Merge pull request #68 from gbouras13/dev

Fixes #57 Fixes #67

Author: gbouras13

README.md

@@ -257,6 +257,15 @@ conda install -c bioconda plassembler
 pip3 install git+https://github.com/rrwick/Unicycler.git
 ```
 
+* You may also run into issues where Plassembler will fail despite the fact Unicycler is installed (thanks Erin Young https://github.com/gbouras13/plassembler/issues/59). Please try running
+
+```bash
+export TERM=xterm-256color
+```
+
+then running `plassembler`
+
+
 **MacOS**
 
 For MacOS environments, the current conda installation method will only install the latest available bioconda Unicycler version of v0.4.8. 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "plassembler"
-version = "1.7.0" # change VERSION too
+version = "1.7.1" # change VERSION too
 description = "Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates"
 authors = ["George Bouras <george.bouras@adelaide.edu.au>"]
 license = "MIT"

src/plassembler/__init__.py

@@ -1570,7 +1570,6 @@ def long(
         canu_nano_or_pacbio = "nanopore"
 
         if pacbio_model != "nothing":
-            pacbio_model = validate_pacbio_model(pacbio_model)
             if pacbio_model == "pacbio-hifi":
                 canu_nano_or_pacbio = "pacbio-hifi"
                 corrected_error_rate = 0.005

src/plassembler/utils/VERSION

@@ -1 +1 @@
-1.7.0
+1.7.1