Alignments made first in makeGeneTreesFastTree

CHANGELOG.rst

@@ -2,6 +2,12 @@
 Change Log
 ==========
 
+-------------------
+3.1.1_ - 2022-12-15
+-------------------
+
+- Separated functions doing alignments and tree making for the sake of compatibility with PHANTASM.
+
 -------------------
 3.1.0_ - 2022-09-10
 -------------------

TUTORIAL.rst

@@ -26,7 +26,7 @@ Next we're going to put a copy of the repository inside this directory. (Note th
 
 Next put the repository into the right release. At the command line, cd into the repository directory (``xgiTutorial/xenoGI``). Then do::
 
-  git checkout v3.1.0
+  git checkout v3.1.1
 
 Next create a second subdirectory of ``xgiTutorial/`` called ``enterics/``. This is the working directory for the data we'll be using.
 

misc/ncbiXmlToWgetScript.py

@@ -0,0 +1,80 @@
+## Takes a list of assemblies from ncbi in xml format, and produces an
+## output file with wget commands for download.
+## Authors: Jacob Fischer, Tona Gonzalez, Rachael Soh, Eliot Bush
+import sys
+import xml.etree.ElementTree as ET
+
+## Example
+
+# Say we have run the following query on ncbi's assembly database:
+# Vibrionaceae [Organism] AND "Sequence from type" [Filter] AND "complete genome" [assembly level]
+
+# We save the search results to file in xml format
+# (e.g. assembly_results.xml). We next must edit assembly_results.xml
+# with a text editor. There needs to be a <data> tag at the very
+# beginning, and </data> at the very end. (For some reason this seems
+# not to be included in what comes down from ncbi). Then we can use this script as follows:
+
+# python3 ncbiXmlToWgetScript.py assembly_results.xml downloadWget.sh GCF
+
+# the final argument specifies whether we'll get GCF (refseq) assemblies or GCA (genbank).
+
+# downloadWget.sh contains wget commands to get all the assemblies. It can be run like this:
+
+# sh downloadWget.sh
+
+## Functions
+
+def createGenomeLinks(xmlFN, outputFN, assemblySource):
+    ''' Parses through xml document output from NCBI assembly search
+    and creates and stores genome links in outputString '''
+
+    tree = ET.parse(xmlFN)
+
+    root = tree.getroot()
+
+    f = open(outputFN,'w')
+
+    if assemblySource == 'GCA':
+        number = 45
+    else:
+        number = 46
+
+    for child in root:
+        link = child[number].text
+
+        if link == None:
+            continue
+
+        i = 0
+        end = '' 
+        copying = False
+        while i != len(link):
+            if copying:
+                end+=link[i]
+                i+=1
+
+            else:
+                if link[i:i+4] == "GCA_" or link[i:i+4] == "GCF_":
+                    end += link[i]
+                    copying = True
+                    i+=1
+                else:
+                    i+=1
+        link = "wget " + link + '/' + end
+
+        f.write(link)
+        f.write('_genomic.gbff.gz\n')
+
+
+    f.close()
+
+## Main
+
+if __name__ == "__main__":
+    xmlFN = sys.argv[1]
+    outputFN = sys.argv[2]
+    assemblySource = sys.argv[3]
+    assert(assemblySource in ['GCA', 'GCF'])
+
+    createGenomeLinks(xmlFN, outputFN, assemblySource)

xenoGI/xenoGI.py

@@ -1,5 +1,5 @@
 """Provides the entry point to xenoGI's functionality."""
-__version__ = "3.1.0"
+__version__ = "3.1.1"
 import sys, glob, os, readline, rlcompleter
 from . import parameters,genbank,blast,trees,genomes,Score,scores,families,islands,analysis,islandBed
 from .Tree import *