add a first documentation for the write_pangenome and write_genome cmds

docs/user/Flat/RGP.md

@@ -2,7 +2,7 @@
 This file is a tsv file that lists all of the detected Regions of Genome Plasticity. This requires to have run the RGP detection analysis by either using the `panrgp` command or the `rgp` command.
 
 It can be written with the following command:
-`ppanggolin write -p pangenome.h5 --regions`
+`ppanggolin write_pangenome -p pangenome.h5 --regions`
 
 The file has the following format :
 
@@ -21,7 +21,7 @@ The file has the following format :
 This is a tsv file with two column. It links the spots of 'summarize_spots' with the RGPs of 'plastic_regions'.
 
 It is written with the following command:
-`ppanggolin write -p pangenome.h5 --spots`
+`ppanggolin write_pangenome -p pangenome.h5 --spots`
 
 |column|description|
 |------|------------|
@@ -33,7 +33,7 @@ It is written with the following command:
 This is a tsv file that will associate each spot with multiple metrics that can indicate the dynamic of the spot.
 
 It is written with the following command:
-`ppanggolin write -p pangenome.h5 --spots`
+`ppanggolin write_pangenome -p pangenome.h5 --spots`
 
 |column| description|
 |-------|------------|
@@ -49,7 +49,7 @@ It is written with the following command:
 #### Borders
 
 Each spot has at least one set of gene families bordering them. To write the list of gene families bordering a spot, you need to use the following option:
-`ppanggolin write -p pangenome.h5 --borders`
+`ppanggolin write_pangenome -p pangenome.h5 --borders`
 
 It will write a .tsv file with 4 columns:
 

docs/user/Flat/dupplication.md

@@ -3,6 +3,6 @@ This file lists the gene families, their duplication ratio, their mean presence
 
 It can be generated using the 'write' subcommand as such : 
 
-`ppanggolin write -p pangenome.h5 --stats`
+`ppanggolin write_pangenome -p pangenome.h5 --stats`
 
 This command will also generate the 'organisms_statistics.tsv' file.

docs/user/Flat/fam2gen.md

@@ -4,4 +4,4 @@ It is basically a three-column file listing the gene family name in the first co
 
 You can obtain it as such :  
 
-`ppanggolin write -p pangenome.h5 --families_tsv`
+`ppanggolin write_pangenome -p pangenome.h5 --families_tsv`

docs/user/Flat/metrics.md

@@ -23,9 +23,11 @@ It could be necessary to get more information about the modules.
 Here we provide information about families, and we separate modules in 
 function of the partition. You can get this supplementary information 
 as such :
-```
+```bash
 ppanggolin metrics -p pangenome.h5 --info_modules
-...
+```
+
+```
 Modules : 3
 Families in Modules : 22  (min : 5, max : 9, sd : 2.08, mean : 7.33)
 	Sheel specific : 36.36  (sd : 4.62, mean : 2.67)

docs/user/Flat/module.md

@@ -1,7 +1,7 @@
 #### Functional modules
 This .tsv file lists the modules and the gene families that belong to them. It lists one family per line, and there are multiple line for each module.
 It is written along with other files with the following command:
-`ppanggolin write -p pangenome.h5 --modules`
+`ppanggolin write_pangenome -p pangenome.h5 --modules`
 
 It follows the following format:
 |column|description|
@@ -12,7 +12,7 @@ It follows the following format:
 #### Modules in organisms
 This .tsv file lists for each organism the modules that are present and how complete they are. Since there are some variability that are allowed in the module predictions, occasionnally some modules can be incomplete in some of the organisms where they are found.
 This file is written along with other files with the following command:
-`ppanggolin write -p pangenome.h5 --modules`
+`ppanggolin write_pangenome -p pangenome.h5 --modules`
 
 And it follows the following format:
 |column|description|
@@ -24,7 +24,7 @@ And it follows the following format:
 #### modules summary
 This .tsv file lists a few characteristics for each detected module. There is one line for each module.
 The file is written along with other files with the following command:
-`ppanggolin write -p pangenome.h5 --modules`
+`ppanggolin write_pangenome -p pangenome.h5 --modules`
 
 And it follows the following format:
 |column|description|
@@ -39,7 +39,7 @@ And it follows the following format:
 This command is available only if both modules and spots have been computed for your pangenome (see the command `all`, or the commands `spot` and `module` for that).
 It indicates which modules are present in which spot and in which RGP.
 The files are written with the following command:
-```ppanggolin write -p pangenome.h5 --spot_modules```
+```ppanggolin write_pangenome -p pangenome.h5 --spot_modules```
 The format of the 'modules_spots.tsv' file is the following:
 
 |column|description|
@@ -56,4 +56,4 @@ The file 'modules_RGP_lists.tsv' lists RGPs that have the same modules. Those RG
 |mod_list| a list of the modules that are in the indicated RGPs|
 |RGP_list| a list of RGP that include exactly the modules listed previously|
 
