From b90714b28410e1f6d62b7cc37d64a521518cfc2a Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Fri, 22 Nov 2024 15:55:21 +1030 Subject: [PATCH] bump dnaapler to v1.0.1 --- HISTORY.md | 7 +++++++ README.md | 2 ++ docs/run.md | 4 ++++ environment.yml | 2 +- 4 files changed, 14 insertions(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index 556647a..db5b79b 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,6 +1,13 @@ History ======= +1.7.4 (2024-11-23) +------------------ + +* Adds `--trna_scan_model` parameter with two accepted options: `--trna_scan_model general` (this will be run by default - what Pharokka has always been running) and `--trna_scan_model bacterial`. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information. +* Bumps the `dnaapler` dependency to v1.0.1 due to a breaking dependency change in `dnaapler`. + + 1.7.3 (2024-07-10) ------------------ diff --git a/README.md b/README.md index aadfdfe..8726178 100644 --- a/README.md +++ b/README.md @@ -399,6 +399,8 @@ options: extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21" --mash_distance MASH_DISTANCE mash distance for the search against INPHARED. Defaults to 0.2. + --trna_scan_model {general,bacterial} + tRNAscan-SE model -V, --version Print pharokka Version --citation Print pharokka Citation ``` diff --git a/docs/run.md b/docs/run.md index cab6a32..dd055d9 100644 --- a/docs/run.md +++ b/docs/run.md @@ -159,6 +159,8 @@ Note 2 things: (1) that you need to leave off the leading hyphen (i.e. `"minNR 2 pharokka.py -i -o -d -t --minced_args "minNR 2 -minRL 21" ``` +As of v1.7.4 you can specify the bacterial `tRNAscan-SE` model using `--trna_scan_model bacterial`. Otherwise, `pharokka` uses the general model by default. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information. + ```bash usage: pharokka.py [-h] [-i INFILE] [-o OUTDIR] [-d DATABASE] [-t THREADS] [-f] [-p PREFIX] [-l LOCUSTAG] [-g GENE_PREDICTOR] [-m] [-s] @@ -217,6 +219,8 @@ options: extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21" --mash_distance MASH_DISTANCE mash distance for the search against INPHARED. Defaults to 0.2. + --trna_scan_model {general,bacterial} + tRNAscan-SE model -V, --version Print pharokka Version --citation Print pharokka Citation ``` \ No newline at end of file diff --git a/environment.yml b/environment.yml index b4da333..87d89d5 100644 --- a/environment.yml +++ b/environment.yml @@ -12,7 +12,7 @@ dependencies: - minced >=0.4.2 - aragorn >=1.2.41 - mash >=2.2 - - dnaapler >=1.0.0 + - dnaapler >=1.0.1 - pyrodigal >=3.1.0 - pyrodigal-gv >=0.2.0 - pycirclize >=0.3.1