Mercurial > repos > jackcurragh > trips_viz_create_annotation

comparison trips_create_annotation/create_annotation_sqlite.py @ 6:8d47b5f57579 draft

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author jackcurragh
date Tue, 07 Jun 2022 11:33:55 +0000
parents cdecd5f9a4d3
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5:cdecd5f9a4d3 6:8d47b5f57579
4 # All start codon positions (including cds_start) should be at the first nucleotide of the codon 4 # All start codon positions (including cds_start) should be at the first nucleotide of the codon
5 # All stop codon positions (including cds_stop) should be at the last nucleotide of the codon 5 # All stop codon positions (including cds_stop) should be at the last nucleotide of the codon
6 import sys 6 import sys
7 import re 7 import re
8 import sqlite3 8 import sqlite3
9 import subprocess 9
10 10 from intervaltree import IntervalTree
11 from intervaltree import Interval, IntervalTree
12 import itertools 11 import itertools
13 from sqlitedict import SqliteDict
14 import os 12 import os
15 13
16 organism = sys.argv[1] 14 organism = sys.argv[1]
17 # This should be a GTF or GFF3 file 15 # This should be a GTF or GFF3 file
18 annotation_file = open(sys.argv[2], "r") 16 annotation_file = open(sys.argv[2], "r")