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        "description": "# ddgen\n\n[![Build Status](https://travis-ci.org/ielis/ddgen.svg?branch=master)](https://travis-ci.org/ielis/ddgen)\n[![PyPI version](https://badge.fury.io/py/ddgen.svg)](https://badge.fury.io/py/ddgen)\n\nLibrary of Python utilities that I needed so many times in the past\n\n\n## Select RefSeq transcript with the highest priority\n\nRefSeq transcripts have following categories: \n- `NM_`, `XM_`, `NR_`, `XR_`\n\nIf we have transcripts from multiple sources, we want to select the one coming from the source with highest priority.\n> E.g. `NM_` has higher priority than `XM_`.\n\nIf we have multiple transcripts from a single source, we want to select the one with smaller integer.\n> E.g. `NM_123.4` has higher priority than `NM_124.4`.\n\n```python\nfrom ddgen.utils import prioritize_refseq_transcripts\n\n# tx will be `NM_123.4`\ntx = prioritize_refseq_transcripts(['NM_123.4', 'NM_124.4', 'XM_100.1'])\n```\n\n\n## Get priority for *Jannovar* variant effects\n\nJannovar assigns one or more effects to a variant. The effects look like\n- `MISSENSE_VARIANT`,\n- `STOP_GAINED`,\n- `SPLICE_DONOR_VARIANT`,\n- `CODING_TRANSCRIPT_VARIANT`, etc.\n\nThe effects are sorted in order of decreasing putative pathogenicity (i.e. `CODING_TRANSCRIPT_VARIANT` is likely to be less deleterious than `STOP_GAINED` in general).\n\nIf the variant affects multiple transcripts, it can have different effects on each of them. In some situations, it might be useful to select and evaluate only the most serious effect.\n\nIn order to make the selection, we work with concept of variant effect *priority*. The lower the number representing the priority, the higher the priority.\n\nWe can do it by comparing effect priorities:\n```python\nfrom ddgen.utils import get_variant_effect_priority, VARIANT_EFFECT_PRIORITIES\n\n# `p` is 21 \np = get_variant_effect_priority('MISSENSE_VARIANT')\n\n# `u` is -1\nu = get_variant_effect_priority('GIBBERISH')\n\n# `p` is 21 again\np = VARIANT_EFFECT_PRIORITIES['MISSENSE_VARIANT']\n```\n\n\n## Connect to H2 database\n\nThe H2 database is a pure Java SQL database, hence it is primarily meant to be used with Java.\nWe can connect to the database from Python, if:\n\n- Java is installed on the local machine\n- the local machine runs UNIX-like OS (sorry, Windows users)\n\nIn that case:\n```python\nfrom ddgen.db import H2DbManager\n\nwith H2DbManager(\"path/to/database.mv.db\", \n                 user=\"sa\", \n                 password=\"sa\") as h2:\n    with h2.get_connection() as conn:\n        with conn.cursor() as cur:\n            # do whatever you want with the connection/cursor\n            cur.execute('SELECT * FROM DB.TABLE;')\n            for i, x in zip(range(5), cur.fetchall()):\n                # print first 5 lines \n                print(x)\n```\n\n## Setup logging\n\nQuick setup of Python built-in `logging` library:\n\n```python\nfrom ddgen.utils import setup_logging\nsetup_logging()\n```\n\n\n",
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