SCRIdb.tools.sample_data_frame

SCRIdb.tools.sample_data_frame(sd)

Constructor for data frame with samples to be processed.

Parameters

sd (DataFrame) – Data frame of fastq samples processed by IGO and transferred to peerd drive. See example below.

Return type

DataFrame

Returns

A list of samples and other information from the database.

Example

>>> from SCRIdb.tools import *
>>> db_connect.conn(os.path.expanduser("~/.config.json"))
>>> f_in=[
            "Sample_CCR7_DC_1_IGO_10587_12",
            "Sample_CCR7_DC_2_IGO_10587_13",
            "Sample_CCR7_DC_3_IGO_10587_14",
            "Sample_CCR7_DC_4_IGO_10587_15"
    ]
>>> f_in = " ".join(f_in)
>>> source_path="/Volumes/peerd/FASTQ/Project_10587/MICHELLE_0194"
>>> target_path="s3://dp-lab-data/sc-seq/Project_10587"
>>> sd = pd.DataFrame(
        {
            "proj_folder": [source_path],
            "s3_loc": [target_path],
            "fastq": [f_in]
        }
    )
>>> sample_data_frame(sd)