Merge pull request #27 from andrewjpage/update_url_issue_26

Update url issue 26

Author: andrewjpage

VERSION

@@ -1 +1 @@
-1.0.1
+1.0.2

tiptoft/Fastq.py

@@ -83,10 +83,12 @@ def read_filter_and_map(self):
                 r += 1
         fh.close()
 
-        self.full_gene_coverage(counter)
+        alleles = self.full_gene_coverage(counter)
         self.logger.info("Number of reads: "+str(counter))
         self.logger.info("Number of matching reads: " +
                          str(match_counter)+"\t"+str(f)+"\t"+str(r))
+		
+        print("\t".join([self.filename, str(len(alleles)), str(match_counter), str(counter), str(match_counter*100/counter)]))
 
         return self
 

tiptoft/RefGenesGetter.py

@@ -36,16 +36,14 @@ def _get_from_plasmidfinder(self, outprefix):
         except Error:
             raise Error('Error mkdir/chdir ' + tmpdir)
 
-        cmd = 'curl -o enterobacteriaceae.fsa https://bitbucket.org/' \
-              'genomicepidemiology/plasmidfinder_db/raw/'\
-              'master/enterobacteriaceae.fsa'
-        print('Downloading data with:', cmd, sep='\n')
-        subprocess.check_call(cmd, shell=True)
+        files_to_download = ['enterobacteriaceae.fsa', 'Inc18.fsa', 'NT_Rep.fsa', 'Rep1.fsa', 'Rep2.fsa', 'Rep3.fsa', 'RepA_N.fsa', 'RepL.fsa', 'Rep_trans.fsa']
 
-        cmd = 'curl -o gram_positive.fsa https://bitbucket.org/'\
-            'genomicepidemiology/plasmidfinder_db/raw/master/gram_positive.fsa'
-        print('Downloading data with:', cmd, sep='\n')
-        subprocess.check_call(cmd, shell=True)
+        for f in files_to_download:
+            cmd = 'curl -o '+str(f)+' https://bitbucket.org/' \
+              'genomicepidemiology/plasmidfinder_db/raw/'\
+              'master/'+str(f)
+            print('Downloading data with:', cmd, sep='\n')
+            subprocess.check_call(cmd, shell=True)
 
         print('Combining downloaded fasta files...')
         fout_fa = pyfastaq.utils.open_file_write(final_fasta)

tiptoft/TipToft.py

@@ -36,12 +36,12 @@ def __init__(self, options):
             self.plasmid_data = str(pkg_resources.resource_filename(
                 __name__, 'data/plasmid_data.fa'))
 
-        if self.output_file and os.path.exists(self.output_file):
-            self.logger.error(
-                "The output file already exists, "
-                "please choose another filename: "
-                + self.output_file)
-            sys.exit(1)
+        #if self.output_file and os.path.exists(self.output_file):
+        #    self.logger.error(
+        #        "The output file already exists, "
+        #        "please choose another filename: "
+        #        + self.output_file)
+        #    sys.exit(1)
 
         if(self.filtered_reads_file and
                 os.path.exists(self.filtered_reads_file)):