Mercurial > repos > bimib > cobraxy
comparison COBRAxy/utils/general_utils.py @ 427:4a385fdb9e58 draft
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| author | francesco_lapi |
|---|---|
| date | Wed, 10 Sep 2025 11:38:08 +0000 |
| parents | ed2c1f9e20ba |
| children | a6e45049c1b9 |
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| 426:00a78da611ba | 427:4a385fdb9e58 |
|---|---|
| 502 | 502 |
| 503 Returns: | 503 Returns: |
| 504 List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas. | 504 List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas. |
| 505 """ | 505 """ |
| 506 with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:] | 506 with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:] |
| 507 | |
| 508 def findIdxByName(header: List[str], name: str, colName="name") -> Optional[int]: | |
| 509 """ | |
| 510 Find the indices of the 'ReactionID' column and a user-specified column name | |
| 511 within the header row of a tabular file. | |
| 512 | |
| 513 Args: | |
| 514 header (List[str]): The header row, as a list of column names. | |
| 515 name (str): The name of the column to look for (e.g. 'GPR'). | |
| 516 colName (str, optional): Label used in error messages for clarity. Defaults to "name". | |
| 517 | |
| 518 Returns: | |
| 519 Tuple[int, int]: A tuple containing: | |
| 520 - The index of the 'ReactionID' column. | |
| 521 - The index of the requested column `name`. | |
| 522 | |
| 523 Raises: | |
| 524 ValueError: If 'ReactionID' or the requested column `name` is not found in the header. | |
| 525 | |
| 526 Notes: | |
| 527 Both 'ReactionID' and the requested column are mandatory for downstream processing. | |
| 528 """ | |
| 529 | |
| 530 col_index = {col_name: idx for idx, col_name in enumerate(header)} | |
| 531 | |
| 532 if name not in col_index or "ReactionID" not in col_index: | |
| 533 raise ValueError(f"Tabular file must contain 'ReactionID' and {name} columns.") | |
| 534 | |
| 535 id_idx = col_index["ReactionID"] | |
| 536 idx_gpr = col_index[name] | |
| 537 | |
| 538 return id_idx, idx_gpr | |
| 539 | |
| 507 | 540 |
| 508 def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree: | 541 def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree: |
| 509 """ | 542 """ |
| 510 Reads the contents of a .svg file, which needs to exist at the given path. | 543 Reads the contents of a .svg file, which needs to exist at the given path. |
| 511 | 544 |