converting to universal format

cjs/.app/database/debug/output/test3/qualitative_reqbt-3-2.csv

@@ -0,0 +1,2 @@
+"EvidFile" "POI" "log10LR"
+"/home/csguest/Desktop/cjs2/cjs/.app/database/debug/tmp/reqbt-3.tsv" "reqbt-3-2" "6.65717772882058e-29"

cjs/cjs.py

@@ -6,15 +6,16 @@ import click
 from database import database
 from automate import automate
 from reqbt import reqbt
-
 from graphs import graphs
+from convert import convert
 
 
 _commands = [
     database,
     automate,
     reqbt,
-    graphs
+    graphs,
+    convert
 ]
 
 # main-entry point to the entire command-line interface

cjs/convert.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+
+# standard library
+import csv
+
+# pip
+import click
+
+import pprint
+from pprint import pprint
+
+# local modules
+import utils.fs
+from utils.fs import search_dir
+
+import utils.io
+from utils.io import write_json
+
+jfs2003id_loci = [
+    'D8S1179',
+    'D21S11',
+    'D7S820',
+    'CSF1PO',
+    'D3S1358',
+    'TH01',
+    'D13S317',
+    'D16S539',
+    'D2S1338',
+    'D19S433',
+    'vWA',
+    'TPOX',
+    'D18S51',
+    'AMEL',
+    'D5S818',
+    'FGA',
+]
+
+@click.group()
+@click.pass_context
+def convert(ctx):
+    pass
+
+@convert.command()
+@click.argument('input_dir', type=click.Path())
+@click.argument('output_dir', type=click.Path())
+@click.pass_context
+def jfs2003id(ctx, input_dir, output_dir):
+    input_files = search_dir(input_dir, '*.csv')
+  
+    output_dict =  {}
+    for file_path in input_files:
+        with open(file_path, 'r') as f:
+            reader = csv.DictReader(f)
+
+            race_list = []
+            for row in reader:
+                tmp_dict = {}
+                name = row['Sample Info']
+                tmp_dict['name'] = name
+                for locus in jfs2003id_loci:
+                    alleles = []
+                    for i in range(2):
+                        key = '%s %d' % (locus, (i+1))
+                        alleles.append(row[key])
+                    tmp_dict[locus] = alleles
+                race_list.append(tmp_dict)
+            output_dict[file_path.stem.split('-')[1]] = race_list
+    write_json('%s/jfs2003id.json' % output_dir, output_dict)
+            
+
+                
+                    
+                    
+                    
+                        
+
+
+    
+

cjs/graphs.py

@@ -5,6 +5,12 @@ import csv
 import math
 from decimal import Decimal
 
+import utils.fs
+from utils.fs import search_dir
+
+import utils.io
+from utils.io import write_csv
+
 import click
 
 @click.group()
@@ -16,19 +22,52 @@ def graphs(ctx):
 @graphs.command()
 @click.pass_context
 def efm(ctx):
+    import natsort
+
     plt.style.use('seaborn-whitegrid')
     # x,y axis values
     x = []
     y = []
 
+    result_files = search_dir('resources/fixed-db-test/', '*.csv')
+    result_values = []
+    output = []
+    for result in result_files:
+        with open(result, 'r') as f:
+            reader = csv.reader(f, delimiter=' ')
+            data = list(reader)
+            evid = data[1][0].split('/')[-1].split('.')[0]
+            comp = data[1][1]
+            lr = data[1][2]
+            y.append(Decimal(lr))
+            print(evid)
+            print(comp)
+            print(lr)
+            row = [evid, comp, lr]
+            output.append(row)
+
+
+
+    output = natsort.natsorted(output, key=lambda x: x[0])
+    
+    output.insert(0, ['evidence_name', 'comparison_name', 'likelihood_ratio'])
+    with open('euroformix_pilot.csv', 'w') as f:
+        writer = csv.writer(f)
+        writer.writerows(output)
+
+
     # open & read the csv file
-    with open('resources/graph_data.csv','r') as csv_file:
+    with open('resources/lowest-with-drop.csv','r') as csv_file:
         csv_reader = csv.reader(csv_file, delimiter=',')
+        next(csv_reader)
 
