Merge branch 'master' into addlusplus

bioforensics · Oct 31, 2023 · 1954c19 · 1954c19
2 parents 04953e6 + 632174e
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diff --git a/README.md b/README.md
@@ -222,11 +222,11 @@ One additional argument can be provided with ```lusstr config --snps```:
 ___
 ## Running the lusSTR SNP workflow
 
-The lusSTR SNP workflow consists of three steps:  
+The lusSTR SNP workflow consists of two steps:  
 (1) ```format```: formatting input and calling alleles if using STRait Razor data  
-(2) ```convert```: applying analytical threshold; converting data to correct format for input into EuroForMix;  
+(2) ```convert```: applying analytical threshold and converting data to correct format for input into EuroForMix
 
-Any or all steps can be run. In order to run all three steps, the following command can be used:  
+Either the first step, format, or both steps can be run. In order to run both steps, the following command can be used:  
 ```
 lusstr snps all
 ```
@@ -238,16 +238,12 @@ The default working directory is the current directory.
 lusstr snps all -w lusstr_files/  
 ```
 
-Individual steps can also be run  
+Individual format step can also be run  
 ```
 lusstr snps format -w lusstr_files/  
 ```
 
-```
-lusstr snps convert -w lusstr_files/  
-```
-
-**In order to run the ```convert``` step, the appropriately formatted ```.csv``` file containing the sequences normally created in the ```format``` step must be present in the working directory. See the below ```Usage``` section for specific information about that file (required columns, etc.).**  
+**In order to run the ```all``` step, the appropriately formatted ```.csv``` file containing the sequences normally created in the ```format``` step must be present in the working directory. See the below ```Usage``` section for specific information about that file (required columns, etc.).**  
 
 ----
 
@@ -256,7 +252,7 @@ lusstr snps convert -w lusstr_files/
 
 ### Formatting input for SNP data  
 
-If inputting data from either the UAS Sample Details Report/Phenotype Report/Sample Report or STRait Razor output, the user must first invoke the ```format``` step to extract necessary information and format for the ```convert``` step.  
+If inputting data from either the UAS Sample Details Report/Phenotype Report/Sample Report or STRait Razor output, the user must first invoke the ```format``` step to extract necessary information and format for the final ```convert``` step.  
 
 The ```format``` command removes unnecessary rows/columns and outputs a table in CSV format containing the following columns:  
 *  Sample ID  
@@ -271,7 +267,7 @@ The ```format``` command removes unnecessary rows/columns and outputs a table in
 
 ### Converting to appropriately formatted files for use in EuroForMix  
 
-This step will convert the table generated in the ```format``` step into the correct format for use in EuroForMix. An analytical threshold can be applied (this is especially useful for data analyzed using STRait Razor) in this step.  
+This final step will convert the table generated in the ```format``` step into the correct format for use in EuroForMix. An analytical threshold can be applied (this is especially useful for data analyzed using STRait Razor) in this step.  
 
 If any samples are to be used as references, their IDs can be provided in the config file to create a separate file appropriately formatted for use as reference profiles in EFM. Any samples not specified as references are assumed to be evidence samples and will be formatted as such.  
 

diff --git a/lusSTR/data/snp_data.json b/lusSTR/data/snp_data.json
@@ -623,7 +623,7 @@
         "ReverseCompNeeded": "Yes",
         "Coord": 50
     },
-    "rs312262906_N29insA": {
+    "rs312262906": {
         "Type": "p",
         "Alleles": ["C", "insA"],
         "ReverseCompNeeded": "No",

diff --git a/lusSTR/tests/data/NA24385 Sample Report 2023_09_07_15_11_11.xlsx b/lusSTR/tests/data/NA24385 Sample Report 2023_09_07_15_11_11.xlsx
diff --git a/lusSTR/tests/data/kinsnps/Kin_pos_1ng_snpsetscombined_evidence.csv b/lusSTR/tests/data/kinsnps/Kin_pos_1ng_snpsetscombined_evidence.csv
@@ -1911,7 +1911,6 @@ Kin_pos_1ng_set1	rs543502	3	4	42.0	33.0	75.0
 Kin_pos_1ng_set1	rs6671673	4	2	45.0	30.0	75.0
 Kin_pos_1ng_set1	rs7176165	4		75.0		75.0
 Kin_pos_1ng_set1	rs7706034	1		75.0		75.0
-Kin_pos_1ng_set1	N29insA	2		76.0		76.0
 Kin_pos_1ng_set1	rs1009930	1		76.0		76.0
 Kin_pos_1ng_set1	rs10167782	4		76.0		76.0
 Kin_pos_1ng_set1	rs10196560	2		76.0		76.0
@@ -1949,6 +1948,7 @@ Kin_pos_1ng_set1	rs2723696	1		76.0		76.0
 Kin_pos_1ng_set1	rs2816999	4	2	40.0	36.0	76.0
 Kin_pos_1ng_set1	rs295340	1		76.0		76.0
 Kin_pos_1ng_set1	rs3018845	2	4	44.0	32.0	76.0
