Few (#292)

* add expressed_sequence_match and contig at level1 * add license for appeaser
NBISweden · Oct 22, 2022 · 2ea395d · 2ea395d
1 parent e0c2cb9
commit 2ea395d
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 4 deletions.
diff --git a/LICENSE-3RD-PARTY.txt b/LICENSE-3RD-PARTY.txt
@@ -0,0 +1,11 @@
+3RD PARTY LICENSES
+
+Note that not all files in the AGAT repository and in the released
+software packages belong to the AGAT project. For 3rd party files,
+the individual licenses apply.
+
+* App-Easer (https://github.com/polettix/App-Easer) used in lib/AGAT/AppEaser.pm
+    Copyright 2021, 2022 by Flavio Poletti flavio@polettix.it
+    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
+    http://www.apache.org/licenses/LICENSE-2.0
+    Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
diff --git a/share/feature_levels.yaml b/share/feature_levels.yaml
@@ -2,15 +2,15 @@
 #                       FEATURE LEVEL DEFINITION FILE
 # -----------------------------------------------------------------------------
 
-# AGAT parser (_sp_ prefix scipts) handles the features (1 line = 1 feature where 
+# AGAT parser (_sp_ prefix scipts) handles the features (1 line = 1 feature where
 # the feature type is indicated within the 3rd column) only if the feature type is
 # declared within this file, otherwise it will be skipped.
-# Features must be linked to one and only one of the 3 available levels: leve1, 
+# Features must be linked to one and only one of the 3 available levels: leve1,
 # level2, level3. It depends is Parent or children are expected by the feature.
 # Please find more info in the corresponding section below.
 
 # Few features (e.g. CDS, UTR) can span multiple lines because are spread over
-# multiple locations within the genome while representing only one biological 
+# multiple locations within the genome while representing only one biological
 # concept. In such case you must also add the information (only if missing) in
 # the "spread feature "section
 
@@ -32,11 +32,13 @@ level1:
   centromere: standalone
   chromosome: topfeature
   conserved_region: standalone
+  contig: topfeature
   dnasei_hypersensitive_site: standalone
   enhancer: standalone
   enhancer_blocking_element: standalone
   epigenetically_modified_region: standalone
   est_match: 1
+  expressed_sequence_match: 1
   gene: 1
   hat_tir_transposon: standalone
   helitron: standalone
@@ -190,4 +192,4 @@ spread:
    utr: 1
    uORF: 1
    3utr: 1
-   5utr: 1
+   5utr: 1