How to parse complex text files using Python?

Question

I'm looking for a simple way of parsing complex text files into a pandas DataFrame. Below is a sample file, what I want the result to look like after parsing, and my current method.

Is there any way to make it more concise/faster/more pythonic/more readable?

I've also put this question on Code Review.

I eventually wrote a blog article to explain this to beginners.

Here is a sample file:

Sample text

A selection of students from Riverdale High and Hogwarts took part in a quiz. This is a record of their scores.

School = Riverdale High
Grade = 1
Student number, Name
0, Phoebe
1, Rachel

Student number, Score
0, 3
1, 7

Grade = 2
Student number, Name
0, Angela
1, Tristan
2, Aurora

Student number, Score
0, 6
1, 3
2, 9

School = Hogwarts
Grade = 1
Student number, Name
0, Ginny
1, Luna

Student number, Score
0, 8
1, 7

Grade = 2
Student number, Name
0, Harry
1, Hermione

Student number, Score
0, 5
1, 10

Grade = 3
Student number, Name
0, Fred
1, George

Student number, Score
0, 0
1, 0

Here is what I want the result to look like after parsing:

                                         Name  Score
School         Grade Student number                 
Hogwarts       1     0                  Ginny      8
                     1                   Luna      7
               2     0                  Harry      5
                     1               Hermione     10
               3     0                   Fred      0
                     1                 George      0
Riverdale High 1     0                 Phoebe      3
                     1                 Rachel      7
               2     0                 Angela      6
                     1                Tristan      3
                     2                 Aurora      9

Here is how I currently parse it:

import re
import pandas as pd


def parse(filepath):
    """
    Parse text at given filepath

    Parameters
    ----------
    filepath : str
        Filepath for file to be parsed

    Returns
    -------
    data : pd.DataFrame
        Parsed data

    """

    data = []
    with open(filepath, 'r') as file:
        line = file.readline()
        while line:
            reg_match = _RegExLib(line)

            if reg_match.school:
                school = reg_match.school.group(1)

            if reg_match.grade:
                grade = reg_match.grade.group(1)
                grade = int(grade)

            if reg_match.name_score:
                value_type = reg_match.name_score.group(1)
                line = file.readline()
                while line.strip():
                    number, value = line.strip().split(',')
                    value = value.strip()
                    dict_of_data = {
                        'School': school,
                        'Grade': grade,
                        'Student number': number,
                        value_type: value
                    }
                    data.append(dict_of_data)
                    line = file.readline()

            line = file.readline()

        data = pd.DataFrame(data)
        data.set_index(['School', 'Grade', 'Student number'], inplace=True)
        # consolidate df to remove nans
        data = data.groupby(level=data.index.names).first()
        # upgrade Score from float to integer
        data = data.apply(pd.to_numeric, errors='ignore')
    return data


class _RegExLib:
    """Set up regular expressions"""
    # use https://regexper.com to visualise these if required
    _reg_school = re.compile('School = (.*)\n')
    _reg_grade = re.compile('Grade = (.*)\n')
    _reg_name_score = re.compile('(Name|Score)')

    def __init__(self, line):
        # check whether line has a positive match with all of the regular expressions
        self.school = self._reg_school.match(line)
        self.grade = self._reg_grade.match(line)
        self.name_score = self._reg_name_score.search(line)


if __name__ == '__main__':
    filepath = 'sample.txt'
    data = parse(filepath)
    print(data)

Solution 1

Update 2019 (PEG parser):

This answer has received quite some attention so I felt to add another possibility, namely a parsing option. Here we could use a PEG parser instead (e.g. parsimonious) in combination with a NodeVisitor class:

from parsimonious.grammar import Grammar
from parsimonious.nodes import NodeVisitor
import pandas as pd
grammar = Grammar(
    r"""
    schools         = (school_block / ws)+

    school_block    = school_header ws grade_block+ 
    grade_block     = grade_header ws name_header ws (number_name)+ ws score_header ws (number_score)+ ws? 

    school_header   = ~"^School = (.*)"m
    grade_header    = ~"^Grade = (\d+)"m
    name_header     = "Student number, Name"
    score_header    = "Student number, Score"

    number_name     = index comma name ws
    number_score    = index comma score ws

    comma           = ws? "," ws?

    index           = number+
    score           = number+

    number          = ~"\d+"
    name            = ~"[A-Z]\w+"
    ws              = ~"\s*"
    """
)

tree = grammar.parse(data)

class SchoolVisitor(NodeVisitor):
    output, names = ([], [])
    current_school, current_grade = None, None

    def _getName(self, idx):
        for index, name in self.names:
            if index == idx:
                return name

    def generic_visit(self, node, visited_children):
        return node.text or visited_children

    def visit_school_header(self, node, children):
        self.current_school = node.match.group(1)

    def visit_grade_header(self, node, children):
        self.current_grade = node.match.group(1)
        self.names = []

    def visit_number_name(self, node, children):
        index, name = None, None
        for child in node.children:
            if child.expr.name == 'name':
                name = child.text
            elif child.expr.name == 'index':
                index = child.text

        self.names.append((index, name))

    def visit_number_score(self, node, children):
        index, score = None, None
        for child in node.children:
            if child.expr.name == 'index':
                index = child.text
            elif child.expr.name == 'score':
                score = child.text

        name = self._getName(index)

