Manual for isa-tab

cubi-tk isa-tab: ISA-tab tooling.

Sub Commands

validate
Validate ISA-tab files for correctness and perform sanity checks.
resolve-hpo
Resolve lists of HPO terms to TSV suitable for copy-and-paste into ISA-tab.
add-ped
Given a germline DNA sequencing ISA-tab file and a PED file, add new lines to the ISA-tab file and update existing ones, e.g., for newly added parents.
annotate
Add annotation to an ISA-tab file, given a tsv file.

Annotate

cubi-tk isa-tab annotate updates material and file nodes in ISA-tab studies and assays with annotations provided as tab-separated text file.

In the annotation file header, target node types need to be indicated in ISA-tab style (i.e. “Source Name”, etc.) while annotations are just named normally. Annotations for materials are automatically recorded as Characteristics, while annotations for files are recorded as Comments. Different node types can be annotated using only one annotation file, as demonstrated in the example below.

By default, if Characteristics or Comments with the same name already exist for a node type, only empty values are updated. Overwriting existing values requires confirmation (–force-update).

Annotations are only applied to one study and assay, since material names are not necessarily unique between the same material types of different studies or different assays (and thus, annotations couldn’t be assigned unambiguously). By default the first study and assay listed in the investigation file are considered for annotation. A specific study and assay may be selected by file name (not path, just as listed in the investigation file) via –target-study or –target-assay, resp.

Example execution:

$ cubi-tk isa-tab annotate investigation.tsv annotation.tsv --target-study s_study.tsv
--target-assay a_assay.tsv

Note: investigation.tsv and annotation.tsv have to be indicated via absolute or relative paths. However, s_study.tsv and a_assay.tsv have to be indicated by name only, just as they are referenced in their corresponding investigation file.

Annotation example tsv file
Source Name Age Sex Sample Name Volume
alpha 18 FEMALE alpha-N1 1000
beta 27 MALE beta-N1 1000
gamma 69 FEMALE gamma-N1 800

More Information

Also see cubi-tk isa-tab CLI documentation and cubi-tk isa-tab --help for more information.