Mercurial > repos > jackcurragh > trips_viz_create_annotation

changeset 6:8d47b5f57579 draft

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Uploaded
author jackcurragh
date Tue, 07 Jun 2022 11:33:55 +0000
parents cdecd5f9a4d3
children 3e35bcc7a778
files trips_create_annotation/create_annotation_sqlite.py trips_create_annotation/trips_create_annotation.xml
diffstat 2 files changed, 1 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/trips_create_annotation/create_annotation_sqlite.py	Fri May 27 10:14:09 2022 +0000
+++ b/trips_create_annotation/create_annotation_sqlite.py	Tue Jun 07 11:33:55 2022 +0000
@@ -6,11 +6,9 @@
 import sys
 import re
 import sqlite3
-import subprocess
 
-from intervaltree import Interval, IntervalTree
+from intervaltree import IntervalTree
 import itertools
-from sqlitedict import SqliteDict
 import os
 
 organism = sys.argv[1]
--- a/trips_create_annotation/trips_create_annotation.xml	Fri May 27 10:14:09 2022 +0000
+++ b/trips_create_annotation/trips_create_annotation.xml	Tue Jun 07 11:33:55 2022 +0000
@@ -1,8 +1,6 @@
 <tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
     <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
     <requirements>
-        <requirement type="package" version="0.19.0">pysam</requirement>
-        <requirement type="package" version="2.0.0">sqlitedict</requirement>
         <requirement type="package" version="3.37.1">sqlite</requirement>
         <requirement type="package" version="3.0.2">python-intervaltree</requirement>