        # build the entire entry
        entry = (self.current_school, self.current_grade, index, name, score)
        self.output.append(entry)

sv = SchoolVisitor()
sv.visit(tree)

df = pd.DataFrame.from_records(sv.output, columns = ['School', 'Grade', 'Student number', 'Name', 'Score'])
print(df)

---

Regex option (original answer)

Well then, watching Lord of the Rings the xth time, I had to bridge some time to the very finale:

---

1. Separate each school
2. ... each grade
3. ... student and scores
4. ... bind them together in a dataframe afterwards

---

a demo on regex101.com

^
School\s*=\s*(?P<school_name>.+)
(?P<school_content>[\s\S]+?)
(?=^School|\Z)

---

another demo on regex101.com

^
Grade\s*=\s*(?P<grade>.+)
(?P<students>[\s\S]+?)
(?=^Grade|\Z)

---

last demo on regex101.com

^
Student\ number,\ Name[\n\r]
(?P<student_names>(?:^\d+.+[\n\r])+)
\s*
^
Student\ number,\ Score[\n\r]
(?P<student_scores>(?:^\d+.+[\n\r])+)

The rest is a generator expression which is then fed into the DataFrame constructor (along with the column names).

---

import pandas as pd, re

rx_school = re.compile(r'''
    ^
    School\s*=\s*(?P<school_name>.+)
    (?P<school_content>[\s\S]+?)
    (?=^School|\Z)
''', re.MULTILINE | re.VERBOSE)

rx_grade = re.compile(r'''
    ^
    Grade\s*=\s*(?P<grade>.+)
    (?P<students>[\s\S]+?)
    (?=^Grade|\Z)
''', re.MULTILINE | re.VERBOSE)

rx_student_score = re.compile(r'''
    ^
    Student\ number,\ Name[\n\r]
    (?P<student_names>(?:^\d+.+[\n\r])+)
    \s*
    ^
    Student\ number,\ Score[\n\r]
    (?P<student_scores>(?:^\d+.+[\n\r])+)
''', re.MULTILINE | re.VERBOSE)


result = ((school.group('school_name'), grade.group('grade'), student_number, name, score)
    for school in rx_school.finditer(string)
    for grade in rx_grade.finditer(school.group('school_content'))
    for student_score in rx_student_score.finditer(grade.group('students'))
    for student in zip(student_score.group('student_names')[:-1].split("\n"), student_score.group('student_scores')[:-1].split("\n"))
    for student_number in [student[0].split(", ")[0]]
    for name in [student[0].split(", ")[1]]
    for score in [student[1].split(", ")[1]]
)

df = pd.DataFrame(result, columns = ['School', 'Grade', 'Student number', 'Name', 'Score'])
print(df)

---

rx_school = re.compile(r'^School\s*=\s*(?P<school_name>.+)(?P<school_content>[\s\S]+?)(?=^School|\Z)', re.MULTILINE)
rx_grade = re.compile(r'^Grade\s*=\s*(?P<grade>.+)(?P<students>[\s\S]+?)(?=^Grade|\Z)', re.MULTILINE)
rx_student_score = re.compile(r'^Student number, Name[\n\r](?P<student_names>(?:^\d+.+[\n\r])+)\s*^Student number, Score[\n\r](?P<student_scores>(?:^\d+.+[\n\r])+)', re.MULTILINE)

---

            School Grade Student number      Name Score
0   Riverdale High     1              0    Phoebe     3
1   Riverdale High     1              1    Rachel     7
2   Riverdale High     2              0    Angela     6
3   Riverdale High     2              1   Tristan     3
4   Riverdale High     2              2    Aurora     9
5         Hogwarts     1              0     Ginny     8
6         Hogwarts     1              1      Luna     7
7         Hogwarts     2              0     Harry     5
8         Hogwarts     2              1  Hermione    10
9         Hogwarts     3              0      Fred     0
10        Hogwarts     3              1    George     0

---

timing

import timeit
print(timeit.timeit(makedf, number=10**4))
# 11.918397722000009 s

---

Solution 2

here is my suggestion using split and pd.concat ("txt" stands for a copy of the original text in the question), basicly the idea is to split by the group words and then concat into data frames, the most inner parsing takes advantage of the fact that the names and grades are in a csv like format. here goes:

import pandas as pd
from io import StringIO

schools = txt.lower().split('school = ')
schools_dfs = []
for school in schools[1:]:
    grades = school.split('grade = ') 
    grades_dfs = []
    for grade in grades[1:]:
        features = grade.split('student number,')
        feature_dfs = []
        for feature in features[1:]:
            feature_dfs.append(pd.read_csv(StringIO(feature)))
        feature_df = pd.concat(feature_dfs, axis=1)
        feature_df['grade'] = features[0].replace('\n','')
        grades_dfs.append(feature_df)
    grades_df = pd.concat(grades_dfs)
    grades_df['school'] = grades[0].replace('\n','')
    schools_dfs.append(grades_df)
schools_df = pd.concat(schools_dfs)

schools_df.set_index(['school', 'grade'])

Solution 3

I would suggest using a parser combinator library like parsy. Compared to using regexes, the result will not be as concise, but it will be much more readable and robust, while still being relatively light-weight.

