iu_get_accessions

Use this script when there are records on the IGVF Portal for which you know their aliases, but want to retreive their DACC accessions. This will only work if the record aliases you provided are registered with the records on the IGVF Portal. Note that if the particular DACC profile at hand doesn’t support the accession property, then the uuid will be returned.

usage: iu_get_accessions.py [-h] [-m IGVF_MODE] -i INFILE -o OUTFILE
                            [-l SUBMITTER_LAB]

Named Arguments

-m, --igvf-mode

The IGVF Portal site (‘prod’, ‘sandbox’, ‘staging, or an explicit host name, i.e. ‘*.demo.igvf.org’) to connect to.

-i, --infile

Input file containing record aliases (one per line). Empty lines and lines beginning with a ‘#’ will be ignored.

-o, --outfile

The output file, which is in the same as the input file except for the addition of the tab-delimited columns - one for each alias.

-l, --submitter-lab

The submitting lab alias prefix (i.e. michael-snyder) for these aliases. No need to set this option if your input file’s aliases are already prefixed with the submitting lab. Furthermore, for any aliases lacking the prefix, the default will be taken from the IGVF_LAB environment variable if not set here.