Merge pull request #281 from icbi-lab/issue-280

Fix #280

Author: grst

scirpy/io/_datastructures.py

@@ -184,9 +184,17 @@ def _split_chains(self) -> Tuple[bool, dict]:
         for tmp_chain in self.chains:
             if "locus" not in tmp_chain:
                 split_chains["extra"].append(tmp_chain)
-            elif tmp_chain["locus"] in self.VJ_LOCI and tmp_chain["productive"]:
+            elif (
+                tmp_chain["locus"] in self.VJ_LOCI
+                and tmp_chain["productive"]
+                and not _is_na2(tmp_chain["junction_aa"])
+            ):
                 split_chains["VJ"].append(tmp_chain)
-            elif tmp_chain["locus"] in self.VDJ_LOCI and tmp_chain["productive"]:
+            elif (
+                tmp_chain["locus"] in self.VDJ_LOCI
+                and tmp_chain["productive"]
+                and not _is_na2(tmp_chain["junction_aa"])
+            ):
                 split_chains["VDJ"].append(tmp_chain)
             else:
                 split_chains["extra"].append(tmp_chain)

scirpy/io/_io.py

@@ -349,7 +349,9 @@ def read_airr(
      * at least one of `junction_aa` or `junction`.
 
     Data should still import if one of these fields is missing, but they are required
-    by most of scirpy's processing functions. 
+    by most of scirpy's processing functions. All chains for which the field
+    `junction_aa` is missing or empty, will be considered as non-productive and 
+    will be moved to the `extra_chains` column.   
 
     {doc_working_model}
 

scirpy/io/_util.py

@@ -13,9 +13,10 @@
        and cells flagged as :term:`Multichain-cell`.
      * Non-productive chains are ignored. 
      * Chain loci must be valid :term:`IGMT locus names<Chain locus>`.
-     * Excess chains, non-productive chains, or chains with invalid loci
-       are serialized to JSON and stored in the `extra_chains` column. They are not 
-       used by scirpy except when exporting the `AnnData` object to AIRR format. 
+     * Excess chains, non-productive chains, chains without a CDR3 sequence, 
+       or chains with invalid loci are serialized to JSON and stored in the 
+       `extra_chains` column. They are not used by scirpy except when exporting 
+       the `AnnData` object to AIRR format. 
 
     For more information, see :ref:`receptor-model`.
 """

