diff options
Diffstat (limited to 'gn3/csvcmp.py')
| -rw-r--r-- | gn3/csvcmp.py | 64 |
1 files changed, 36 insertions, 28 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index ac09cc3..82d74d0 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -1,50 +1,59 @@ +"""This module contains functions for manipulating and working with csv +texts""" import json import os import uuid from gn3.commands import run_cmd -def extract_strain_name(csv_header, data, seek="Strain Name"): +def extract_strain_name(csv_header, data, seek="Strain Name") -> str: + """Extract a strain's name given a csv header""" for column, value in zip(csv_header.split(","), data.split(",")): if seek in column: return value return "" -def create_dirs_if_not_exists(dirs: list): +def create_dirs_if_not_exists(dirs: list) -> None: + """Create directories from a list""" for dir_ in dirs: if not os.path.exists(dir_): os.makedirs(dir_) def remove_insignificant_edits(diff_data, epsilon=0.001): - _mod = [] + """Remove or ignore edits that are not within ε""" + __mod = [] for mod in diff_data.get("Modifications"): original = mod.get("Original").split(",") current = mod.get("Current").split(",") - for i, (x, y) in enumerate(zip(original, current)): - if (x.replace('.', '').isdigit() and - y.replace('.', '').isdigit() and - abs(float(x) - float(y)) < epsilon): - current[i] = x + for i, (_x, _y) in enumerate(zip(original, current)): + if ( + _x.replace(".", "").isdigit() + and _y.replace(".", "").isdigit() + and abs(float(_x) - float(_y)) < epsilon + ): + current[i] = _x if not (__o := ",".join(original)) == (__c := ",".join(current)): - _mod.append({ - "Original": __o, - "Current": __c, - }) - diff_data['Modifications'] = _mod + __mod.append( + { + "Original": __o, + "Current": __c, + } + ) + diff_data["Modifications"] = __mod return diff_data -def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"): +def csv_diff(base_csv, delta_csv, tmp_dir="/tmp") -> dict: + """Diff 2 csv strings""" base_csv_list = base_csv.strip().split("\n") delta_csv_list = delta_csv.strip().split("\n") - base_csv_header, delta_csv_header, header = "", "", "" + base_csv_header, delta_csv_header = "", "" for i, line in enumerate(base_csv_list): if line.startswith("Strain Name,Value,SE,Count"): - header = line - base_csv_header, delta_csv_header= line, delta_csv_list[i] + base_csv_header, delta_csv_header = line, delta_csv_list[i] break longest_header = max(base_csv_header, delta_csv_header) @@ -53,22 +62,21 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"): base_csv = base_csv.replace("Strain Name,Value,SE,Count", longest_header, 1) else: - delta_csv = delta_csv.replace("Strain Name,Value,SE,Count", - longest_header, 1) + delta_csv = delta_csv.replace( + "Strain Name,Value,SE,Count", longest_header, 1 + ) file_name1 = os.path.join(tmp_dir, str(uuid.uuid4())) file_name2 = os.path.join(tmp_dir, str(uuid.uuid4())) - with open(file_name1, "w") as f_: + with open(file_name1, "w", encoding="utf-8") as _f: _l = len(longest_header.split(",")) - f_.write(fill_csv(csv_text=base_csv, - width=_l)) - with open(file_name2, "w") as f_: - f_.write(fill_csv(delta_csv, - width=_l)) + _f.write(fill_csv(csv_text=base_csv, width=_l)) + with open(file_name2, "w", encoding="utf-8") as _f: + _f.write(fill_csv(delta_csv, width=_l)) # Now we can run the diff! _r = run_cmd(cmd=('"csvdiff ' - f'{file_name1} {file_name2} ' + f"{file_name1} {file_name2} " '--format json"')) if _r.get("code") == 0: _r = json.loads(_r.get("output")) @@ -86,6 +94,7 @@ def csv_diff(base_csv, delta_csv, tmp_dir="/tmp"): def fill_csv(csv_text, width, value="x"): + """Fill a csv text with 'value' if it's length is less than width""" data = [] for line in csv_text.strip().split("\n"): if line.startswith("Strain") or line.startswith("#"): @@ -95,6 +104,5 @@ def fill_csv(csv_text, width, value="x"): for i, val in enumerate(_n): if not val.strip(): _n[i] = value - data.append( - ",".join(_n + [value] * (width - len(_n)))) + data.append(",".join(_n + [value] * (width - len(_n)))) return "\n".join(data) |