         #loop through all rows. Puts column (0) in x, & column (1) in y.
         for i, row in enumerate(csv_reader):
-            y.append(math.log10(Decimal(row[0])))
-            x.append(math.log10(Decimal(row[1])))
+            x.append(Decimal(row[0]))
+
+    print(len(x))
+    print(len(y))
+    x = x[0:1244]
 
     plt.rcParams['axes.facecolor'] = '#ededed'
     plt.ticklabel_format(style='sci', axis='x')
@@ -38,8 +77,8 @@ def efm(ctx):
     plt.scatter(x,y, s=0.75, color='black')
 
     # naming the x,y axis
-    plt.xlabel('LR - EuroForMix v2.1.0')
-    plt.ylabel('LR - Forensic Statistical Tool v2.0')
+    plt.xlabel('LR - Forensic Statistical Tool v1.5 - With CheckFrequencyForRemoval')
+    plt.ylabel("LR - EuroForMix v2.1.0 - Nate's Settings")
 
     # giving a title to the graph
     plt.title('EuroForMix Vs. Forensic Statistical Tool')
@@ -48,4 +87,4 @@ def efm(ctx):
     plt.legend()
 
     # function to show the plot
-    plt.show()
+    plt.show()

cjs/resources/comparison_profiles/non_contributors/jfs2003id-african_americans.csv

@@ -0,0 +1,259 @@
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+OT05894,14,15,29,37,8,12,7,10,15,15,7,7,12,13,11,11,20,22,11,14,18,18,8,11,13.2,16,X,Y,12,13,23,25
+OT05896,14,15,30,30,10,10,11,12,15,17,8,9,12,12,11,11,20,22,14,14,15,18,8,10,18,18,X,Y,11,12,19,25
+OT05897,13,13,27,30,8,8,12,13,16,18,7,8,11,12,11,13,16,21,14,14.2,16,18,11,11,15,17,X,Y,12,12,22,23
+OT05898,13,15,29,32.2,8,13,8,11,14,15,8,9,12,13,11,11,23,23,14,16.2,15,17,6,9,17,17,X,Y,8,12,19,22
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+OT05901,13,16,27,28,9,9,10,11,15,18,7,7,8,11,9,10,23,25,15.2,16.2,18,18,6,11,18,18,X,Y,11,12,22,23
+OT06795,11,17,29,30,11,11,12,12,17,17,7,9,8,9,12,13,20,24,13,16.2,17,18,8,9,13,14,X,Y,11,13,23,26
+PT84214,14,15,28,32.2,10,10,11,12,16,17,6,8,12,12,12,13,20,21,14,14.2,17,17,10,11,12,13.2,X,Y,12,12,21,24
+PT84215,12,14,31.2,32,8,9,7,11,15,16,8,9.3,12,12,9,11,19,23,13,14,14,16,8,11,15,16,X,Y,12,12,22,22
+PT84216,13,14,30,30,10,10,10,10,15,16,7,8,11,12,12,13,19,21,12,13,13,18,6,8,12,16,X,Y,12,13,24,24
+PT84222,12,16,28,30,9,11,10,12,15,15,7,8,12,13,9,10,23,23,14,14,17,18,9,10,15,17,X,Y,12,14,23,23.2
+PT84223,14,15,29,29,8,10,12,12,17,17,7,7,11,11,11,13,19,21,12,13,16,19,8,11,15,19,X,Y,11,12,21,22
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+PT84225,13,13,31,31,10,11,10,12,17,18,7,7,9,11,9,12,23,24,12,13,14,16,10,12,15,17,X,Y,12,12,24,25
+PT84226,14,14,28,32.2,10,10,11,12,16,16,8,9.3,8,12,11,12,23,25,13,14,15,18,8,11,17,17,X,Y,11,12,23,26
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+PT84231,14,15,27,29,8,9,11,12,15,17,7,9,12,12,12,13,17,24,11,13.2,16,18,8,11,14,17,X,Y,8,13,22,24
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+PT84234,13,15,29,31,10,11,10,12,15,16,6,7,13,13,9,11,19,22,11,13,16,16,6,6,15,16,X,Y,12,13,19.2,25
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+PT84240,11,13,28,29,9,10,10,11,16,17,6,9,11,12,12,13,18,24,11,14.2,16,17,9,11,14,19,X,Y,12,12,23,27
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+PT84242,13,13,30,30,8,11,9,10,16,17,7,9.3,12,12,8,11,24,24,13.2,14,14,17,8,9,12,17,X,Y,11,13,23,25
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cjs/resources/comparison_profiles/non_contributors/jfs2003id-caucasians.csv

