added benchmarking datasets

data/v1.3/Map_Reads.py

@@ -37,16 +37,16 @@
 map_threads = total_threads/par_threads
 map_threads = int(map_threads)
 
-Reads = ['PacBio', 'ONT']
+Reads = ['PacBio_I', 'PacBio_II', 'ONT']
 Graph = 'Graphs/MHC-CHM13.0.gfa.gz'
 R = ['0', '1000', '10000', '100000', '1000000', '2000000000']
 
 Metadata = []
 for read in Reads:
-    if read == 'PacBio':
-        Read = 'Reads/MHC_CHM13_' + read + '_filt.fq.gz'
-    elif read == 'ONT':
-        Read = 'Reads/MHC_CHM13_' + read + '_filt.part_001.fq.gz ' + ' Reads/MHC_CHM13_' + read + '_filt.part_002.fq.gz'
+    if read == 'PacBio_I':
+        Read = 'Reads/MHC_CHM13_' + read.split('_')[0] + '_filt.fq.gz'
+    else:
+        Read = 'Reads/MHC_CHM13_' + read.split('_')[0] + '_filt.part_001.fq.gz ' + ' Reads/MHC_CHM13_' + read.split('_')[0] + '_filt.part_002.fq.gz'
     for r in R:
         Metadata.append([read, r, Read])
 
@@ -67,7 +67,7 @@ def Map_Reads(Metadata):
     print(out)
     # add 6th line from out to count_recomb
     R = ""
-    if read == 'PacBio':
+    if read == 'PacBio_I':
         out = out.split('\n')
         val = re.findall(r'R: (\d+.\d+)', out[5])
         R = val[0]

data/v1.3/Plot_Map.py

@@ -12,7 +12,7 @@
 from pylatexenc.latex2text import LatexNodes2Text
 
 
-Reads = ['PacBio', 'ONT']
+Reads = ['PacBio_I', 'PacBio_II', 'ONT']
 R = ['0', '1000', '10000', '100000', '1000000', '2000000000']
 R_labels = ['$0$', '$10^3$', '$10^4$', '$10^5$', '$10^6$', '$\infty$']
 R_labels_ = [LatexNodes2Text().latex_to_text(r) for r in R_labels]
@@ -41,6 +41,12 @@
     fig.set_size_inches(6, 4)
 
     table = Table(title="Reads: " + read)
+    if read == 'PacBio_I':
+        table = Table(title="Reads: PacBio Sequel II (SRR11292121)")
+    elif read == 'PacBio_II':
+        table = Table(title="Reads: PacBio Sequel II (SRX5633451)")
+    elif read == 'ONT':
+        table = Table(title="Reads: Oxford Nanopore (SRR23365080)")
     table.add_column("Recombination Penalty", justify="right", style="cyan", no_wrap=True)
     table.add_column("Complete support", justify="right", style="blue", no_wrap=True)
     for i in range(len(R)):