-This information can also be visualized through figures that can be drawn with `ppanggolin draw --spots` (see [Spot plots](https://github.com/labgem/PPanGGOLiN/wiki/Outputs#spot-plots), and which can display modules.
+This information can also be visualized through figures that can be drawn with `ppanggolin draw --spots` (see [Spot plots](https://github.com/labgem/PPanGGOLiN/wiki/Outputs#spot-plots), and which can display modules.)

docs/user/Flat/orgStat.md

@@ -24,6 +24,6 @@ This file is made of 15 columns described in the following table
 
 It can be generated using the 'write' subcommand as such : 
 
-`ppanggolin write -p pangenome.h5 --stats`
+`ppanggolin write_pangenome -p pangenome.h5 --stats`
 
 This command will also generate the 'mean_persistent_duplication.tsv' file.

docs/user/Flat/partition.md

@@ -2,4 +2,4 @@ Those files will be stored in the 'partitions' directory and will be named after
 
 You can generate those files as such :  
 
-` ppanggolin write -p pangenome.h5 --partitions`
+` ppanggolin write_pangenome -p pangenome.h5 --partitions`

docs/user/Flat/presAbs.md

@@ -5,12 +5,12 @@ This file is basically a presence absence matrix. The columns are the genomes us
 
 It can be generated using the 'write' subcommand as such : 
 
-`ppanggolin write -p pangenome.h5 --Rtab`
+`ppanggolin write_pangenome -p pangenome.h5 --Rtab`
 
 ### matrix
 
 This file is a .csv file following a format alike the gene_presence_absence.csv file generated by [roary](https://sanger-pathogens.github.io/Roary/), and works with [scoary](https://github.com/AdmiralenOla/Scoary) if you want to do pangenome-wide association studies.
 
 It can be generated using the 'write' subcommand as such : 
 
-`ppanggolin write -p pangenome.h5 --csv`
+`ppanggolin write_pangenome -p pangenome.h5 --csv`

docs/user/Outputs.md

@@ -5,9 +5,9 @@ PPanGGOLiN provides multiple outputs to describe a pangenome. In this section th
 
 In most cases it will provide with a HDF-5 file named "pangenome.h5". This file stores all the information about your pangenome and the analysis that were run. If given to ppanggolin through most of the subcommands, it will read information from it. This is practical as you can regenerate figures or output files, or rerun parts of the analysis without redoing everything.
 
-In this section, each parts will describe a possible output of PPanGGOLiN, and will be commented with the command line that generates it using the HDF5 file, which is assumed to be called 'pangenome.h5'.
+In this section, each part will describe a possible output of PPanGGOLiN, and will be commented with the command line that generates it using the HDF5 file, which is assumed to be called 'pangenome.h5'.
 
-When using the same subcommand (like 'write' or 'draw' that can help you generate multiple file each), you can provide multiple options to write all of the file formats that you desire at once.
+When using the same subcommand (like 'write_pangenome' or 'draw' that can help you generate multiple file each), you can provide multiple options to write all of the file formats that you desire at once.
 
 ## PPanGGOLiN figures outputs
 
@@ -27,7 +27,10 @@ When using the same subcommand (like 'write' or 'draw' that can help you generat
 ```{include} Figures/rarefaction.md
 ```
 
-## Write
+## `write_pangeome`: Write flat output describing the pangenome
+
+Writes 'flat' files that describe the pangenome and its elements.
+
 ### Organisms statistics
 ```{include} Flat/orgStat.md
 ```
@@ -39,7 +42,6 @@ The pangenome's graph can be given through multiple data formats, in order to ma
 ```{include} graphOut/GEXF.md
 ```
 
-
 #### json
 ```{include} graphOut/JSON.md
 ```
@@ -51,14 +53,6 @@ The pangenome's graph can be given through multiple data formats, in order to ma
 ```{include} Flat/dupplication.md
 ```
 
-### partitions
-```{include} Flat/partition.md
-```
-
-### projection
-```{include} Flat/projection.md
-```
-
 ### Gene families and genes
 ```{include} Flat/fam2gen.md
 ```
@@ -71,6 +65,26 @@ The pangenome's graph can be given through multiple data formats, in order to ma
 ```{include} Flat/module.md
 ```
 
+### partitions
+```{include} Flat/partition.md
+```
+
+## `write_genomes`: Write genomes with pangenome annotations
+
+Writes 'flat' files that represent the genomes along with their associated pangenome elements.
+
+
+
+### tables
+```{include} Flat/tables.md
+```
+### gff
+```{include} Flat/gff.md
+```
+### proksee
+```{include} Flat/proksee.md
+```
+
 ## Fasta
 ```{include} sequence/fasta.md
 ```