MLST database updated (metamlstDB_2021). DB now downloaded through Ze…

…nodo
SegataLab · Dec 29, 2020 · adc4ca7 · adc4ca7
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Showing 4 changed files with 16 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -10,19 +10,24 @@ MetaMLST performs an *in-silico* Multi Locus Sequence Typing (MLST) Analysis on
 
 ### How can I use it? ###
 
-Check out the [**Quick Start**](https://github.com/SegataLab/metamlst/wiki#-quick-start) or refer to the [**Wiki**](https://github.com/SegataLab/metamlst/wiki/) for the *documentation*. You can also try the [**examples**](https://www.dropbox.com/s/xmbjj37k612f0rr/metamlst_examples.zip?dl=1), or take a look to the [**Examples**](https://github.com/SegataLab/metamlst/wiki/Examples) section
+Check out the [**Quick Start**](https://github.com/SegataLab/metamlst/wiki#-quick-start) or refer to the [**Wiki**](https://github.com/SegataLab/metamlst/wiki/) for the *documentation*. You can also try the [**examples**](https://zenodo.org/record/4399251/files/metamlst_examples.zip?download=1), or take a look to the [**Examples**](https://github.com/SegataLab/metamlst/wiki/Examples) section
 
 ### How it works? ###
 
 MetaMLST reconsctructs the MLST loci-sequences using the closest reference from the publicly available datsets (PubMLST) and traces the most abundant strain of each species:
 ![MetaMLST pipeline schema](http://segatalab.github.io/images/metamlst_working_concept.jpg)
 
-### Where can I get support? ###
+### Databases ###
 
-* Bugs and Support: [**MetaMLST Users Support Group**](https://groups.google.com/forum/#!forum/metamlst)
-* Project page at [SegataLab](http://segatalab.cibio.unitn.it/tools/metamlst/index.html)
-* Project [Wiki](https://github.com/SegataLab/metamlst/wiki/)
+MetaMLST automatically downloads the latest version of its database. You can also manually download databases from [here](https://zenodo.org/record/4399251#.X-uTwVn0muU). 
+The latest database is: **metamlstDB_2021**.
 
 ### Publication ###
 
 * Moreno Zolfo, Adrian Tett, Olivier Jousson, Claudio Donati and Nicola Segata - **[MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples](http://nar.oxfordjournals.org/content/early/2016/09/19/nar.gkw837.full)** - *Nucleic Acids Research, 2016* DOI: 10.1093/nar/gkw837
+
+### Where can I get support? ###
+
+* Bugs and Support: [**MetaMLST Users Support Group**](https://groups.google.com/forum/#!forum/metamlst)
+* Project page at [SegataLab](http://segatalab.cibio.unitn.it/tools/metamlst/index.html)
+* Project [Wiki](https://github.com/SegataLab/metamlst/wiki/)
diff --git a/metaMLST_functions.py b/metaMLST_functions.py
@@ -25,8 +25,8 @@
 	from io import StringIO
 
 __author__ = 'Moreno Zolfo (moreno.zolfo@unitn.it)'
-__version__ = '1.2.1'
-__date__ = '21 May 2020'
+__version__ = '1.2.2'
+__date__ = '29 December 2020'
 
 def byte_to_megabyte(byte):
     """
@@ -38,9 +38,9 @@ def byte_to_megabyte(byte):
 
 def check_install():
 	import zipfile,os
-	METAMLST_DBPATH=os.path.abspath(os.path.dirname(__file__))+'/metamlst_databases/metamlstDB_2019.db'
+	METAMLST_DBPATH=os.path.abspath(os.path.dirname(__file__))+'/metamlst_databases/metamlstDB_2021.db'
 	METAMLST_DBFOLDER=os.path.abspath(os.path.dirname(__file__))+'/metamlst_databases/'
-	METAMLST_URL='https://www.dropbox.com/s/d6mkjha1k7ob383/metamlstDB_2019.db.zip?dl=1'
+	METAMLST_URL='https://zenodo.org/record/4399251/files/metamlstDB_2021.db.zip?download=1'
 
 	if not os.path.isdir(METAMLST_DBFOLDER):
 		os.mkdir(METAMLST_DBFOLDER,mode=0o775)

diff --git a/metamlst-index.py b/metamlst-index.py
@@ -6,9 +6,7 @@
 	import sys,os,subprocess,sqlite3,argparse,re
 	from metaMLST_functions import *
 except ImportError as e:
-	print("Error while importing python modules! Remember that this script requires: sys,os,subprocess,sqlite3,argparse,re")
-
-
+	print("Error while importing python modules! Remember that this script requires: sys, os, subprocess, sqlite3, argparse, re and pysam. Error:"+str(e))
 	sys.exit(1)
 
 try:

diff --git a/metamlst.py b/metamlst.py
@@ -13,7 +13,7 @@
 	import sys
 	from metaMLST_functions import *
 except ImportError as e:
-	print ("Error while importing python modules! Remember that this script requires: sys,os,subprocess,sqlite3,argparse,re\nError: "+str(e))
+	print ("Error while importing python modules! Remember that this script requires: sys, os, subprocess, sqlite3, argparse, re and pysam\nError: "+str(e))
 	sys.exit(1)
 
 try: