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Qualimap: address NBSP as thousand separators (#2282)
* Qualimap: address NBSP as thousand separators in rnaseqqc * [automated] Update CHANGELOG.md * Qualimap: address NBSP in BamQC as well * Fix changelog * Fix changelog * Determine decimal format once per file. Reuse function between BamQC and rnaseqqc submodules. More efficient parsing, only call re once per line * Handle error of mixed formats * Update multiqc/modules/qualimap/__init__.py Co-authored-by: Phil Ewels <phil.ewels@seqera.io> --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,94 @@ | ||
| import logging | ||
| from typing import Dict, Union | ||
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| from .qualimap import MultiqcModule | ||
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| __all__ = ["MultiqcModule"] | ||
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| log = logging.getLogger(__name__) | ||
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| def parse_numerals( | ||
| preparsed_d: Dict[str, str], | ||
| float_metrics: Dict[str, str], | ||
| int_metrics: Dict[str, str], | ||
| rate_metrics: Dict[str, str], | ||
| fpath: str, | ||
| ) -> Dict[str, Union[int, float, str]]: | ||
| """ | ||
| Take pre-parsed Qualimap report (keys to string values), and properly parse | ||
| numeral values, taking regional formats into account. | ||
| """ | ||
| # Determine if decimal separator is dot or comma | ||
| decimalcomma = None | ||
| for k in rate_metrics: | ||
| if k in preparsed_d: | ||
| val = preparsed_d[k] | ||
| if "," in val and "." in val: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as both . and , are " | ||
| f"found in a rational value: {val}" | ||
| ) | ||
| return {} | ||
| if "," in val: | ||
| if decimalcomma is False: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as differently formatted" | ||
| f"rational values are found" | ||
| ) | ||
| return {} | ||
| decimalcomma = True | ||
| if "." in val: | ||
| if decimalcomma is True: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as differently formatted" | ||
| f"rational values are found" | ||
| ) | ||
| return {} | ||
| decimalcomma = False | ||
| if decimalcomma is None: | ||
| # All expected float numbers are integer, so attempt to instead determine the | ||
| # thousands separator from large int values. | ||
| for k in int_metrics: | ||
| if k in preparsed_d: | ||
| val = preparsed_d[k] | ||
| if "," in val and "." in val: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as both . and , are " | ||
| f"found in a rational value: {val}" | ||
| ) | ||
| return {} | ||
| if "," in val: | ||
| if decimalcomma is True: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as differently formatted" | ||
| f"rational values are found" | ||
| ) | ||
| return {} | ||
| decimalcomma = False | ||
| if "." in val: | ||
| if decimalcomma is False: | ||
| log.error( | ||
| f"Couldn't determine decimal separator for file {fpath}, as differently formatted" | ||
| f"rational values are found" | ||
| ) | ||
| return {} | ||
| decimalcomma = True | ||
| if decimalcomma is None: | ||
| log.debug(f"Couldn't determine decimal separator for file {fpath}") | ||
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| d = {} | ||
| for k, v in preparsed_d.items(): | ||
| v = v.strip("X").strip("%") | ||
| if k in float_metrics or k in rate_metrics or k in int_metrics: | ||
| if decimalcomma is True: | ||
| v = v.replace(".", "").replace(",", ".") | ||
| v = v.replace(",", "") | ||
| if k in int_metrics: | ||
| d[int_metrics[k]] = int(v) | ||
| elif k in float_metrics: | ||
| d[float_metrics[k]] = float(v) | ||
| elif k in rate_metrics: | ||
| d[rate_metrics[k]] = float(v) | ||
|
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| return d |