Edited --read_type to accept any minimap2 command-line option

README.md

@@ -1,6 +1,6 @@
 # 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 concatination. 
+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 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/)
 
@@ -43,7 +43,7 @@ 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.
-For this version, the `--read_type` argument could be either `short`, `long-hifi` or `long-ont`. You could also use `--threads 40` to be used with minimap2.
+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
 ```

read2tree/Mapper.py

@@ -112,14 +112,12 @@ def _call_wrapper(self, ref_file_handle, reads, tmp_output_folder):
         sam_file= output_folder+"/"+ref_file_handle.split('/')[-1].split('.')[0]+".sam"
 
         #self._output_shell(minimap2_ex+" -ax sr "+ ref_file_handle+ " -t " + str(self.args.threads) + " "+reads+" | "+samtools_ex+" view -F 4 -bh -S -t" + str(self.args.threads)+ " > " + bam_file)
-        if 'short' in self.args.read_type:
-            minimap_argm =" -ax sr"
-        elif 'long-hifi' in self.args.read_type:
-            minimap_argm = " -ax map-hifi "
-        elif 'long-ont' in self.args.read_type:
-            minimap_argm = " -ax map-ont "
-        else:
-            self.logger.error(" read_type is not valid" +self.args.read_type+" please use one of these: short long-ont  long-hifi ")
+
+        rt = (self.args.read_type or "").strip()
+        if not rt:
+            self.logger.error("read_type is not set, please use one of these: -ax short, -ax long-ont, -ax long-hifi")
+        minimap_argm = f" {rt} "
+
         if isinstance(reads,list):
             reads_str=" ".join(reads)
         elif isinstance(reads,str):

read2tree/main.py

@@ -73,9 +73,9 @@ def parse_args(argv, exe_name, desc):
                             help='[Default is none] Reads to be mapped to reference. If paired '
                                  'end add separated by space.')
 
-    arg_parser.add_argument('--read_type', default='short',
-                            help='[Default is short] Type of reads to '
-                                 'use for mapping: short, long-hifi or long-ont corresponding to  sr,  map-hifi, or map-ont   in minimap2.')
+    arg_parser.add_argument('--read_type', default='-ax sr',
+                            help='[Default is -ax sr] Minimap2 command-line options for mapping reads to reference. '
+                                 'Examples:  -ax sr  ,  -ax map-hifi  ,  -ax map-pb  or  -ax map-ont  ')
 
     arg_parser.add_argument('--threads', type=int, default=1,
                             help='[Default is 1] Number of threads for the mapping ')