e.write("<td>"+ gaps+ '</td>'+ '\n')
        e.write(table2)
        e.write(html_string)
        e.write("</head>" + "\n")
        e.write("{% endblock content %}"+"\n")
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  • \$\begingroup\$ Could you show us how the output html is rendered? \$\endgroup\$
    – dfhwze
    Sep 14, 2019 at 18:33
  • 2
    \$\begingroup\$ Sure I will add rendered one in couple of minutes. \$\endgroup\$
    – catuf
    Sep 14, 2019 at 19:17
  • 1
    \$\begingroup\$ What he meant is, how and when do you call this function? It is odd that you are programatically creating a template with data in it. There seems to be a fundamental misunderstanding here. Anyhow, first thing I'd do is separating the parsing from the rendering. \$\endgroup\$
    – Holli
    Sep 14, 2019 at 23:01
  • \$\begingroup\$ As you can see in this script. I receive the result file as a string from the needle program and call this function. \$\endgroup\$
    – catuf
    Sep 15, 2019 at 0:42

1 Answer 1

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Functions

Right now, write_html manages both parsing and writing to a file. Separate this function into two functions, perhaps parse_data and write_data.

String Formatting

This

s = "<pre>" + line + "</pre>"
e.write("<td>" + sequence_1 + '</td>' + '\n')

can be written like this

s = f"<pre>{line}></pre>"
e.write(f"<td>{sequence_1}</td>\n")

The f"" allows you to directly implement variables into your strings.

Simplification

This

elif line.startswith('# Gaps:'):
    line = line.split()
    gaps = line[2]

can be written like this

elif line.startswith('# Gaps:'):
    gaps = line.split()[2]

The same with these two:

if line.startswith('# 1:'):
    sequence_1 = line.split()[2]
elif line.startswith('# 2:'):
    sequence_2 = line.split()[2]

Variable Assignments

This

sequence_1 = ''
sequence_2 = ''
identity = ''
similarity = ''
gaps = ''
html_string = ''

can be written like this

sequence_1, sequence_2, identity, gaps, similarity, html_string = '', '', '', '', '', ''

Type Hints

You can use type hints to make it clear what is being accepted as parameters, and what is being returned by the function.

From this

def write_html(result):

to this

def write_html(result: str) -> None:

Docstrings

You should include a docstring at the beginning of every function, method, class, and module you write. This will allow documentation to identify what these are supposed to do.

def write_html(result: str) -> None:
    """
    (Description about this method here)
    """
    ... code here ...
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