From d210346aff0d021170cc9525eb1be99c8d8172c4 Mon Sep 17 00:00:00 2001 From: Torsten Seemann Date: Sat, 14 Feb 2015 18:14:52 +1100 Subject: [PATCH] Remove achievements from TODO list --- doc/ToDoList.txt | 5 ----- 1 file changed, 5 deletions(-) diff --git a/doc/ToDoList.txt b/doc/ToDoList.txt index af07b7c..49d75ab 100644 --- a/doc/ToDoList.txt +++ b/doc/ToDoList.txt @@ -2,7 +2,6 @@ Prokka Wishlist --------------- -* New --hmms option to prioritise a custom HMM [Connor Driscoll] * New --first-blast option, like --proteins? * New --last-blast option eg. "nr" [Check who emailed me this] * annotate possible frame-shifts @@ -11,17 +10,13 @@ Prokka Wishlist * reconsider !~m/a-z/ rule in cleanup_product() [Roderick Felsheim] * all Kingdom=ALL or ANY for metagenomes [Andreas Bremges] * make --cleanup option for /product names [Andreas Bremges] -* check databases exist before spawning blast/hmmer * locus_tag rules: http://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf -* Add .PTT file output [Andrew Buultjens] * Bug: "existing RNA (repeat_region)" CRISPR is not RNA ? -* Allow --proteins to be a .GBK or .GFF3 file ie. extract the CDS annotations * Factor out some functions into modules! * Check for large genomic tracts which are unannotated. Sometimes Prodigal misses big genes. * Add an example input/output so users can check their copy is producing similar results. * Output potential homopolymer assembly errors near CDS flanks * Add the CLUSTERS "PHA" library to Viruses mode. * Option to include ribosomal binding sites (RBS) as features. -* Check input contigs for runs of Ns, and either complain, or split the file, or additionally create a .AGP scaffold file. (Mitchell Stanton-Cook has done this, need to incorporate) * Add hyperlinks to tool references in Manual