Bump to 2.9.0-gv

apcamargo · Jun 11, 2022 · 8555819 · 8555819
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diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,7 @@
+VERSION 2.9.0-gv
+
+* Added two gene models for phages using the genetic code 11 to the metagenome mode.
+
 VERSION 2.8.0-gv
 
 * Added four gene models to the metagenome mode: three with the genetic code 11 and one with the genetic code 15.

diff --git a/README.md b/README.md
@@ -8,22 +8,22 @@ A fork of [Prodigal](https://github.com/hyattpd/Prodigal) meant to improve gene
 * [Topaz (genetic code 15)](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full)
 * [Agate (genetic code 15)](https://www.biorxiv.org/content/10.1101/2021.08.26.457843v1.full)
 * Gut phages (genetic code 15)
-* Gut phages (genetic code 11) × 3
+* Gut phages (genetic code 11) × 5
 
 ## Installation
 
-`prodigal-gv` can be installed via [Conda/Mamba](https://anaconda.org/bioconda/prodigal-gv), pre-build binaries ([Linux](https://github.com/apcamargo/prodigal-gv/releases/download/2.8.0/prodigal-gv-linux) and [macOS](https://github.com/apcamargo/prodigal-gv/releases/download/2.8.0/prodigal-gv-macos)), or built from scratch:
+`prodigal-gv` can be installed via [Conda/Mamba](https://anaconda.org/bioconda/prodigal-gv), pre-build binaries ([Linux](https://github.com/apcamargo/prodigal-gv/releases/download/2.9.0/prodigal-gv-linux) and [macOS](https://github.com/apcamargo/prodigal-gv/releases/download/2.9.0/prodigal-gv-macos)), or built from scratch:
 
 ```
 # Conda/Mamba:
 conda install -c bioconda prodigal-gv
 
 # Pre-built binary (Linux):
-curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.8.0/prodigal-gv-linux -o prodigal-gv
+curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.9.0/prodigal-gv-linux -o prodigal-gv
 chmod +x prodigal-gv
 
 # Pre-built binary (macOS):
-curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.8.0/prodigal-gv-macos -o prodigal-gv
+curl -L https://github.com/apcamargo/prodigal-gv/releases/download/2.9.0/prodigal-gv-macos -o prodigal-gv
 chmod +x prodigal-gv
 
 # Buld from scratch

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-v2.8.0-gv: June 2022
+v2.9.0-gv: June 2022
diff --git a/main.c b/main.c
@@ -28,7 +28,7 @@
 #include "fptr.h"
 
 
-#define VERSION "2.8.0-gv"
+#define VERSION "2.9.0-gv"
 #define DATE "June, 2022"
 
 #define MIN_SINGLE_GENOME 20000

diff --git a/metagenomic.c b/metagenomic.c
@@ -85,6 +85,8 @@ void initialize_metagenomic_bins(struct _metagenomic_bin *meta) {
   initialize_metagenome_57(meta[57].tinf);
   initialize_metagenome_58(meta[58].tinf);
   initialize_metagenome_59(meta[59].tinf);
+  initialize_metagenome_60(meta[60].tinf);
+  initialize_metagenome_61(meta[61].tinf);
 
   sprintf(meta[0].desc, "%d|%s|%s|%.1f|%d|%d", 0,
           "Mycoplasma_bovis_PG45",
@@ -266,4 +268,10 @@ void initialize_metagenomic_bins(struct _metagenomic_bin *meta) {
   sprintf(meta[59].desc, "%d|%s|%s|%.1f|%d|%d", 59,
           "Gut_phage_code_11c",
           "V", 29.95, meta[59].tinf->trans_table, meta[59].tinf->uses_sd);
+  sprintf(meta[60].desc, "%d|%s|%s|%.1f|%d|%d", 60,
+          "Gut_phage_code_11d",
+          "V", 36.40, meta[60].tinf->trans_table, meta[60].tinf->uses_sd);
+  sprintf(meta[61].desc, "%d|%s|%s|%.1f|%d|%d", 61,
+          "Gut_phage_code_11e",
+          "V", 32.35, meta[61].tinf->trans_table, meta[61].tinf->uses_sd);
 }
diff --git a/metagenomic.h b/metagenomic.h
@@ -29,7 +29,7 @@
 #include "node.h"
 
 #define NUM_BIN 6
-#define NUM_META 60
+#define NUM_META 62
 #define SAMPLE_LEN 120
 #define MAX_SAMPLE 200
 

diff --git a/training.c b/training.c
diff --git a/training.h b/training.h
@@ -113,5 +113,7 @@ void initialize_metagenome_56(struct _training *);
 void initialize_metagenome_57(struct _training *);
 void initialize_metagenome_58(struct _training *);
 void initialize_metagenome_59(struct _training *);
+void initialize_metagenome_60(struct _training *);
+void initialize_metagenome_61(struct _training *);
 
 #endif