GNUVID DB update v1.4

ahmedmagds · Aug 26, 2020 · a5d1e08 · a5d1e08
1 parent eeb58bd
commit a5d1e08
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Showing 10 changed files with 7,655 additions and 519 deletions.
diff --git a/...9_acknowledgement_table_2020_07_21_17.pdf → ...9_acknowledgement_table_2020_08_22_23.pdf b/...9_acknowledgement_table_2020_07_21_17.pdf → ...9_acknowledgement_table_2020_08_22_23.pdf
diff --git a/README.md b/README.md
diff --git a/bin/Extract_fasta_sequence_blast_report.py b/bin/Extract_fasta_sequence_blast_report.py
@@ -11,7 +11,7 @@
     "--version",
     help="print version and exit",
     action="version",
-    version="%(prog)s 1.3",
+    version="%(prog)s 1.4",
 )
 PARSER.add_argument(
     "output_folder", type=str, help="output folder name & quality report prefix"

diff --git a/bin/GNUVID.py b/bin/GNUVID.py
@@ -58,7 +58,7 @@
 
 PARSER = argparse.ArgumentParser(
     prog="GNUVID.py",
-    description="GNUVID v1.3 utilizes the natural\
+    description="GNUVID v1.4 utilizes the natural\
  variation in public genomes of SARS-CoV-2 to rank gene sequences based on the number of observed exact \
  matches (the GNU score) in all known genomes of SARS-CoV-2. It types the genomes based on their unique \
  gene allele sequences. It types (using a whole genome MLST) your query genome in seconds.",
@@ -119,7 +119,7 @@
     "--version",
     help="print version and exit",
     action="version",
-    version="%(prog)s 1.3",
+    version="%(prog)s 1.4",
 )
 PARSER.add_argument(
     "reference",
@@ -1032,7 +1032,7 @@
     QUERYFILE_OBJECT.close()
 logging.info("Typed the query isolate/s and wrote Query_isolates_GNUVID_ST_Report.txt")
 logging.info("Done in --- {:.3f} seconds ---".format(time.time() - START_TIME))
-logging.info("""Thanks for using GNUVID v1.3, I hope you found it useful.
+logging.info("""Thanks for using GNUVID v1.4, I hope you found it useful.
 Please cite WhatsGNU 'Moustafa AM and Planet PJ 2020, Genome Biology;21:58'.
 Please also cite BLAST+ 'Camacho et al. 2009, BMC Bioinformatics;10:421' if you use GNUVID.
 Please also cite GISAID 'Shu Y. and McCauley J. 2017, EuroSurveillance; 22:13'

diff --git a/bin/GNUVID_database_customizer.py b/bin/GNUVID_database_customizer.py
@@ -43,7 +43,7 @@
 from collections import OrderedDict
 
 PARSER = argparse.ArgumentParser(
-    prog="GNUVID_database_customizer.py", description="Database_customizer script for GNUVID v1.3.",)
+    prog="GNUVID_database_customizer.py", description="Database_customizer script for GNUVID v1.4.",)
 GROUP = PARSER.add_mutually_exclusive_group()
 GROUP.add_argument("-g", "--GenBank_RefSeq", help="fna files from GenBank or RefSeq", action="store_true",)
 GROUP.add_argument("-p", "--prokka", help="fna files from prokka", action="store_true",)

diff --git a/db/GNUVID_07172020_DB_isolates_report.txt → db/GNUVID_08172020_DB_isolates_report.txt b/db/GNUVID_07172020_DB_isolates_report.txt → db/GNUVID_08172020_DB_isolates_report.txt
diff --git a/db/GNUVID_07172020_comp_db.txt.gz → db/GNUVID_08172020_comp_db.txt.gz b/db/GNUVID_07172020_comp_db.txt.gz → db/GNUVID_08172020_comp_db.txt.gz
diff --git a/db/MST_07172020.png b/db/MST_07172020.png
diff --git a/db/MST_07172020.pdf → db/MST_08172020.pdf b/db/MST_07172020.pdf → db/MST_08172020.pdf
diff --git a/db/MST_08172020.png b/db/MST_08172020.png