add missing fasta cmd documentation

docs/index.md

@@ -73,6 +73,7 @@ user/PangenomeAnalyses/pangenomeAnalyses
 user/RGP/rgpAnalyses
 user/Modules/moduleAnalyses
 user/writeGenomes
+user/writeFasta
 user/align
 user/projection
 user/genomicContext

docs/user/writeFasta.md

@@ -0,0 +1,76 @@
+
+# Write pangenome sequences
+
+The `fasta` command can be used to write sequences of the pangenome or specific parts of the pangenome in FASTA format. 
+
+Most options require a partition.
+
+Available partitions are:
+* `all` for the entire pangenome.
+* `Persistent` for persistent families
+* `Shell` for shell genes or families
+* `Cloud` for cloud genes or families
+* `rgp` for genes or families found in RGPs
+* `core` for core genes or families
+* `softcore` for softcore genes or families
+
+When using the `softcore` filter, the `--soft_core` option can be used to modify the threshold used to determine what is part of the softcore. It is set to 0.95 by default.
+
+## Genes
+
+This option can be used to write the nucleotide CDS sequences. It can be used as such, to write all of the genes of the pangenome for example:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_GENES --genes all
+```
+
+Or to write only the persistent genes:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_GENES --genes persistent
+```
+
+
+## Protein families
+
+This option can be used to write the protein sequences of the representative sequences for each family. It can be used as such for all families:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_PROT --prot_families all
+```
+
+or for all of the shell families for example:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_PROT --prot_families shell
+```
+
+
+## Gene families
+
+This option can be used to write the gene sequences of the representative sequences for each family. It can be used as such:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_GENES_FAMILIES --gene_families all
+```
+
+or for the cloud families for example:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_GENES_FAMILIES --gene_families cloud
+```
+
+## Regions
+
+This option can be used to write the nucleotide sequences of the detected RGPs.
+It requires the fasta sequences used to compute the pangenome, as originally provided when you computed your pangenome.
+
+This command has only two filters:
+* all, for all regions
+* complete, for only the 'complete' regions which are not on a contig border
+
+It can be used as such:
+
+```bash
+ppanggolin fasta -p pangenome.h5 --output MY_REGIONS --regions all --fasta genomes.fasta.list
+```