scirpy/tests/data/airr/tra_issue_280.tsv

@@ -0,0 +1,6 @@
+cell_id	sequence_id	UMI_sequence	consensus_count	duplicate_count	sequence	locus	stop_codon	vj_in_frame	productive	rev_comp	v_call	d_call	j_call	sequence_alignment	germline_alignment	sequence_alignment_aa	germline_alignment_aa	v_alignment_start	v_alignment_end	d_alignment_start	d_alignment_end	j_alignment_start	j_alignment_end	v_sequence_alignment	v_sequence_alignment_aa	v_germline_alignment	v_germline_alignment_aa	d_sequence_alignment	d_sequence_alignment_aa	d_germline_alignment	d_germline_alignment_aa	j_sequence_alignment	j_sequence_alignment_aa	j_germline_alignment	j_germline_alignment_aa	fwr1	fwr1_aa	cdr1	cdr1_aa	fwr2	fwr2_aa	cdr2	cdr2_aa	fwr3	fwr3_aa	fwr4	fwr4_aa	cdr3	cdr3_aa	junction	junction_length	junction_aa	junction_aa_length	v_score	d_score	j_score	v_cigar	d_cigar	j_cigar	v_support	d_support	j_support	v_identity	d_identity	j_identity	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	fwr1_start	fwr1_end	cdr1_start	cdr1_end	fwr2_start	fwr2_end	cdr2_start	cdr2_end	fwr3_start	fwr3_end	fwr4_start	fwr4_end	cdr3_start	cdr3_end	np1	np1_length	np2	np2_length
+AACCGAAAGCT	CAATCGGT|CELL_ID=AACCGAAAGCT|PRFREQ=0.9390439525184472|CONSCOUNT=2927|DUPCOUNT=1	CAATCGGT	2927	1	TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGTGCCAGCTCTCTCGGGGGGGAGAGTCAAAACACCTTGTACTTTGGTGCGGGCACCCGACTATCGGTGCTAG	TRB	F	T	T	T	TRBV12-2*01	TRBD2*01	TRBJ2-4*01	TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGTGCCAGCTCTCTCGGGGGGGAGAGTCAAAACACCTTGTACTTTGGTGCGGGCACCCGACTATCGGTGCTAG	TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGTGCCAGCTCTCTCGGGGGGGNNAGTCAAAACACCTTGTACTTTGGTGCGGGCACCCGACTATCGGTGCTAG	SVQQFDDYHSEMNMSALELEDSAVYFCASSLGGESQNTLYFGAGTRLSVL	SVQQFDDYHSEMNMSALELEDSAVYFCASSLGGXSQNTLYFGAGTRLSVL	1	93	94	100	103	151	TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGTGCCAGCTCTCTC	SVQQFDDYHSEMNMSALELEDSAVYFCASSL	TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGTGCCAGCTCTCTC	SVQQFDDYHSEMNMSALELEDSAVYFCASSL	GGGGGGG	GG	GGGGGGG	GG	AGTCAAAACACCTTGTACTTTGGTGCGGGCACCCGACTATCGGTGCTAG	SQNTLYFGAGTRLSVL	AGTCAAAACACCTTGTACTTTGGTGCGGGCACCCGACTATCGGTGCTAG	SQNTLYFGAGTRLSVL									TCAGTCCAACAGTTTGATGACTATCACTCTGAGATGAACATGAGTGCCTTGGAGCTAGAGGACTCTGCCGTGTACTTCTGT	SVQQFDDYHSEMNMSALELEDSAVYFC	TTTGGTGCGGGCACCCGACTATCGGTGCTA	FGAGTRLSVL	GCCAGCTCTCTCGGGGGGGAGAGTCAAAACACCTTGTAC	ASSLGGESQNTLY	TGTGCCAGCTCTCTCGGGGGGGAGAGTCAAAACACCTTGTACTTT	45	CASSLGGESQNTLYF	15	146.741	14.146	94.899	192N93M58S	93S6N7M51S1N	102S49M	7.31E-35	2.16E+02	1.65E-20	100.000	100.000	100.000	1	93	193	285	94	100	7	13	103	151	1	49									1	81	121	150	82	120		0	AG	2
+AACCGAAAGCT	CATACACG|CELL_ID=AACCGAAAGCT|PRFREQ=0.88|CONSCOUNT=785|DUPCOUNT=4	CATACACG	785	4	GGACGATTCACAAACTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGTGCAGCAAGGGGTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	TRA	F	T	T	T	"TRAV14-1*01,TRAV14-2*01,TRAV14-2*03"		"TRAJ31*01,TRAJ31*02"	GGACGATTCACAAACTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGTGCAGCAAGGGGTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	GGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGTGCAGCAAGNNNTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	GRFTNFFNKREKKLSLHITDSQPGDSATYFCAARGNRIFFGDGTQLVVKP	GRFTIFFNKREKKLSLHITDSQPGDSATYFCAAXXNRIFFGDGTQLVVKP	1	101			105	151	GGACGATTCACAAACTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGTGCAGCAAG	GRFTNFFNKREKKLSLHITDSQPGDSATYFCAA	GGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGTGCAGCAAG	GRFTIFFNKREKKLSLHITDSQPGDSATYFCAA					TAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	NRIFFGDGTQLVVKP	TAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	NRIFFGDGTQLVVKP									GGACGATTCACAAACTTCTTCAATAAAAGGGAGAAAAAGCTCTCCTTGCACATCACAGACTCTCAGCCTGGAGACTCAGCTACCTACTTCTGT	GRFTNFFNKREKKLSLHITDSQPGDSATYFC	TTTGGTGATGGGACGCAGCTGGTGGTGAAGCCC	FGDGTQLVVKP	GCAGCAAGGGGTAACAGAATCTTC	AARGNRIF	TGTGCAGCAAGGGGTAACAGAATCTTCTTT	30	CAARGNRIFF	10	156.089		91.054	177N101M50S2N		104S10N47M	1.12E-37		2.36E-19	99.010		100.000	1	101	178	278					105	151	11	57									1	93	118	150	94	117	GGG	3		