+Kin_pos_1ng_set1	rs312262906	2		76.0		76.0
 Kin_pos_1ng_set1	rs340828	3	1	46.0	30.0	76.0
 Kin_pos_1ng_set1	rs369005	2	4	39.0	37.0	76.0
 Kin_pos_1ng_set1	rs3923451	4		76.0		76.0

diff --git a/lusSTR/tests/data/kinsnps/evidence.csv b/lusSTR/tests/data/kinsnps/evidence.csv
@@ -1,5 +1,4 @@
 Sample Name	Marker	Allele 1	Allele 2	Height 1	Height 2
-Kin_pos_1ng	N29insA	2		76.0	
 Kin_pos_1ng	rs1000022	2	4	176.0	142.0
 Kin_pos_1ng	rs1000137	4	2	66.0	36.0
 Kin_pos_1ng	rs10002268	4		365.0	
@@ -4521,6 +4520,7 @@ Kin_pos_1ng	rs3117915	1	3	85.0	117.0
 Kin_pos_1ng	rs3118520	3		554.0	
 Kin_pos_1ng	rs312154	4	3	69.0	51.0
 Kin_pos_1ng	rs312185	1	2	152.0	146.0
+Kin_pos_1ng	rs312262906	2		76.0	
 Kin_pos_1ng	rs312272	2		32.0	
 Kin_pos_1ng	rs3124028	4		96.0	
 Kin_pos_1ng	rs3124041	3		221.0	

diff --git a/lusSTR/tests/data/kinsnps/multiplerefs.csv b/lusSTR/tests/data/kinsnps/multiplerefs.csv
@@ -1,5 +1,4 @@
 Sample Name	Marker	Allele 1	Allele 2
-Kin_pos_reference	N29insA	2	2
 Kin_pos_reference	rs1000022	2	4
 Kin_pos_reference	rs1000137	4	2
 Kin_pos_reference	rs10002268	4	4
@@ -4521,6 +4520,7 @@ Kin_pos_reference	rs3117915	1	3
 Kin_pos_reference	rs3118520	3	3
 Kin_pos_reference	rs312154	4	3
 Kin_pos_reference	rs312185	1	2
+Kin_pos_reference	rs312262906	2	2
 Kin_pos_reference	rs312272	2	2
 Kin_pos_reference	rs3124028	4	4
 Kin_pos_reference	rs3124041	3	3
@@ -9235,7 +9235,6 @@ Kin_pos_reference	rs999717	1	2
 Kin_pos_reference	rs999813	4	3
 Kin_pos_reference	rs9999446	1	3
 Kin_pos_reference	rs9999662	1	1
-Kin_pos_1ng	N29insA	2	2
 Kin_pos_1ng	rs1000022	2	4
 Kin_pos_1ng	rs1000137	4	2
 Kin_pos_1ng	rs10002268	4	4
@@ -13757,6 +13756,7 @@ Kin_pos_1ng	rs3117915	1	3
 Kin_pos_1ng	rs3118520	3	3
 Kin_pos_1ng	rs312154	4	3
 Kin_pos_1ng	rs312185	1	2
+Kin_pos_1ng	rs312262906	2	2
 Kin_pos_1ng	rs312272	2	2
 Kin_pos_1ng	rs3124028	4	4
 Kin_pos_1ng	rs3124041	3	3

diff --git a/lusSTR/tests/data/kinsnps/reference.csv b/lusSTR/tests/data/kinsnps/reference.csv
@@ -1,5 +1,4 @@
 Sample Name	Marker	Allele 1	Allele 2
-Kin_pos_reference	N29insA	2	2
 Kin_pos_reference	rs1000022	2	4
 Kin_pos_reference	rs1000137	4	2
 Kin_pos_reference	rs10002268	4	4
@@ -4521,6 +4520,7 @@ Kin_pos_reference	rs3117915	1	3
 Kin_pos_reference	rs3118520	3	3
 Kin_pos_reference	rs312154	4	3
 Kin_pos_reference	rs312185	1	2
+Kin_pos_reference	rs312262906	2	2
 Kin_pos_reference	rs312272	2	2
 Kin_pos_reference	rs3124028	4	4
 Kin_pos_reference	rs3124041	3	3

diff --git a/lusSTR/tests/data/kinsnps/snps_kin_all.txt b/lusSTR/tests/data/kinsnps/snps_kin_all.txt
@@ -10225,6 +10225,8 @@ Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs3124028	0	G	G	Kintelligence	Contains untyped allele
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312272	32	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312272	10	T	T	Kintelligence	Contains untyped allele
+Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312262906	76	C	C	Phenotype	
+Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312262906	0	A	A	Phenotype	Contains untyped allele
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312185	152	A	A	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312185	146	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312154	69	T	T	Kintelligence	
@@ -20075,5 +20077,3 @@ Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs100
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000137	36	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000022	176	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000022	142	T	T	Kintelligence	
-Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	N29insA	76	C	C	Kintelligence	
-Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	N29insA	0	A	A	Kintelligence	Contains untyped allele
diff --git a/lusSTR/tests/data/kinsnps/snps_kin_filtered.txt b/lusSTR/tests/data/kinsnps/snps_kin_filtered.txt
@@ -6692,6 +6692,7 @@ Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs3124041	221	G	G	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs3124028	96	T	T	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312272	32	C	C	Kintelligence	
+Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312262906	76	C	C	Phenotype	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312185	152	A	A	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312185	146	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs312154	69	T	T	Kintelligence	
@@ -13115,4 +13116,3 @@ Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs100
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000137	36	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000022	176	C	C	Kintelligence	
 Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	rs1000022	142	T	T	Kintelligence	
-Kin_pos_reference	Kintelligence Test	Verogen Kintelligence Analysis Method	N29insA	76	C	C	Kintelligence