Values Embedded in Other Values

Scenario

You have a column of file names that secretly also contain other values like specimen ID and sequencing library.

File Name
BSID1234_SL1234.bam
BSID1235_SL1235.bam
BSID1236_SL1236.bam
BSID1237_SL1237.bam

Correct Output

BIOSPECIMEN.ID	SEQUENCING.LIBRARY_NAME	GENOMIC_FILE.FILE_NAME
BSID1234	SL1234	BSID1234_SL1234.bam
BSID1235	SL1235	BSID1235_SL1235.bam
BSID1236	SL1236	BSID1236_SL1236.bam
BSID1237	SL1237	BSID1237_SL1237.bam

Solution with Regular Expressions

operations = [
    keep_map(
        in_col="File Name",
        out_col=CONCEPT.GENOMIC_FILE.FILE_NAME
    ),
    value_map(
        in_col="File Name",
        out_col=CONCEPT.BIOSPECIMEN.ID,
        m=r'^([^_]+).+$'
    ),
    value_map(
        in_col="File Name",
        out_col=CONCEPT.SEQUENCING.LIBRARY_NAME,
        m=r'^[^_]+_(.+)$'
    )
]

Solution with Functions

operations = [
    keep_map(
        in_col="File Name",
        out_col=CONCEPT.GENOMIC_FILE.FILE_NAME
    ),
    value_map(
        in_col="File Name",
        out_col=CONCEPT.BIOSPECIMEN.ID,
        m=lambda x: x.split('_')[0]
    ),
    value_map(
        in_col="File Name",
        out_col=CONCEPT.SEQUENCING.LIBRARY_NAME,
        m=lambda x: x.split('_')[1].split('.')[0]
    )
]