Removing the display of the dataframe with the weights in the output

README.md

@@ -145,113 +145,67 @@ species.
     ##  1   mlplasmids
     ##  6
     ## 
-    ## [Wed Jan 22 13:31:18 2020]
-    ## Job 5: Extracting the links from the graph test/faecium_graph.gfa
+    ## [Wed Jan 22 13:56:34 2020]
+    ## Job 1: Extracting the nodes from the graph test/faecium_graph.gfa
     ## 
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
-    ## [Wed Jan 22 13:31:23 2020]
-    ## Finished job 5.
+    ## [Wed Jan 22 13:56:38 2020]
+    ## Finished job 1.
     ## 1 of 6 steps (17%) done
     ## 
-    ## [Wed Jan 22 13:31:23 2020]
-    ## Job 1: Extracting the nodes from the graph test/faecium_graph.gfa
+    ## [Wed Jan 22 13:56:38 2020]
+    ## Job 5: Extracting the links from the graph test/faecium_graph.gfa
     ## 
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
-    ## [Wed Jan 22 13:31:26 2020]
-    ## Finished job 1.
+    ## [Wed Jan 22 13:56:41 2020]
+    ## Finished job 5.
     ## 2 of 6 steps (33%) done
     ## 
-    ## [Wed Jan 22 13:31:26 2020]
+    ## [Wed Jan 22 13:56:41 2020]
     ## Job 3: Running mlplasmids to obtain the plasmid prediction using the nodes extracted from the graph. If this is the first time running mlplasmids, installation can take a few minutes
     ## 
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
-    ## [Wed Jan 22 13:31:40 2020]
+    ## [Wed Jan 22 13:56:54 2020]
     ## Finished job 3.
     ## 3 of 6 steps (50%) done
     ## 
-    ## [Wed Jan 22 13:31:40 2020]
+    ## [Wed Jan 22 13:56:54 2020]
     ## Job 2: Extracting the sd k-mer coverage from the chromosome-predicted contigs
     ## 
     ## R script job uses conda environment but R_LIBS environment variable is set. This is likely not intended, as R_LIBS can interfere with R packages deployed via conda. Consider running `unset R_LIBS` or remove it entirely before executing Snakemake.
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
     ## WARNING: ignoring environment value of R_HOME
-    ## [Wed Jan 22 13:31:52 2020]
+    ## [Wed Jan 22 13:57:07 2020]
     ## Finished job 2.
     ## 4 of 6 steps (67%) done
     ## 
-    ## [Wed Jan 22 13:31:52 2020]
+    ## [Wed Jan 22 13:57:07 2020]
     ## Job 4: Searching for plasmid-like walks using a greedy approach
     ## 
     ## R script job uses conda environment but R_LIBS environment variable is set. This is likely not intended, as R_LIBS can interfere with R packages deployed via conda. Consider running `unset R_LIBS` or remove it entirely before executing Snakemake.
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
     ## WARNING: ignoring environment value of R_HOME
-    ## [Wed Jan 22 13:32:28 2020]
+    ## [Wed Jan 22 13:57:50 2020]
     ## Finished job 4.
     ## 5 of 6 steps (83%) done
     ## 
-    ## [Wed Jan 22 13:32:28 2020]
+    ## [Wed Jan 22 13:57:50 2020]
     ## Job 0: Generating weights for the set of new edges connecting plasmid unitigs
     ## 
     ## R script job uses conda environment but R_LIBS environment variable is set. This is likely not intended, as R_LIBS can interfere with R packages deployed via conda. Consider running `unset R_LIBS` or remove it entirely before executing Snakemake.
     ## Activating conda environment: /home/sergi/gplas/.snakemake/conda/70552874
     ## WARNING: ignoring environment value of R_HOME
     ## NULL
-    ##    From_to To_from weight
-    ## 1       18      33    116
-    ## 2       18      47    142
-    ## 3       18      31     94
-    ## 4       18      60    100
-    ## 5       18      50    108
-    ## 6       18      52    314
-    ## 7       18      57    360
-    ## 8       18      54    148
-    ## 9       18      46     38
-    ## 10      33      47    100
-    ## 11      31      33     88
-    ## 12      33      60     90
-    ## 13      33      50     92
-    ## 14      33      52    124
-    ## 15      33      57    136
-    ## 16      33      54     50
-    ## 17      33      46     46
-    ## 18      31      47    142
-    ## 19      47      60    152
-    ## 20      47      50    164
-    ## 21      47      52    106
-    ## 22      47      57    140
-    ## 23      47      54     50
-    ## 24      46      47     64
-    ## 25      31      60    220
-    ## 26      31      50    186
-    ## 27      31      52     92
-    ## 28      31      57    108
-    ## 29      31      54     42
-    ## 30      31      46    120
-    ## 31      50      60    232
-    ## 32      52      60     94
-    ## 33      57      60    110
-    ## 34      54      60     38
-    ## 35      46      60    118
-    ## 36      50      52     98
-    ## 37      50      57    118
-    ## 38      50      54     42
-    ## 39      46      50    108
-    ## 40      52      57    342
-    ## 41      52      54    130
-    ## 42      46      52     40
-    ## 43      54      57    252
-    ## 44      46      57     44
-    ## 45      46      54     14
     ##       Algorithm Modularity Original_component Decision
     ## 1      Walktrap       0.13                  1 No_split
     ## 2 Leading-eigen       0.13                  1 No_split
     ## 3       Louvain       0.13                  1 No_split
     ## null device 
     ##           1 
-    ## [Wed Jan 22 13:32:45 2020]
+    ## [Wed Jan 22 13:58:04 2020]
     ## Finished job 0.
     ## 6 of 6 steps (100%) done
-    ## Complete log: /home/sergi/gplas/.snakemake/log/2020-01-22T133118.420801.snakemake.log
+    ## Complete log: /home/sergi/gplas/.snakemake/log/2020-01-22T135633.934474.snakemake.log
     ##   _______ .______    __           ___           _______.
     ##  /  _____||   _  \  |  |         /   \         /       |
     ## |  |  __  |  |_)  | |  |        /  ^  \       |   (----`
@@ -431,24 +385,20 @@ Mandatory arguments:
 Optional arguments:
 
   - **-n**: Project name given to gplas. Default: ‘unnamed’
-
   - **-t**: Threshold to predict plasmid-derived sequences. Integer
     value ranging from 0 to 1. Default mlplasmids threshold: 0.5 Default
     plasflow threshold: 0.7
-
   - **-x**: Number of times gplas finds plasmid paths per each plasmid
     starting node. Integer value ranging from 1 to infinite. Default: 20
-
   - **-f**: Gplas filtering threshold score to reject possible outcoming
     edges. Integer value ranging from 0 to 1. Default: 0.1
-
   - **-q**: Modularity threshold to split components present in the
     plasmidome network. Integer value ranging from 0 to 1. Default: 0.2
-   
-    For benchmarking purposes you can pass a complete genome to gplas
-    and will generate a precision and completeness. Using this you can
-    assess the performance of gplas on a small set of genomes in which
-    perhaps you have generated long-reads.
+
+For benchmarking purposes you can pass a complete genome to gplas and
+will generate a precision and completeness. Using this you can assess
+the performance of gplas on a small set of genomes in which perhaps you
+have generated long-reads.
 
   - **-r**: Path to the complete reference genome corresponding to the
     graph given. For optimal results using this benchmarking flag,