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How to use the snakemake.io.AnnotatedString function in snakemake

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github epruesse / ymp / src / ymp / snakemake.py View on Github external
def format_annotated(self, item, expand_args):
        """Wrapper for :meth:format preserving *AnnotatedString* flags

        Calls :meth:format to format *item* into a new string and copies
        flags from original item.

        This is used by :meth:expand
        """
        updated = self.format(item, **expand_args)
        if isinstance(item, AnnotatedString):
            updated = AnnotatedString(updated)
            try:
                updated.flags = deepcopy(item.flags)
            except TypeError:
                log.debug(
                    "Failed to deepcopy flags for item {} with flags{}"
                    "".format(item, item.flags)
                )
            updated.flags = copy(item.flags)
        return updated
github epruesse / ymp / src / ymp / snakemake.py View on Github external
def format_annotated(self, item, expand_args):
        """Wrapper for :meth:format preserving *AnnotatedString* flags

        Calls :meth:format to format *item* into a new string and copies
        flags from original item.

        This is used by :meth:expand
        """
        updated = self.format(item, **expand_args)
        if isinstance(item, AnnotatedString):
            updated = AnnotatedString(updated)
            try:
                updated.flags = deepcopy(item.flags)
            except TypeError:
                log.debug(
                    "Failed to deepcopy flags for item {} with flags{}"
                    "".format(item, item.flags)
                )
            updated.flags = copy(item.flags)
        return updated

snakemake

Workflow management system to create reproducible and scalable data analyses

GitHub
MIT
Latest version published 11 days ago

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