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.
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.