Show the transcript translocation in the docs.

docs/tutorial.rst

@@ -273,10 +273,14 @@ depending on presence of a single allele of a missense or truncating variant
 >>> from gpsea.analysis.clf import monoallelic_classifier
 >>> is_missense = variant_effect(VariantEffect.MISSENSE_VARIANT, tx_id)
 >>> truncating_effects = (
+...    VariantEffect.TRANSCRIPT_ABLATION,
+...    VariantEffect.TRANSCRIPT_TRANSLOCATION,
 ...    VariantEffect.FRAMESHIFT_VARIANT,
+...    VariantEffect.START_LOST,
 ...    VariantEffect.STOP_GAINED,
 ...    VariantEffect.SPLICE_DONOR_VARIANT,
 ...    VariantEffect.SPLICE_ACCEPTOR_VARIANT,
+...    # more effects could be listed here ...
 ... )
 >>> is_truncating = anyof(variant_effect(e, tx_id) for e in truncating_effects)
 >>> gt_clf = monoallelic_classifier(

docs/user-guide/analyses/partitioning/genotype/variant_predicates.rst

@@ -26,13 +26,11 @@ The predicates operate on several lines of information:
 +------------------------+-------------------------------------------------------------------------------------------------+
 | Protein data           | variant is located in a region encoding a protein domain, protein feature type                  |
 +------------------------+-------------------------------------------------------------------------------------------------+
-| Genome                 | overlap with a genomic region of interest                                                       |
-+------------------------+-------------------------------------------------------------------------------------------------+
 
 
 The scope of the builtin predicates is fairly narrow
 and likely insufficient for real-life analyses.
-However, the predicates can be chained into a compound predicate
+However, several predicates can be "chained" into a compound predicate using a boolean logic,
 to achive more expressivity for testing complex conditions,
 such as "variant is a missense or synonymous variant located in exon 6 of `NM_013275.6`".
 
@@ -41,8 +39,9 @@ such as "variant is a missense or synonymous variant located in exon 6 of `NM_01
 Examples
 ********
 
-Here we show examples of several simple variant predicates and 
-how to chain them for testing complex conditions.
+Here we show how to use the builtin predicates for simple tests
+and how to build a compound predicate from the builtin predicates,
+for testing complex conditions.
 
 
 Load cohort
@@ -112,10 +111,10 @@ See the :mod:`gpsea.analysis.predicate` module
 for a complete list of the builtin predicates.
 
 
-Predicate chain
-===============
+Compound predicates
+===================
 
-Using the builtin predicates, we can build a logical chain to test complex conditions.
+A compound predicate for testing complex conditions can be built from two or more predicates.
 For instance, we can test if the variant meets any of several conditions:
 
 >>> import gpsea.analysis.predicate as vp
@@ -130,7 +129,13 @@ or *all* conditions:
 >>> missense_and_exon20.test(variant)
 True
 
-All variant predicates overload Python ``&`` (AND) and ``|`` (OR) operators, to allow chaining.
+All variant predicates overload Python ``&`` (AND) and ``|`` (OR) operators,
+to combine a predicate pair into a compound predicate.
+
+.. note::
+
+  Combining three or or more predicates can be achieved with :func:`~gpsea.analysis.allof`
+  and :func:`~gpsea.analysis.anyof` functions.
 
 Therefore, there is nothing that prevents us to combine the predicates into multi-level tests, 
 e.g. to test if the variant is a *"chromosomal deletion" or a deletion which removes at least 50 bp*:

docs/user-guide/analyses/phenotype-scores.rst

@@ -121,17 +121,19 @@ In this example, the point mutation is a mutation that meets the following condi
 '((change length == 0 AND reference allele length == 1) AND MISSENSE_VARIANT on NM_001042681.2)'
 
 
-For the loss of function predicate, the following variant effects are considered loss of function:
+For the loss-of-function predicate, the following is a non-exhausting list
+of variant effects considered as a loss-of-function:
 
 >>> lof_effects = (
+...     VariantEffect.TRANSCRIPT_TRANSLOCATION,
 ...     VariantEffect.TRANSCRIPT_ABLATION,
 ...     VariantEffect.FRAMESHIFT_VARIANT,
 ...     VariantEffect.START_LOST,
 ...     VariantEffect.STOP_GAINED,
 ... )
 >>> lof_mutation = anyof(variant_effect(eff, tx_id) for eff in lof_effects)
 >>> lof_mutation.description
-'(TRANSCRIPT_ABLATION on NM_001042681.2 OR FRAMESHIFT_VARIANT on NM_001042681.2 OR START_LOST on NM_001042681.2 OR STOP_GAINED on NM_001042681.2)'
+'(TRANSCRIPT_TRANSLOCATION on NM_001042681.2 OR TRANSCRIPT_ABLATION on NM_001042681.2 OR FRAMESHIFT_VARIANT on NM_001042681.2 OR START_LOST on NM_001042681.2 OR STOP_GAINED on NM_001042681.2)'
 
 
 The genotype predicate will bin the patient into two classes: a point mutation or the loss of function: