updating documentation to include pygmes and protein mode

docs/Makefile

@@ -16,4 +16,5 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	eukcc -h > _static/eukcc-help.txt 
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/eukcc-help.txt

@@ -0,0 +1,61 @@
+usage: eukcc [-h] --db DB [--outdir OUTDIR] [--config CONFIG] [--ncores int]
+             [--ncorespplacer int] [--hmm HMM] [--training] [--proteins]
+             [--bed file.bed] [--force] [--keeptemp] [--fplace] [--noglob]
+             [--quiet] [--debug] [--HPA] [--nPlacements n] [--minGenomes n]
+             [--fullineage] [--minPlacementLikelyhood float] [--mindist n]
+             [--touch] [--gmes] [--pygmes] [--diamond DIAMOND] [--plot] [-v]
+             fasta
+
+Evaluate completeness and contamination of a MAG. Args that start with '--'
+(eg. --db) can also be set in a config file (specified via --config). Config
+file syntax allows: key=value, flag=true, stuff=[a,b,c] (for details, see
+syntax at https://goo.gl/R74nmi). If an arg is specified in more than one
+place, then commandline values override config file values which override
+defaults.
+
+positional arguments:
+  fasta                 Run script on this bin (fasta file)
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --db DB               Path to EukCC DB
+  --outdir OUTDIR, -o OUTDIR
+                        Location for the output. Names will be prefixed using
+                        the bin filenames
+  --config CONFIG, -c CONFIG
+                        Config file to define parameters, YAML
+  --ncores int, -n int  set number of cores for GeneMark-ES, pplacer and Hmmer
+  --ncorespplacer int   Pplacer requires a lot of memory. If you want you can
+                        set less cores for pplacer, which improves memory
+                        consumption significantly
+  --hmm HMM             run hmmer on all these HMMs instead
+  --training            Run EukCC in training mode (needed to create a new
+                        release of the DB)
+  --proteins            Input fasta is proteins
+  --bed file.bed, -b file.bed
+                        You can pass a bedfile of the protein location to omit
+                        fragmented proteins being detected twice
+  --force, -f           Force rerun of computation even if output is newer
+                        than input. Don't resume previous run.
+  --keeptemp            Keep all temporary files, by default EukCC will remove
+                        some temp files
+  --fplace, -p          Force rerun of placement and subsequent steps
+  --noglob, -g          Do not expand paths using glob
+  --quiet, -q           Silcence most output
+  --debug, -d           Debug and thus ignore safety
+  --HPA                 Set placement method to HPA
+  --nPlacements n       Set number of proteins to support location in tree
+                        (default: 2)
+  --minGenomes n        Minimal number of genomes to support a set (default:
+                        3)
+  --fullineage          Output full lineage for MAGs
+  --minPlacementLikelyhood float
+                        minimal pplacer likelyhood (default: 0.4)
+  --mindist n           Distance to collapse hits (default: 2000)
+  --touch               Do not run, but touch all output files
+  --gmes                only run GeneMark-ES
+  --pygmes              Use pygmes, will improve eukccs capability of running
+                        on highly fragmented bins but will take longer
+  --diamond DIAMOND     required to use pygmes option
+  --plot                produce plots
+  -v, --version         show program's version number and exit

docs/index.rst

@@ -13,6 +13,7 @@ EukCC
 
     Install <install.rst>
     Tutorial <usage/tutorial.rst>
+    EukCC options <usage/options.rst>
     FAQ <FAQ.rst>
 
 

docs/usage/options.rst

@@ -0,0 +1,77 @@
+EukCC options explained
+============================
+
+EukCC in genome (default) mode
+--------------------------------
+When launching EukCC without special 
+parameters, it will assume that a 
+genomic fasta file was passed as input.
+Thus GeneMark-ES will be used 
+to predict proteins. 
+
+.. code-block:: shell
+
+    eukcc --db eukccdb -o . genome.fna
+
+
+EukCC in protein mode
+---------------------------
+If proteins for a genome or MAG were already predicted
+using a nother pipeline, EukCC can be used to 
+estimate the completeness and contamination.
+
+For this EukCC requires at least the proteins as Fasta
+file. Internally EukCC ignores repeated proteins that
+occure very close to each other on a genomic level. This
+is due to common gene prediction errors and subsequent 
+duplicated hits with profile hmms. Thus it is possible
+to pass the genomic coordinates for each protein as a bed
+file to EukCC. Such a file can easily be prepared from 
+gtf or gff files. If no bed file is provided, this step 
+will be skipped.
+
+
+.. code-block:: shell
+
+    eukcc --db eukccdb -o . \
+          --protein genome.faa \
+          --bed coordinates.bed
+        
+
+
+EukCC using pygmes
+---------------------------
+GeneMark-ES uses a self training step to generate a model
+for the provided genome. Somtimes highly fragmented or
+incomplete genomes can fail to provided enough training data
+for GeneMark-ES model creation to succeed. 
+
+In these cases EukCC can rely on pygmes to select a suitable 
+model from previous analysed genomes. This allows to estimate 
+genome completeness also for very incomplete genomes.
+
+For pygmes to select a suitable model the user needs to provide
+a diamond data base with taxonomic information.
+Such a database can be downloaded here:
+
+.. code-block:: shell
+
+    wget -O uniref50_pygmes.dmnd http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/uniref50_20200213_tax.dmnd
+
+EukCC can then be launched with:
+
+
+.. code-block:: shell
+
+    eukcc --db eukccdb -o . \
+        --pygmes \
+        --diamond uniref50_pygmes.dmnd \
+        genome.fna
+
+    
+EukCC -h
+------------------------
+
+
+.. include:: ../_static/eukcc-help.txt
+