From e2d43806dc0e9f56677c0d2f75d741e6637bffc5 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 16 Mar 2022 15:13:40 +0100 Subject: [PATCH] Fix ``sff_extract`` tool, drop type annotation I don't think this tool is really used much, but it is loaded in `tool_conf.xml`. https://github.com/galaxyproject/galaxy/pull/11877 added type annotations, and that's a syntax error on 2.7 The alternative would be to fix the rest of the tool for 3.x, but I think we're just wasting our time there and we shouldn't touch this again. --- tools/filters/sff_extract.py | 5 ++--- tools/filters/sff_extractor.xml | 2 -- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/tools/filters/sff_extract.py b/tools/filters/sff_extract.py index ddc3c8fd280..a1d9435d66a 100644 --- a/tools/filters/sff_extract.py +++ b/tools/filters/sff_extract.py @@ -31,7 +31,6 @@ import struct import subprocess import sys import tempfile -from typing import Dict, List __author__ = 'Jose Blanca and Bastien Chevreux' __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux' @@ -43,9 +42,9 @@ __status__ = 'beta' fake_sff_name = 'fake_sff_name' # readname as key: lines with matches from SSAHA, one best match -ssahapematches: Dict[str, List] = {} +ssahapematches = {} # type: ignore # linker readname as key: length of linker sequence -linkerlengths: Dict[str, int] = {} +linkerlengths = {} # type: ignore # set to true if something really fishy is going on with the sequences stern_warning = True diff --git a/tools/filters/sff_extractor.xml b/tools/filters/sff_extractor.xml index d26b6e5ca2e..236669327dd 100644 --- a/tools/filters/sff_extractor.xml +++ b/tools/filters/sff_extractor.xml @@ -57,5 +57,3 @@ Clippings (XML) - -