150 (#152)

* fix #150 and move troubleshooting section from README to doc

* add how to cite section in doc

README.md

@@ -468,62 +468,6 @@ chromosomes](https://www.biorxiv.org/content/10.1101/2020.09.04.283127v1.full.pd
 
 ## Troubleshooting
 
-### AGAT throws features out, because the feature type is not yet taken into account
-Feature types (primary_tag) handled by AGAT are defined within json files. Most common features are already defined in those files. If you encounter files with feature types not accepted, AGAT will inform you and throw the features out. To keep those feature you must inform properly AGAT how to handle them.
-First access the json files by running:
-```
-			agat_convert_sp_gxf2gxf.pl --expose
-```
+See Troubleshooting section form the doc [here](https://agat.readthedocs.io/en/latest/troubleshooting.html).
 
-Then open the file corresponding to the feature type you want to add:
-* Feature level1 (e.g. gene, match, region):
-  My feature has no parent
-  => features_level1.json
-* Feature level2 (e.g. mrna, match_part, trna):
-  My feature has one parent and the parent is a level 1 feature.
-  => features_level2.json.
-* Feature level3 (e.g. exon, intron, cds):
-  My feature has one parent (the parent has also a parent) and no children
-  => features_level3.json.
-* Feature level3 discontinuous (e.g. cds, utr):
-  A single feature that exists over multiple genomic locations
-  => features_spread.json.
-
-Then add the feature type information by adding a paired-value like this:
-```
-	"bigRNA":"gene",
-```
-Where `bigRNA`is the feature type and `gene`the parent feature type expected.
-/!\\ For level1 feature type the second value can be:
- * topfeature: feature does not expect children, and will be written first in the sequence
- * standalone: feature does not expect children
- * other values do not have any meaning but a value is required, write whatever you want. 
-
-### AGAT throws features out, because child features are not provided
-Features level1 (e.g. gene, match, chromosome) may require to have child features or not depending of the information stored into the `features_level1.json` file. If a child is required, and the GFF file does not contain it, the level1 feature will be thrown away. You must modify the json file to add the the term `standalone` to inform AGAT that this feature level1 do not require any child. (This work only on feature level1, not level2 or level3). To access the json files run the following command:
-```
-# export the json files
-agat_convert_sp_gxf2gxf.pl --expose
-```
-Then open the `features_level1.json` and put the value `standalone` as value to the required feature.
-Finally run your scripts in the same folder as the modified json files are standing.
 
-### Use a version of AGAT from a specific branch
-```
-# install AGAT dependencies
-conda install -c bioconda agat
-# clone the repo
-git clone https://github.com/NBISweden/AGAT.git
-# if the branch you want is not the master (replace BRANCHE_NAME by the one you wish to use)
-git checkout BRANCHE_NAME
-# move into AGAT folder
-cd AGAT 
-# Check all the dependencies*
-perl Makefile.PL
-# Compile
-make
-# Test
-make test
-# Install
-make install                                    
-```

docs/how_to_cite.md

@@ -0,0 +1,7 @@
+## How to cite?
+
+This work has not been published yet(I will think about it). But if you wish to cite AGAT you can do it as follow (Adapt the version for the one you have used): 
+
+```
+Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format.  
+(Version v0.7.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717

docs/index.rst

@@ -25,6 +25,7 @@ Contents
    why_this_tool.md
    agat_for_you.md
    troubleshooting.md
+   how_to_cite.md
 
 .. toctree::
    :maxdepth: 2

docs/troubleshooting.md

@@ -39,3 +39,41 @@ agat_convert_sp_gxf2gxf.pl --expose
 ```
 Then open the `features_level1.json` and put the value `standalone` as value to the required feature.
 Finally run your scripts in the same folder as the modified json files are standing.
+
+### How to use a version of AGAT from a specific branch
+```
+# install AGAT dependencies
+conda install -c bioconda agat
+# clone the repo
+git clone https://github.com/NBISweden/AGAT.git
+# if the branch you want is not the master (replace BRANCHE_NAME by the one you wish to use)
+git checkout BRANCHE_NAME
+# move into AGAT folder
+cd AGAT 
+# Check all the dependencies*
+perl Makefile.PL
+# Compile
+make
+# Test
+make test
+# Install
+make install                                    
+```
+
+### How to fix Bio::Root::Exception met in AGAT
+
+They are bioperl error messages. Encountered error can be:  
+```
+MSG: Failed validation of sequence '[unidentified sequence]'. Invalid characters 
+```
+or  
+```
+MSG: Each line of the file must be less than 65,536 characters.
+```
+
+Bio::DB::Fasta from Bioperl cannot handle line with more than 65,536 characters. So you must fold you fasta sequence before to run AGAT's scripts:
+```
+# Fold to 80 characters by line. 
+# Be careful if you have long headers that can be folded over several lines. You must first shorten them, or fold with higher value.
+fold input.fa > output.fa
+```