add output.md to output

docs/output.md

@@ -15,6 +15,8 @@ gene.coords.gbk is the gene information
 
 
 
+
+
 ## hit_table.tsv :
 
 The results of the queries to the GMGC.
@@ -27,17 +29,16 @@ There are five columns in the file.
 - gene_dna : the dna sequence of the hitted gene in GMGC
 - gene_protein : the protein sequence of the hitted gene in GMGC
 
-#### Align_category
+Align_category
 
 - EXACT : above 95% nucleotide identity with at least 95% coverage
-
 - SIMILAR : above 80% nucleotide identity with at least 80% coverage
-
 - MATCH : above 50% nucleotide identity with at least 50% coverage
-
 - NO MATCH : no match in GMGC
 
-
+
+
+
 
 ## genome_bin.tsv
 
@@ -50,6 +51,8 @@ There are two columns in the file.
 
 
 
+
+
 ## summary.txt
 
 Summary of the query

gmgc_finder/main.py

@@ -12,10 +12,13 @@
 from tqdm import tqdm
 import gzip
 import bz2
+import subprocess
+from os import path
+import tempfile
+
 from .alignment import identity_coverage
 from .gmgc_finder_version import __version__
 
-import tempfile
 
 def parse_args(args):
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -34,8 +37,7 @@ def parse_args(args):
     return parser.parse_args()
 
 def gene_prediction(fasta_input,output):
-    import subprocess
-    from os import path
+
     print('Start gene prediction...')
 
 
@@ -280,6 +282,8 @@ def main(args=None):
                 print(s)
                 ofile.write(s+'\n')
 
+        subprocess.call('cp docs/output.md {}'.format(out), shell=True)
+