Add jobs option

README.md

@@ -1,4 +1,4 @@
-## PROST python package v0.2.12
+## PROST python package v0.2.13
 
 PRotein Ortholog Search Tool is a new homolog detection tool that utilizes ESM-1b language model and iDCT quantization method.
 PROST is fast and accurate compared to traditional tools. 
@@ -18,13 +18,13 @@ Following commands can be used to create databases and perform homology search.
 ```
 prost makedb db/sp.fa db/sp.prdb
 prost makedb db/covid.fa db/covid.prdb
-prost search --thr 0.05 db/covid.prdb db/sp.prdb results
-prost searchsp --thr 0.05 db/covid.prdb results
+prost search --thr 0.05 --jobs 8 db/covid.prdb db/sp.prdb results
+prost searchsp --thr 0.05 --jobs 8 db/covid.prdb results
 prost tosjonwp -a -i 'info' results.tsv website
 ```
 
 * `makedb`: creates a PROST database from given fasta file. The fasta file usually contains more than one entry.
-* `search`: searches a query database agains a target database. Query database can contain one or more sequences embedded using makedb command. `--thr` can be used to specify an e-value threshold. The default threshold is 0.05.
+* `search`: searches a query database agains a target database. Query database can contain one or more sequences embedded using makedb command. `--thr` can be used to specify an e-value threshold. The default threshold is 0.05. You can paralelize the search by using `--jobs` option.
 * `searchsp`: searches a query database agains a SwissProt February 2023 database. Performs GO enrichment analysis on found homologs. Query database can contain one or more sequences embedded using makedb command. Again `--thr` can be used to specify an e-value threshold.  `--gothr` can be used to specifiy different e-value threshold for GO enrichment analysis. 
 `searchsp` produces a tab seprataed file `.tsv` This file can be converted into a `.json` file that can be used with the tool [JSONWP](https://jsonwp.onrender.com/) using the command `prost tojsonwp -i 'Here is an info string to shown on website' results.tsv website`
 Here is an example result:

bin/prost

@@ -493,16 +493,17 @@ PROST [python package](https://github.com/MesihK/prost) can be used to generate
 
 @click.command()
 @click.option('--thr', default=0.05, help='E-value threshold for homolog detection')
+@click.option('-n', '--jobs', default=1, help='Number of jobs to run in parallel')
 @click.argument('querydb', type=click.Path(exists=True,file_okay=True,dir_okay=False))
 @click.argument('targetdb', type=click.Path(exists=True,file_okay=True,dir_okay=False))
 @click.argument('out', type=click.Path(exists=False,file_okay=True,dir_okay=False))
-def search(thr, querydb, targetdb, out):
+def search(thr, jobs, querydb, targetdb, out):
     '''Search a query database in target database.
 This command searches a query database against a target database.
 Both databases should be created using makedb command.
 Databases can contain one or more sequences.
 An e-value threshold can be specified with --thr flag. The default e-value threshold is 0.05'''
-    goList,homologList = _search(thr,None,querydb,targetdb,None)
+    goList,homologList = _search(thr,None,querydb,targetdb,None,jobs)
     print(f'Saving results into {out}.tsv.')
     toTSV(goList,homologList,out)
     print(f'You can use `prost tojsonwp` command to convert {out}.tsv results into a webpage!')

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyprost
-version = 0.2.12
+version = 0.2.13
 author = Mesih Kilinc
 author_email = mesih@iastate.edu
 description = PRotein Ortholog Search Tool