ProtGraph Release 0.3.11 (#73)

* Rewritten compacting of FASTAs to also work memory efficient on very large FASTAs

* Added more information to -qs

* Fixed #68 , we also now consider IDs if they are available in those features

* Fixes #66. We now allow as in the features to select to be added in the graph, the features to be used for counting.

This allows us for further tools to use this information to not only limit on variants, but by arbitrary features

* Enhancing #66, we also are now able to set a limit on variable or fixed modifications

* Changed version in apsw to be more explicit (closes #49), removed if-main in script

* Bumped Version to 0.3.10

* Extended PTMs to allow multiple at once (untested) #67

* Added protein n/c-term ptms, still needs testing if graphs are correctly generated. #67

* Finished PTMs on ProteinGraphs.

fixes #67

ProtGraph can now add multiple PTMs (even on same AminoAcids) in various combinations into ProteinGraphs. It can be set for N/C-Terminal Peptide/Protein PTMs as well as on single aminoacids. Documnetation is still missing

* Fixed qualifier generation error. Now N/C-PEP/PRO-Term PTMs are annotated correctly in the FASTA-Header

* Updated Tests and CLI-Documentation

* Append PTMs to also allow only N/CTerminal AA Varbiable Modification

* Safety Check on Fixed Mods, here N/C-Terminal AAs mods are note allows

* Fixed Syntax

* Added cases to also handle empty cells with less exceptions

* Linting

* Updated Tests, added python 3.11 and 3.12 tests

* Removed blank line

* Bug Fix, where variable Mods where not correctly added to ProteinGraphs

* Fixed error in FIXMOD Qualifier Info

* Bumped Version to 0.3.11

Author: Luxxii

protgraph/annotate_ptms.py

@@ -43,7 +43,7 @@ def _flatten_list(double_list: list):
 def _create_feature(start_pos, end_pos, mod_type, amino_acid, delta):
     ''' A wrapper to return a VARMOD or FIXMOD feature '''
     return FeatureTable(
-        location=FeatureLocation(start_pos, end_pos), type=mod_type, strand=None, id=None,
+        location=FeatureLocation(start_pos, end_pos), type=mod_type, id=None,
         qualifiers=dict(note="{}:{}".format(amino_acid, delta))
     )
 
@@ -193,7 +193,7 @@ def _apply_varmod(graph_entry, var_mods, mass_factor):
                 for in_edge in node.in_edges():
                     for delta_idx, delta in enumerate(deltas):
                         edges_to_add.append((in_edge.source, offset + len(nodes_to_clone)*delta_idx + vc))
-                        qualifier_info.append(_create_feature(spos, epos, "VARMOD", aa, delta))
+                        qualifier_info.append([_create_feature(spos, epos, "VARMOD", aa, delta)])
 
                         if "cleaved" in graph_entry.es[0].attributes():
                             cleaved_info.append(in_edge["cleaved"])
@@ -264,7 +264,7 @@ def _apply_varmod(graph_entry, var_mods, mass_factor):
                     if filter_ingoing_edges(in_edge.source_vertex["position"]):
                         for delta_idx, delta in enumerate(deltas):
                             edges_to_add.append((in_edge.source, offset + len(nodes_to_clone)*delta_idx + vc))
-                            qualifier_info.append(_create_feature(spos, epos, "VARMOD", aa, delta))
+                            qualifier_info.append([_create_feature(spos, epos, "VARMOD", aa, delta)])
 
                             if "cleaved" in graph_entry.es[0].attributes():
                                 cleaved_info.append(in_edge["cleaved"])
@@ -368,9 +368,9 @@ def _apply_varmod(graph_entry, var_mods, mass_factor):
         for e in end_node.in_edges():
             for offset in range(len(deltas)):
                 edges_to_add.append((e.source, vc + offset))
-                qualifier_info.append(
+                qualifier_info.append([
                     _create_feature(end_node["position"], end_node["position"]+1, "VARMOD", "CPEPTERM", delta)
-                )
+                ])
                 if "cleaved" in graph_entry.es[0].attributes():
                     cleaved_info.append(e["cleaved"])
 

setup.py

@@ -11,7 +11,7 @@
 
 setup(
     name='protgraph',
-    version='0.3.10',
+    version='0.3.11',
     author="Dominik Lux",
     description="ProtGraph, a graph generator for proteins.",
     long_description=long_description,