Parsing is in general quite a hard task, and an approach that is good for people at beginner level for general programming might be hard to find.

EDIT: Some actual example code that does minimal parsing of your supplied example. It does not pass to pandas, or even match up names to scores, or students to grades etc. - it just returns a hierarchy of objects starting with School at the top, with the relevant attributes as you would expect:

from parsy import string, regex, seq
import attr


@attr.s
class Student():
    name = attr.ib()
    number = attr.ib()


@attr.s
class Score():
    score = attr.ib()
    number = attr.ib()


@attr.s
class Grade():
    grade = attr.ib()
    students = attr.ib()
    scores = attr.ib()


@attr.s
class School():
    name = attr.ib()
    grades = attr.ib()


integer = regex(r"\d+").map(int)
student_number = integer
score = integer
student_name = regex(r"[^\n]+")
student_def = seq(student_number.tag('number') << string(", "),
                  student_name.tag('name') << string("\n")).combine_dict(Student)
student_def_list = string("Student number, Name\n") >> student_def.many()
score_def = seq(student_number.tag('number') << string(", "),
                score.tag('score') << string("\n")).combine_dict(Score)
score_def_list = string("Student number, Score\n") >> score_def.many()
grade_value = integer
grade_def = string("Grade = ") >> grade_value << string("\n")
school_grade = seq(grade_def.tag('grade'),
                   student_def_list.tag('students') << regex(r"\n*"),
                   score_def_list.tag('scores') << regex(r"\n*")
                   ).combine_dict(Grade)

school_name = regex(r"[^\n]+")
school_def = string("School = ") >> school_name << string("\n")
school = seq(school_def.tag('name'),
             school_grade.many().tag('grades')
             ).combine_dict(School)


def parse(text):
    return school.many().parse(text)

This is much more verbose than a regex solution, but much closer to a declarative definition of your file format.

Solution 4

In a similar manner to your original code I define the parsing regex's

import re
import pandas as pd

parse_re = {
    'school': re.compile(r'School = (?P<school>.*)$'),
    'grade': re.compile(r'Grade = (?P<grade>\d+)'),
    'student': re.compile(r'Student number, (?P<info>\w+)'),
    'data': re.compile(r'(?P<number>\d+), (?P<value>.*)$'),
}

def parse(line):
    '''parse the line by regex search against possible line formats
       returning the id and match result of first matching regex,
       or None if no match is found'''
    return reduce(lambda (i,m),(id,rx): (i,m) if m else (id, rx.search(line)), 
                  parse_re.items(), (None,None))

then loop through the lines gathering the information about each student. Once the record is complete (when we have Score the record is complete) we append the record to a list.

A small state machine that is driven by the line by line regex matches collates each record. In particular we have to save the students in a grade by number as their Score and Name are provided separately in the input file.

results = []
with open('sample.txt') as f:
    record = {}
    for line in f:
        id, match = parse(line)

        if match is None:
            continue

        if id == 'school':
            record['School'] = match.group('school')
        elif id == 'grade':
            record['Grade'] = int(match.group('grade'))
            names = {}  # names is a number indexed dictionary of student names
        elif id == 'student':
            info = match.group('info')
        elif id == 'data':
            number = int(match.group('number'))
            value = match.group('value')
            if info == 'Name':
                names[number] = value
            elif info == 'Score':
                record['Student number'] = number
                record['Name'] = names[number]
                record['Score'] = int(value)
                results.append(record.copy())

Finally the list of records is converted to a DataFrame.

df = pd.DataFrame(results, columns=['School', 'Grade', 'Student number', 'Name', 'Score'])
print df

Outputs:

            School  Grade  Student number      Name  Score
0   Riverdale High      1               0    Phoebe      3
1   Riverdale High      1               1    Rachel      7
2   Riverdale High      2               0    Angela      6
3   Riverdale High      2               1   Tristan      3
4   Riverdale High      2               2    Aurora      9
5         Hogwarts      1               0     Ginny      8
6         Hogwarts      1               1      Luna      7
7         Hogwarts      2               0     Harry      5
8         Hogwarts      2               1  Hermione     10
9         Hogwarts      3               0      Fred      0
10        Hogwarts      3               1    George      0

Some optimizations would be to compare the most common regex's first and to explicitly skip blank lines. Building the dataframe as we go would avoid extra copies of the data but I gather that appending to a dataframe is an expensive operation.

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