add --signgularity

README.md

@@ -318,6 +318,7 @@ usage: VIRTUS_wrapper.py [-h] \
                         [--fastq] \
                         [--figsize FIGSIZE] \
                         [--th_cov TH_COV] [--th_rate TH_RATE] \
+                        [--singularity] \
                         input_path
 
 positional arguments:
@@ -337,6 +338,7 @@ optional arguments:
   --figsize FIGSIZE     (default:6,6)
   --th_cov TH_COV       threshold of max viral coverage to plot, test (default:10)
   --th_rate TH_RATE     threshold of max rate virus/human to plot, test (default:0.0001)
+  --singularity         run with singularity (default:False)
 ```
 example
 ```

wrapper/summary.csv

@@ -1,11 +1,11 @@
 virus,Ctrl_1_cov,Ctrl_2_cov,Flu_1_cov,Flu_2_cov,Ctrl_1_rate,Ctrl_2_rate,Flu_1_rate,Flu_2_rate,u-value,p-value,FDR
-"NC_007360.1_Influenza_A_virus_(A/Goose/Guangdong/1/96(H5N1))_nucleocapsid_protein_(NP)_gene,_complete_cds",7.53994,18.7859,79.0415,52.7796,2.0898752524203576e-08,2.0557772102157603e-07,0.00017833350419595113,5.705166243157474e-05,4.0,0.2452781168067728,0.27253124089641423
-"NC_007372.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_2,_complete_sequence",0.0,66.1256,99.5728,99.4874,0.0,7.537849770791118e-07,0.0001770468108072655,0.0001739883316582788,4.0,0.2452781168067728,0.27253124089641423
-"NC_001501.1_Moloney_murine_leukemia_virus,_complete_genome",0.0,99.808,0.0,99.808,0.0,0.00010224065325473046,0.0,0.00010721235153450432,2.5,1.0,1.0
-"NC_007366.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_4,_complete_sequence",0.0,88.6493,99.546,99.319,0.0,2.7752992337912757e-06,0.001292302052174779,0.001175295727694479,4.0,0.2452781168067728,0.27253124089641423
-"NC_004907.1_Influenza_A_virus_(A/Hong_Kong/1073/99(H9N2))_segment_7,_complete_sequence",0.0,26.0488,90.2439,64.7805,0.0,3.08366581532364e-07,0.00017954321592890345,0.00011777617866775727,4.0,0.2452781168067728,0.27253124089641423
-"NC_007369.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_5,_complete_sequence",0.0,95.6577,99.4891,99.3614,0.0,3.3920323968560035e-06,0.0015065639948394136,0.0014216742588635755,4.0,0.2452781168067728,0.27253124089641423
-"NC_007368.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_6,_complete_sequence",8.86162,95.8419,99.0457,98.9775,2.0898752524203576e-08,1.130677465618668e-06,0.0005835539425968027,0.0005348199832909638,4.0,0.2452781168067728,0.27253124089641423
-"NC_007370.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_8,_complete_sequence",0.0,96.0674,98.5393,98.3146,0.0,1.7131476751798e-06,0.0008950437164526317,0.0008666710694272907,4.0,0.2452781168067728,0.27253124089641423
-"NC_002016.1_Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1))_segment_7,_complete_sequence",0.0,31.4508,98.5394,97.7605,0.0,3.4262953503596e-07,0.00010884106382753628,0.0001308585341241699,4.0,0.2452781168067728,0.27253124089641423
-"NC_007367.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_7,_complete_sequence",0.0,97.7605,99.3184,99.0263,0.0,2.192829024230144e-06,0.0011559565424916634,0.0011260270173726686,4.0,0.2452781168067728,0.27253124089641423
+"NC_007368.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_6,_complete_sequence",8.86162,95.8419,99.0457,98.9775,2.0898752524203576e-08,1.130677465618668e-06,0.0005835539425968,0.0005348199832909,4.0,0.2452781168067728,0.27253124089641423
+"NC_002016.1_Influenza_A_virus_(A/Puerto_Rico/8/1934(H1N1))_segment_7,_complete_sequence",0.0,31.4508,98.5394,97.7605,0.0,3.4262953503596e-07,0.0001088410638275,0.0001308585341241,4.0,0.2452781168067728,0.27253124089641423
+"NC_007360.1_Influenza_A_virus_(A/Goose/Guangdong/1/96(H5N1))_nucleocapsid_protein_(NP)_gene,_complete_cds",7.53994,18.7859,79.0415,52.7796,2.0898752524203576e-08,2.05577721021576e-07,0.0001783335041959,5.7051662431574736e-05,4.0,0.2452781168067728,0.27253124089641423
+"NC_007370.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_8,_complete_sequence",0.0,96.0674,98.5393,98.3146,0.0,1.7131476751798e-06,0.0008950437164526,0.0008666710694272,4.0,0.2452781168067728,0.27253124089641423
+"NC_004907.1_Influenza_A_virus_(A/Hong_Kong/1073/99(H9N2))_segment_7,_complete_sequence",0.0,26.0488,90.2439,64.7805,0.0,3.08366581532364e-07,0.0001795432159289,0.0001177761786677,4.0,0.2452781168067728,0.27253124089641423
+"NC_007367.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_7,_complete_sequence",0.0,97.7605,99.3184,99.0263,0.0,2.192829024230144e-06,0.0011559565424916,0.0011260270173726,4.0,0.2452781168067728,0.27253124089641423
+"NC_007366.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_4,_complete_sequence",0.0,88.6493,99.546,99.319,0.0,2.775299233791276e-06,0.0012923020521747,0.0011752957276944,4.0,0.2452781168067728,0.27253124089641423
+"NC_001501.1_Moloney_murine_leukemia_virus,_complete_genome",0.0,99.808,0.0,99.808,0.0,0.0001022406532547,0.0,0.0001072123515345,2.5,1.0,1.0
+"NC_007369.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_5,_complete_sequence",0.0,95.6577,99.4891,99.3614,0.0,3.392032396856004e-06,0.0015065639948394,0.0014216742588635,4.0,0.2452781168067728,0.27253124089641423
+"NC_007372.1_Influenza_A_virus_(A/New_York/392/2004(H3N2))_segment_2,_complete_sequence",0.0,66.1256,99.5728,99.4874,0.0,7.537849770791119e-07,0.0001770468108072,0.0001739883316582,4.0,0.2452781168067728,0.27253124089641423