feat: use primer3-py for primer3 instead of the executable #101
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| @@ -208,7 +208,7 @@ def __str__(self) -> str: | |||
| """ | |||
| # If the bases field is None, replace with MISSING_BASES_STRING | |||
| bases: str = self.bases if self.bases is not None else MISSING_BASES_STRING | |||
| return f"{bases}\t{self.tm}\t{self.penalty}\t{self.span}" | |||
| return f"{bases}\t{self.tm:.2f}\t{self.penalty:.2f}\t{self.span}" | |||
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #101 +/- ##
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Coverage ? 96.87%
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Files ? 26
Lines ? 1695
Branches ? 184
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Hits ? 1642
Misses ? 31
Partials ? 22 ☔ View full report in Codecov by Sentry. |
| for tag, value in assembled_primer3_tags.items(): | ||
| tag_str = f"{tag}" | ||
| if tag_str.startswith("SEQUENCE"): | ||
| seq_args[tag_str] = value | ||
| else: | ||
| global_args[tag] = value |
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This works ... but I think we could probably also add a is_global_arg() to Primer3InputTag that does this more efficiently (e.g. based on ordinal) or split Primer3InputTag into two classes - one for globals and one for sequence tags?
| for key, value in design_primers_retval.items(): | ||
| # Because Primer3 will emit both the input given and the output generated, we | ||
| # discard the input that is echo'ed back by looking for tags (keys) | ||
| # that do not match any Primer3InputTag | ||
| if not any(key == item.value for item in Primer3InputTag): | ||
| primer3_results[key] = value |
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Is this actually needed? I don't think there's any harm in allow the inputs to be present in the dict() used below.
If you feel strongly about this .. perhaps we have a more efficient way than looping through all the values in Primer3InputTag - e.g. create a _ALL_INPUT_TAG_STRINGS set and at the class level and check for membership?
| def primer3_error(message: str) -> None: | ||
| """Formats the Primer3 error and raises a ValueError.""" | ||
| error_message = f"{message}: " | ||
| # add in any reported PRIMER_ERROR | ||
| if "PRIMER_ERROR" in primer3_results: | ||
| error_message += primer3_results["PRIMER_ERROR"] | ||
| # add in any error lines | ||
| if len(error_lines) > 0: | ||
| error_message += "\n".join(f"\t\t{e}" for e in error_lines) | ||
| # raise the exception now | ||
| raise ValueError(error_message) |
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I think this can be inline at the single call site now?
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