fix bugs in multithreading mafft and enhance readme

README.md

@@ -1,11 +1,11 @@
 # read2tree 
 
-read2tree is a software tool that allows to obtain alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bipasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtereing, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatenation. 
+read2tree is a software tool that allows obtaining alignment matrices for tree inference. For this purpose it makes use of the OMA database and a set of reads. Its strength lies in the fact that it bypasses the several standard steps when obtaining such a matrix in regular analysis. These steps are read filtering, assembly, gene prediction, gene annotation, all vs all comparison, orthology prediction, alignment and concatenation. 
 
 read2tree works in linux with  [![Python 3.10.8](https://img.shields.io/badge/python-3.10.8-blue.svg)](https://www.python.org/downloads/release/python-310/)
 
 ## New release 
-We are now realasing Read2Tree v2.0.0 with improved spead and logging. As the aligner, we are now using minimap2 [minimap2](https://github.com/lh3/minimap2). Also, MAFFT and IQtree are now using multiple threads. We would suggest to run r2t with `--debug` which helps to debug later. Please note that arguments have slightly changed in this release(see below for details). 
+We are now releasing Read2Tree v2.0.0 with improved speed and logging. As the aligner, we are now using minimap2 [minimap2](https://github.com/lh3/minimap2). Also, MAFFT and IQtree are now using multiple threads. We would suggest running r2t with `--debug` which helps to debug later. Please note that arguments have slightly changed in this release(see below for details). 
 
 
 ## Read2Tree Talk:
@@ -45,7 +45,7 @@ conda install -c conda-forge biopython numpy Cython ete3 lxml tqdm scipy pyparsi
 conda install -c bioconda dendropy pysam
 ```
 
-Besides, you need softwares including [mafft](http://mafft.cbrc.jp/alignment/software/) (multiple sequence aligner), [iqtree](http://www.iqtree.org/) (phylogenomic inference), [minimap2](https://github.com/lh3/minimap2) (long and short read mappers), and [samtools](http://www.htslib.org/download/) which could be installed using conda.
+Besides, you need software packages including [mafft](http://mafft.cbrc.jp/alignment/software/) (multiple sequence aligner), [iqtree](http://www.iqtree.org/) (phylogenomic inference), [minimap2](https://github.com/lh3/minimap2) (long and short read mappers), and [samtools](http://www.htslib.org/download/) which could be installed using conda.
 For this version, the `--read_type` argument accepts any minimap2 options string that defines how reads are aligned to the reference. For example, it could be `-ax sr`, `-ax map-hifi` or `-ax map-ont`. You can also pass `--threads 40` to be used with minimap2.
 ```
 conda install -c bioconda mafft iqtree minimap2 samtools
@@ -163,6 +163,13 @@ Hint: As read2tree exploits the `progress` package, the user can benefit from co
 To see the details of arguments, please take look at our wiki [page](https://github.com/DessimozLab/read2tree/wiki/Details-of-arguments)
 
 ## Possible issues
+It seems that minimap2 doesn't have the preset option  `-x sr` for short reads in older versions like 2.1. Then, you might get
+```
+Shell err: b"[E::main] unknown preset 'sr'\n"
+```
+
+Updating minimap2 to version 2.30 should fix the issue.
+
 
 Installing on MAC sometimes drops this error:
 
@@ -180,8 +187,12 @@ export LANG=en_US.UTF-8
 
 ## Change log
 
+- version 2.0.1:
+  - fixing a few bugs
+- version 2.0.0:
+  - pre-release: improve logging and make minimap2 as default aligner
 - version 1.5:
-  - using minimap2 as the read mapper 
+  - using minimap2 as the read mapper in the minimap2 branch
 - version 0.1.5:
   - fix issue with UnknownSeq being removed in Biopython>1.80
   - removing unused modeltester wrappers

read2tree/Aligner.py

@@ -292,9 +292,11 @@ def _align_worker(self, og_set):
             mafft_wrapper = Mafft(value.aa, datatype=DataType.PROTEIN)
             mafft_wrapper.options.options['--localpair'].set_value(True)
             mafft_wrapper.options.options['--maxiterate'].set_value(1000)
-            mafft_wrapper.options.options['--thread'].set_value(self.args.threads)
+            mafft_wrapper.options.options['--thread'].set_value(int(self.args.threads))
             logger.info("aligning OG {} with {} proteins".format(key, len(value.aa)))
             alignment = mafft_wrapper()
+            #logger.debug("MAFFT command line : {} {}".format(mafft_wrapper.cli.exe ,mafft_wrapper.command())) 
+
             codons = self._get_codon_dict_og(value)
             align = Alignment()
             align.aa = alignment

read2tree/__init__.py

@@ -6,7 +6,7 @@
 from pkg_resources import resource_string
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
-__version__ = '2.0.0'
+__version__ = '2.0.1'
 __copyright__ = 'read2tree (C) 2017-{:d} David Dylus,  Adrian M. Altenhoff, Sina Majidian  ' \
                 .format(date.today().year)
 

read2tree/wrappers/abstract_cli.py

@@ -212,7 +212,7 @@ def __call__(self, cmd=None, wait=False, **flags):
         if flags:
             cmd = ' '.join([cmd.strip(), _kwargs_to_args(flags, self._hyphen_policy)])
         self.cmd = '{} {}'.format(self.exe, cmd)
-        logger.debug('Running following command: {}'.format(self.cmd))
+        logger.info('Running following command: {}'.format(self.cmd))
 
         # spawn
         self.process = Popen(shlex.split(self.cmd),

read2tree/wrappers/options.py

@@ -99,7 +99,7 @@ def _type(self):
         return Real
 
     def get_value(self):
-        return float(self._value)
+        return self._value
 
 
 class StringOption(TypedValueOption):