@@ -0,0 +1,303 @@
+Sample Info,D8S1179 1,D8S1179 2,D21S11 1,D21S11 2,D7S820 1,D7S820 2,CSF1PO 1,CSF1PO 2,D3S1358 1,D3S1358 2,TH01 1,TH01 2,D13S317 1,D13S317 2,D16S539 1,D16S539 2,D2S1338 1,D2S1338 2,D19S433 1,D19S433 2,vWA 1,vWA 2,TPOX 1,TPOX 2,D18S51 1,D18S51 2,AMEL 1,AMEL 2,D5S818 1,D5S818 2,FGA 1,FGA 2
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+UA16927,10,15,28,30,12,12,11,12,15,17,7,9.3,11,14,12,12,17,19,13,15,16,17,8,12,15,18,X,X,9,13,24,25
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+UT57319,10,14,30,31,8,10,10,12,17,18,9.3,9.3,10,13,11,13,17,24,15,15,17,18,11,11,13,14,X,X,11,12,21,21
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cjs/resources/comparison_profiles/non_contributors/jfs2003id-hispanics.csv

@@ -0,0 +1,141 @@
+Sample Info,D8S1179 1,D8S1179 2,D21S11 1,D21S11 2,D7S820 1,D7S820 2,CSF1PO 1,CSF1PO 2,D3S1358 1,D3S1358 2,TH01 1,TH01 2,D13S317 1,D13S317 2,D16S539 1,D16S539 2,D2S1338 1,D2S1338 2,D19S433 1,D19S433 2,vWA 1,vWA 2,TPOX 1,TPOX 2,D18S51 1,D18S51 2,AMEL 1,AMEL 2,D5S818 1,D5S818 2,FGA 1,FGA 2
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-11-2.csv

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+"EvidFile" "POI" "log10LR"
+"/home/dev/cjs2/cjs/.app/database/testing/tmp/reqbt-11.tsv" "reqbt-11-2" "1681539049.06188"

cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-110-1.csv

@@ -0,0 +1,2 @@
+"EvidFile" "POI" "log10LR"
+"/home/dev/cjs2/cjs/.app/database/testing/tmp/reqbt-110.tsv" "reqbt-110-1" "4369108154.02722"

cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-110-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-111-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-111-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-112-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-112-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-113-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-113-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-114-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-114-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-115-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-115-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-116-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-116-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-117-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-117-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-118-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-118-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-118-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-119-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-119-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-119-3.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-12-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-12-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-120-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-120-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-120-3.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-121-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-121-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-121-3.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-122-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-122-2.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-122-3.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-123-1.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-123-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-123-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-124-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-124-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-124-3.csv

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+"EvidFile" "POI" "log10LR"
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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-125-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-125-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-125-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-126-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-126-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-126-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-127-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-127-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-127-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-128-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-128-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-128-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-129-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-129-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-129-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-13-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-13-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-130-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-130-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-130-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-131-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-131-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-131-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-132-1.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-132-2.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-132-3.csv

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cjs/resources/efm_results/fixed-db-test/qualitative_reqbt-133-1.csv

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