Merge pull request #12 from luispedro/main

Minor touch ups and refactoring

Author: cocodyq

.github/workflows/test_gmsc_mapper.yml

@@ -8,9 +8,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9"]
-
-
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

README.md

@@ -3,7 +3,7 @@
 GMSC-mapper is a command line tool to query the Global Microbial smORFs Catalog (GMSC).
 
 GMSC-mapper can be used to 
-- Find query smORFs (< 100aa) homologous to Global Microbial smORFs Catalog (GMSC) by alignment.
+- Find query smORFs (&lt; 100aa) homologous to Global Microbial smORFs Catalog (GMSC) by alignment.
   - Support 3 types of input:
     - contigs (GMSC-mapper will predict smORFs from contigs first)
     - amino acid sequences
@@ -21,7 +21,7 @@ Clone GMSC-mapper repository
 git clone https://github.com/BigDataBiology/GMSC-mapper.git
 ```
 
-Create conda environment(only support python v3.8/v3.9)
+Create conda environment(only support python v3.8-10)
 
 ```bash
 conda create -n gmscmapper python=3.8

gmsc_mapper/filter_length.py

@@ -1,24 +1,21 @@
-message_error = '''GMSC-mapper Error: Input sequences are all more than 303nt or 100aa,which will be filtered. 
-                   Please check if your input consist of contigs, which should use -i not --nt-genes or --aa-genes as input.\n'''
+message_error = '''GMSC-mapper Error: Input sequences are all more than 303nt or 100aa,which will be filtered.
+Please check if your input consist of contigs, which should use -i not --nt-genes or --aa-genes as input.\n'''
 
 def filter_length(queryfile, tmpdirname, N):
     import sys
     import gzip
     from os import path
     from .fasta import fasta_iter
-    
     filtered_file = path.join(tmpdirname, "filtered.faa.gz")
 
     with gzip.open(filtered_file, 'wt',compresslevel=1) as of:
-        all_longer_flag = 1
-        
+        all_longer_flag = True
         for ID, seq in fasta_iter(queryfile):
             if len(seq) < N:
-                all_longer_flag = 0
+                all_longer_flag = False
                 of.write(f'>{ID}\n{seq}\n')
-        
+
         if all_longer_flag:
             sys.stderr.write(message_error)
             sys.exit(1)
-    
     return filtered_file