schrodinger.seam.io.textio module

schrodinger.seam.io.textio.resolve_path(path_template: Union[str, Path]) Path

Resolve a path template containing $SEAM_JOBDIR to an actual path.

If SEAM_JOBDIR is set, it will be used as the base directory. Otherwise, falls back to the current working directory.

Parameters:

path_template – Path template potentially containing $SEAM_JOBDIR

Returns:

Resolved Path object.

schrodinger.seam.io.textio.move_to_finaldest(src_path: str, dest_path: str) str

Moves a file from a source path to a destination path using Beam’s filesystem abstractions. Expands environment variables in source path.

class schrodinger.seam.io.textio.WriteToText(file_name: str, header: Optional[str] = None, overwrite: bool = True, **kwargs)

Bases: _LocalOnlyPTransform, WriteToText

Write a PCollection of strings to a file.

This is meant as a replacement for beam’s WriteToText transform, which is doesn’t work in the Schrodinger environment due to a multiproc requirement.

Note: the header will only be written if the file overwrite is True.