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Clarify pseudocigar_chrom_col docs when no full location is set #95

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Clarify pseudocigar_chrom_col docs when no full location is set #95

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9 changes: 5 additions & 4 deletions src/pmotools/pmo_builder/mhap_table_to_pmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ def mhap_table_to_pmo(
:type microhaplotype_name_col: str, optional
:param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
:type pseudocigar_col: str, optional
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col. chrom_col can only be set together with start_col and end_col, so use pseudocigar_chrom_col when there is no full microhaplotype location
:type pseudocigar_chrom_col: str, optional
:param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
:type pseudocigar_start_col: str, optional
Expand Down Expand Up @@ -233,7 +233,7 @@ def create_representative_microhaplotype_dict(
:type microhaplotype_name_col: str, optional
:param pseudocigar_col: the name of the column containing a pseudocigar for the microhaplotype
:type pseudocigar_col: str, optional
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col
:param pseudocigar_chrom_col: column for the pseudocigar ref_loc chromosome; defaults to chrom_col. chrom_col can only be set together with start_col and end_col, so use pseudocigar_chrom_col when there is no full microhaplotype location
:type pseudocigar_chrom_col: str, optional
:param pseudocigar_start_col: column for the pseudocigar ref_loc start (required if pseudocigar_col is set)
:type pseudocigar_start_col: str, optional
Expand Down Expand Up @@ -273,8 +273,9 @@ def create_representative_microhaplotype_dict(
):
raise ValueError(
"pseudocigar_col is set, so a Pseudocigar ref_loc must be "
"constructable: set a chromosome (pseudocigar_chrom_col or "
"chrom_col), pseudocigar_start_col, and pseudocigar_end_col."
"constructable: set a chromosome (pseudocigar_chrom_col, or "
"chrom_col together with start_col and end_col), "
"pseudocigar_start_col, and pseudocigar_end_col."
)

def get_if_present(row, col):
Expand Down
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