Merge pull request #212 from gbouras13/1.1.0

log the inputs

README.md

@@ -21,6 +21,7 @@ Table of Contents
 - [Version Log](#version-log)
 - [System](#system)
 - [Time](#time)
+- [Benchmarking](#Benchmarking)
 - [Bugs and Suggestions](#bugs-and-suggestions)
 - [Citation](#citation)
 
@@ -215,6 +216,14 @@ pharokka has been tested on Linux and MacOS (M1 and Intel).
 
 On a standard 16GB RAM laptop specifying 8 threads, pharokka should take between 3-10 minutes to run for a single phage, depending on the genome size.
 
+# Benchmarking
+
+The 673 crAss-like phage genomes were taken from Yutin, N., Benler, S., Shmakov, S.A. et al. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat Commun 12, 1044 (2021). https://doi.org/10.1038/s41467-021-21350-w
+
+
+
+
+
 # Bugs and Suggestions
 
 If you come across bugs with pharokka, or would like to make any suggestions to improve the program, please open an issue or email [email protected]

bin/input_commands.py

@@ -22,7 +22,7 @@ def get_input():
 	parser.add_argument('-p', '--prefix', action="store", help='Prefix for output files. This is not required.',  default='Default')
 	parser.add_argument('-l', '--locustag', action="store", help='User specified locus tag for the gff/gbk files. This is not required. A random locus tag will be generated instead.',  default='Default')
 	parser.add_argument('-g', '--gene_predictor', action="store", help='User specified gene predictor. Use "-g phanotate" or "-g prodigal". Defaults to phanotate (not required unless prodigal is desired).',  default='phanotate' )
-	parser.add_argument('-m', '--meta', help='Metagenomic mode', action="store_true")
+	parser.add_argument('-m', '--meta', help='meta mode for metavirome imput samples', action="store_true")
 	parser.add_argument('-c', '--coding_table', help='translation table for prodigal. Defaults to 11. Experimental only.', action="store", default = "11")
 	parser.add_argument('-e', '--evalue', help='E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05.', action="store", default = "1E-05")
 	parser.add_argument('-V', '--version', help='Version', action='version', version=v)

bin/pharokka.py

@@ -59,6 +59,8 @@
     logging.captureWarnings(True)
     logger.info("Starting pharokka v" + v)
 
+    logging.info("Input args: %r", args)
+
     # check the database is installed
     print("Checking database installation")
     logger.info("Checking database installation")