The easiest way to interact with the BioLite catalog is using the catalog script packaged wit BioLite:
$ catalog -h
usage: catalog [-h] {insert,all,search,sizes} ...
Command-line tool for interacting with the agalma catalog.
agalma maintains a 'catalog' stored in an SQLite database of metadata
associated with your raw Illumina data, including:
- A unique ID that you make up to reference this data set.
- Paths to the FASTQ files containing the raw forward and reverse reads.
- The species name and NCBI ID.
- The sequencing center where the data was collected.
optional arguments:
-h, --help show this help message and exit
commands:
{insert,all,search,sizes}
insert Add a new record to the catalog, or overwrite the
existing record with the same id.
all List all catalog entries.
search Search all fields (except 'paths') for entries
matching the provided pattern, which can include * as
a wildcard.
sizes List all paths in the catalog, ordered by size on
disk.
The documentation below describes the catalog module, for manually interacting with the catalog from within a Python script.
The BioLite catalog table pairs metadata with the raw NGS data files (identified by their absolute path on disk). It includes the following:
The catalog acts as a bridge between the BioLite diagnostics and a more detailed laboratory information management system (LIMS) for tracking provenance of sample preparation and data collection upstream of and during sequencing. It contains the minimal context needed to associate diagnostics reports of downstream analyses with the raw sequence data, but without replicating or reimplementing the full functionality of a LIMS.
Bases: tuple
A named tuple for holding records from the catalog Table.
Alias for field number 5
Alias for field number 0
Alias for field number 4
Alias for field number 6
Alias for field number 7
Alias for field number 3
Alias for field number 11
Alias for field number 1
Alias for field number 12
Alias for field number 10
Alias for field number 9
Alias for field number 2
Alias for field number 13
Alias for field number 8
Insert or update a catalog entry, where keyword arguments specify the column/value pairs. If an entry for the given ID already exists, then the specified column/values pairs are used to update the entry. If the ID does not exist, a new entry is created with the specified values.
Returns a CatalogRecord object for the given catalog ID, or :keyword:None if the ID is not found in the catalog.
Yields a list of CatalogRecord objects for all entries in the catalog, ordered with the default ordering that SQLite provides.
Yields a list of CatalogRecord objects for all entries in the catalog with an indexed column matching the given search string. The indexed columns are all the columns in the catalog except paths.