2022-02-23: 0.4.1 (GUI). Fixed bug in upload_tcr_details

README.md

@@ -389,7 +389,7 @@ Note that the third example there uses the preferred allele option and specifies
 * `-jt` - length of J gene substring that has to be matched to avoid throwing a warning (decrease to get fewer notices about short J matches), default = 3
 
 # GUI-stitchr 
-### 0.4.0
+### 0.4.1
 
 A graphical interface has been developed for users that are less comfortable at the command line, or who prefer a more immediately interactive session. It can be launched from inside the Scripts directory like so:
 

Scripts/gui-stitchr.py

@@ -17,7 +17,7 @@
 import collections as coll
 import warnings
 
-__version__ = '0.4.0'
+__version__ = '0.4.1'
 __author__ = 'Jamie Heather'
 __email__ = 'jheather@mgh.harvard.edu'
 
@@ -98,12 +98,13 @@ def change_receptors(receptor_str):
     return new_receptor
 
 
-def upload_tcr_details(path_to_file, receptor_type):
+def upload_tcr_details(path_to_file, receptor_type, stated_species):
     """
     Read suitably formatted TCRs in template format to the GUI
     :param path_to_file: str detailing the full path to the input file
     :param receptor_type: str detailing the receptor in use, i.e. either 'TRA/TRB' or 'TRG/TRD'
-    :return: str of receptor type again, in case it switches during the course of reading the TCR file in
+    :param stated_species: str of the species on record before the upload, to remain if one not inferred
+    :return: strs of receptor type and species again, in case they switch during the course of reading the TCR file in
     """
 
     # This section uses the Thimble format input file to populate the GUI fields
@@ -119,6 +120,7 @@ def upload_tcr_details(path_to_file, receptor_type):
             inferred_species = species_inference
             window['species_choice'].update(inferred_species)
         else:
+            inferred_species = stated_species
             sg.Popup("Cannot infer species name from file name:\nplease set manually.")
 
         with open(path_to_file, 'r') as in_file:
@@ -361,7 +363,7 @@ def upload_tcr_details(path_to_file, receptor_type):
                          'using the first alphabetically.')
                 example_matches.sort()
 
-            receptor, species = upload_tcr_details(examples_path + example_matches[0], receptor)
+            receptor, species = upload_tcr_details(examples_path + example_matches[0], receptor, species)
 
     elif event == 'change_receptor':
 
@@ -391,7 +393,7 @@ def upload_tcr_details(path_to_file, receptor_type):
 
     elif event == 'Upload TCR details':
 
-        receptor = upload_tcr_details(values['uploaded_tcr'], receptor)
+        receptor, species = upload_tcr_details(values['uploaded_tcr'], receptor, species)
 
     elif event == 'find_preferred_alleles':
 

Templates/GUI-Examples/human_TRG-TRD.tsv

@@ -1,2 +1,2 @@
 TCR_name	TRGV	TRGJ	TRG_CDR3	TRDV	TRDJ	TRD_CDR3	TRGC	TRDC	TRG_leader	TRD_leader	Linker	Link_order	TRG_5_prime_seq	TRG_3_prime_seq	TRD_5_prime_seq	TRD_3_prime_seq
-Y00482/X14547	TRGV5*01	TRGJ1*02	CATWAPNYYKKLF	TRDV2*03	TRDJ1*01	CACDTLRTGGRLYTDKLIF	TRGC1*01	TRDC*01	TRGV5*01	TRDV2*03	P2A	GD
+Y00482/X14547	TRGV5*01	TRGJ1*02	CATWAPNYYKKLF	TRDV2*03	TRDJ1*01	CACDTLRTGGRLYTDKLIF	TRGC1*01	TRDC*01	TRGV5*01	TRDV2*03	P2A	GD