GOLDEN

1. Intro

Golden is a small databanks entries retriever. It searches and displays entries on indexed databanks `flat' files.

This package currently contains the following programs : golden ... Entries retriever. goldin ... Indexes generator.

Queries/Indexes can be made using entry name, primary accession numbers or even both (by default).

Currently supported formats : Genbank, Embl, Pir codata, and assimiled.

2. Installation

To install golden and goldin just do :

./configure
make
[sudo] make install

golden functionalities can also be exported to python (in order to be called from your python script). In order to do that, you must of course have python installed on your machine.

These python "bindings" or "exports" were tested with python 2.7 up to python 3.11.

They are available on PyPi (for python3 only). To install them, just do (after installing python):

pip3 install --user golden-seq-retriever

You must then export the GOLDENDATA environment variable to point to where the indexes are.

3. Use of golden bindings from a python script

There are 2 functions that allow to perform queries:

• access to query a single entry.

• access_multi to query multiple entries. Am "EntryIterator" is provided in order to iterate over all retrieved entries.

For a matter of performance, access_multi must be preferred if you have more than 1 entry to retrive. Below is a small example

import Golden
Golden.access("uniprot:A0A6C0J8N5")

for a single query

import entryIterator
it=entryIterator.entryIterator("uniprot:A0A6C0J8N5 uniprot:A0A6C0BRH4 uniprot:A0A6C0BRH4")
for entry in it:
    print(entry)

to make it easy to iterate over retrieved entries. Or

import Golden
entries_str=access_multi("uniprot:A0A6C0J8N5\nuniprot:A0A6C0BRH4\nuniprot:A0A6C0BRH4\n")
print(entries_str)

to get back a character string containing all entries.

Any remark/suggestion/problem should be reported to [email protected].