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Retrieves isolation sources from NCBI given the set of sequences with specified accession numbers. Both nucleotide and protein accessions are accepted.

Project description

**GetIsolationSources** is a small command line utility that, given fasta files containing GenBank IDs in sequence descriptions, generates a per sequence list of isolation sources and their distribution (i.e. number of sequences per isolation source).

It searches for IDs using regular expressions in accordance with [NCBI specifications](http://www.ncbi.nlm.nih.gov/Sequin/acc.html), so the format of description strings does not matter.

To obtain needed information it uses automated Entrez queries, so you need a working Internet connection to perform the analysis. Queries are made in accordance with NCBI load-balance regulations, therefore processing several thousand records may take several minutes or even longer.

It is distributed as a source code supporting python setup tools.

**GetIsolationSources uses [BioPython](http://biopython.org/wiki/Main_Page).** So if you're using source code distribution, the latest version of [BioPython](http://biopython.org/wiki/Main_Page) should be installed.

[**Downaloads**](https://github.com/allista/GetIsolationSource/releases)

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**GetIsolationSources** by [**Allis Tauri**](https://github.com/allista) is licensed under the [MIT](https://github.com/allista/GetIsolationSources/blob/master/LICENSE) license.

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
GetIsolationSources-1.5.2.tar.gz (7.4 kB) Copy SHA256 hash SHA256 Source None Jul 11, 2017

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