+AACCGAAAGCT	CGTTACCC|CELL_ID=AACCGAAAGCT|PRFREQ=0.8305084745762712|CONSCOUNT=49|DUPCOUNT=1	CGTTACCC	49	1	AGCTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAGGACAGCAAGGGGTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	TRA	T	F	F	T	"TRAV14-1*01,TRAV14N-1*01"		"TRAJ31*01,TRAJ31*02"	CTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAGGACAGCAAGGGGTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	CTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAGGACAGCANNNNNTAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	LTVWEGETAILNCSYEDSKG*QNLLW*WDAAGGEA	LTVWEGETAILNCSYEDSXX*QNLLW*WDAAGGEA	1	57			63	109	CTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAGGACAGCA	LTVWEGETAILNCSYEDS	CTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAGGACAGCA	LTVWEGETAILNCSYEDS					TAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	*QNLLW*WDAAGGEA	TAACAGAATCTTCTTTGGTGATGGGACGCAGCTGGTGGTGAAGCCCA	*QNLLW*WDAAGGEA	CTCTGACAGTCTGGGAAGGAGAGACCGCAATTCTGAACTGCAGTTATGAG	LTVWEGETAILNCSYE	GACAGCA	DS															90.649		91.054	2S28N57M52S195N		64S10N47M	3.89E-18		1.69E-19	100.000		100.000	3	59	29	85					65	111	11	57	3	52	53	59											AGGGG	5		
+AACCGAAAGCT	CAGATGAC|CELL_ID=AACCGAAAGCT|PRFREQ=0.9730586370839936|CONSCOUNT=8396|DUPCOUNT=2	CAGATGAC	8396	2	GCTCGTGGGCTCGGNGATGNGTATAAGGGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCACATATAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	TRB	F	T	T	T	"TRBV16*01,TRBV16*02,TRBV16*04"		TRBJ2-1*01	AAGGGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCACATATAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	AAGGGACAAGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCANNNNTAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	KGQEATLWCEPISGHSAVFWYRQTTYNYAEQFFGPGTRLTVL	KGQEATLWCEPISGHSAVFWYRQTXXNYAEQFFGPGTRLTVL	1	73			78	127	AAGGGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCA	KGQEATLWCEPISGHSAVFWYRQT	AAGGGACAAGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCA	KGQEATLWCEPISGHSAVFWYRQT					TAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	NYAEQFFGPGTRLTVL	TAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	NYAEQFFGPGTRLTVL	AAGGGACAGGAAGCAACTCTGTGGTGTGAGCCAATT	KGQEATLWCEPI	TCAGGACATAGTGCT	SGHSA	GTTTTCTGGTACAGACAGACCA	VFWYRQT													112.462		96.822	24S42N73M54S175N		101S50M	1.52E-24		4.34E-21	98.630		100.000	25	97	43	115					102	151	1	50	25	60	61	75	76	97									CATA	4		
+AACCGAAAGCT	CAGTGCTC|CELL_ID=AACCGAAAGCT|PRFREQ=0.9697986577181208|CONSCOUNT=578|DUPCOUNT=1	CAGTGCTC	578	1	NCTCGTNGGCTCGGNGATGTGTATAAGNGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCACATATAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	TRB	F	T	T	T	"TRBV16*01,TRBV16*02,TRBV16*04"		TRBJ2-1*01	AAGNGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCACATATAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	AAGGGACAAGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCANNNNTAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	KXQEATLWCEPISGHSAVFWYRQTTYNYAEQFFGPGTRLTVL	KGQEATLWCEPISGHSAVFWYRQTXXNYAEQFFGPGTRLTVL	1	73			78	127	AAGNGACAGGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCA	KXQEATLWCEPISGHSAVFWYRQT	AAGGGACAAGAAGCAACTCTGTGGTGTGAGCCAATTTCAGGACATAGTGCTGTTTTCTGGTACAGACAGACCA	KGQEATLWCEPISGHSAVFWYRQT					TAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	NYAEQFFGPGTRLTVL	TAACTATGCTGAGCAGTTCTTCGGACCAGGGACACGACTCACCGTCCTAG	NYAEQFFGPGTRLTVL	AAGNGACAGGAAGCAACTCTGTGGTGTGAGCCAATT	KXQEATLWCEPI	TCAGGACATAGTGCT	SGHSA	GTTTTCTGGTACAGACAGACCA	VFWYRQT													109.346		96.822	24S42N73M54S175N		101S50M	1.32E-23		4.34E-21	97.260		100.000	25	97	43	115					102	151	1	50	25	60	61	75	76	97									CATA	4		

scirpy/tests/test_io.py

@@ -347,6 +347,14 @@ def test_read_tracer():
     assert cell2["IR_VDJ_1_j_call"] == "TRBJ2-5"
 
 
+@pytest.mark.conda
+def test_read_airr_issue280():
+    """Test that reading the example shown in issue #280 works."""
+    anndata = read_airr(TESTDATA / "airr" / "tra_issue_280.tsv")
+    assert anndata.obs["IR_VDJ_1_junction_aa"][0] == "CASSLGGESQNTLYF"
+    assert anndata.obs["IR_VJ_1_junction_aa"][0] == "CAARGNRIFF"
+
+
 @pytest.mark.conda
 def test_read_airr():
     # Test that reading the files one-by-one or at once yields the same results