add experiment parameter for reference

Strideradu · Oct 25, 2018 · 8732331 · 8732331
1 parent bdde9e5
commit 8732331
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Showing 6 changed files with 48 additions and 18 deletions.
diff --git a/README.md b/README.md
@@ -15,7 +15,7 @@ Usage
 ----------
 At this stage, our tool consists three part:
 
-####Suffix array filter
+#### Suffix array filter
 
 A prebuild excecuteble file using GCC 4.8.2 can found under /sa_filter/
 
@@ -30,7 +30,7 @@ To excecute (although this will be included in the script)
 ```
 The program will do all against all to compare shared kmer
 
-####Modified YASS for group hits
+#### Modified YASS for group hits
 
 A prebuild excecuteble file using GCC 4.8.2 can found under /yass/
 
@@ -47,7 +47,7 @@ The output format is (seperated by tab)
 query_id, query length, target_id, target_length, groups(x, diagonal, length)
 ```
 
-####Python script
+#### Python script
 
 To run GroupK, after build the two program above
 ```

diff --git a/Script/.idea/workspace.xml b/Script/.idea/workspace.xml
diff --git a/Script/GroupK.py b/Script/GroupK.py
@@ -64,7 +64,7 @@
 with open(group_output, "w") as fout:
     for query_id in filter_dict.keys():
         record = record_dict[query_id]
-        query_save = save_path + "query_k{}_c{}.fasta".format(k, threshold)
+        query_save = os.path.join(save_path, "query_k{}_c{}.fasta".format(k, threshold))
         record.description = ""
         SeqIO.write(record, query_save, "fasta")
 
@@ -73,10 +73,10 @@
         for target_id in target_list:
             record = record_dict[target_id]
             target_output.append(record)
-        target_save = save_path + "target_k{}_c{}.fasta".format(k, threshold)
+        target_save = os.path.join(save_path, "target_k{}_c{}.fasta".format(k, threshold))
         SeqIO.write(target_output, target_save, "fasta")
 
-        temp_output = save_path + "groups_temp_k{}_c{}.out".format(k, threshold)
+        temp_output = os.path.join(save_path, "groups_temp_k{}_c{}.out".format(k, threshold))
         yass_command = yass_path + ' -p "{}" -m {} -i {} -o {} {} {}'.format('#' * args.k2, args.accuracy, args.gap,
                                                                              temp_output, query_save, target_save)
         process = subprocess.Popen(yass_command, stdout=subprocess.PIPE, shell=True)

diff --git a/experiment/Ecoli_15Xof150X_ROC.xlsx b/experiment/Ecoli_15Xof150X_ROC.xlsx
diff --git a/experiment/Ecoli_30X_sim_ROC_min100.xlsx b/experiment/Ecoli_30X_sim_ROC_min100.xlsx
diff --git a/experiment/Human_foot_3_bacteria.xlsx b/experiment/Human_foot_3_bacteria.xlsx