Merge branch 'no_overhangs'

ryandkuster · Apr 3, 2024 · bd78b7c · bd78b7c
2 parents fc08561 + 28f1810
commit bd78b7c
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Showing 9 changed files with 62 additions and 75 deletions.
diff --git a/readsynth.py b/readsynth.py
@@ -300,12 +300,6 @@ def create_adapters(args):
     a2 = ['CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG',
           'CTGTCTCTTATACACATCTCCGAGCCCACGAGACATCTCGTATGCCGTCTTCTGCTTG',
           'rs2']
-    m1 = list(args.motif_dt1.keys())[0]
-    m2 = list(args.motif_dt2.keys())[0]
-    a1[0] = a1[0] + args.m1[0][:args.motif_dt1[m1]]
-    a1[1] = args.m1[0][args.motif_dt1[m1]+1:] + a1[1]
-    a2[0] = a2[0] + args.m2[0][:args.motif_dt2[m2]]
-    a2[1] = args.m2[0][args.motif_dt2[m2]+1:] + a2[1]
 
     return [a1], [a2]
 
@@ -545,11 +539,16 @@ def process_df(df, digest_file, args):
     df = df.reset_index(drop=True)
 
     """
-    add a quick step that removes appropriate over/underhang
+    add a quick step that calculates length based on the adjusted length
+    of sequences after removal of appropriate over/underhang
     """
 
+    df['seq_backup'] = df['seq'].copy()
+    df['revc_backup'] = df['revc'].copy()
+
     for mot, front in args.motif_dt.items():
         back = args.motif_len[mot] - front
+
         df.loc[(df['m1'] == mot) & (df['reverse'] == 0), 'seq'] = \
             df['seq'].str[front:]
         if back != 0:
@@ -572,9 +571,11 @@ def process_df(df, digest_file, args):
             df.loc[(df['m2'] == mot) & (df['reverse'] == 1), 'revc'] = \
                 df['revc'].str[:-back]
 
-
     df['length'] = df['seq'].str.len()
-    #df = df[(df['seq'].str.len() > 0) & (df['revc'].str.len() > 0)]
+    df['seq'] = df['seq_backup']
+    df['revc'] = df['revc_backup']
+    df.drop('seq_backup', axis=1, inplace=True)
+    df.drop('revc_backup', axis=1, inplace=True)
 
     df = df.sort_values(by=['length'])
     df = df.reset_index(drop=True)

diff --git a/test/test_data/genomes/hhai_hhai_process_df_test.csv b/test/test_data/genomes/hhai_hhai_process_df_test.csv
@@ -1,17 +1,17 @@
 seq,start,end,m1,m2,internal,reverse,revc,length
-CAAAAAAAAAAGCG,10,24,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,48,62,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,62,76,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,180,194,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CTTTTTTTTTTGCG,10,24,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,48,62,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,62,76,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,180,194,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CAAAAAAAAAAGCGCAAAAAAAAAAGCG,48,76,GCGC,GCGC,1,0,CTTTTTTTTTTGCGCTTTTTTTTTTGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCG,100,128,GCGC,GCGC,0,0,CTTTTTTTTTTTTAATTTTTTTTTTGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCG,152,180,GCGC,GCGC,0,0,CTTTTTTTTTTTTAATTTTTTTTTTGCG,28
-CTTTTTTTTTTGCGCTTTTTTTTTTGCG,48,76,GCGC,GCGC,1,1,CAAAAAAAAAAGCGCAAAAAAAAAAGCG,28
-CTTTTTTTTTTTTAATTTTTTTTTTGCG,100,128,GCGC,GCGC,0,1,CAAAAAAAAAATTAAAAAAAAAAAAGCG,28
-CTTTTTTTTTTTTAATTTTTTTTTTGCG,152,180,GCGC,GCGC,0,1,CAAAAAAAAAATTAAAAAAAAAAAAGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,152,194,GCGC,GCGC,1,0,CTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCG,42
-CTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCG,152,194,GCGC,GCGC,1,1,CAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,42
+GCGCAAAAAAAAAAGCGC,10,24,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,48,62,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,62,76,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,180,194,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCTTTTTTTTTTGCGC,10,24,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,48,62,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,62,76,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,180,194,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCAAAAAAAAAAGCGCAAAAAAAAAAGCGC,48,76,GCGC,GCGC,1,0,GCGCTTTTTTTTTTGCGCTTTTTTTTTTGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,100,128,GCGC,GCGC,0,0,GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,152,180,GCGC,GCGC,0,0,GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,28
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTGCGC,48,76,GCGC,GCGC,1,1,GCGCAAAAAAAAAAGCGCAAAAAAAAAAGCGC,28
+GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,100,128,GCGC,GCGC,0,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,28
+GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,152,180,GCGC,GCGC,0,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,152,194,GCGC,GCGC,1,0,GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,42
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,152,194,GCGC,GCGC,1,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,42
diff --git a/test/test_data/genomes/hhai_hhai_raw_digest_test1.fasta.csv b/test/test_data/genomes/hhai_hhai_raw_digest_test1.fasta.csv
@@ -1,17 +1,17 @@
 seq,start,end,m1,m2,internal,reverse,revc,length
-CAAAAAAAAAAGCG,10,24,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,48,62,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,62,76,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CAAAAAAAAAAGCG,180,194,GCGC,GCGC,0,0,CTTTTTTTTTTGCG,14
-CTTTTTTTTTTGCG,10,24,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,48,62,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,62,76,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CTTTTTTTTTTGCG,180,194,GCGC,GCGC,0,1,CAAAAAAAAAAGCG,14
-CAAAAAAAAAAGCGCAAAAAAAAAAGCG,48,76,GCGC,GCGC,1,0,CTTTTTTTTTTGCGCTTTTTTTTTTGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCG,100,128,GCGC,GCGC,0,0,CTTTTTTTTTTTTAATTTTTTTTTTGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCG,152,180,GCGC,GCGC,0,0,CTTTTTTTTTTTTAATTTTTTTTTTGCG,28
-CTTTTTTTTTTGCGCTTTTTTTTTTGCG,48,76,GCGC,GCGC,1,1,CAAAAAAAAAAGCGCAAAAAAAAAAGCG,28
-CTTTTTTTTTTTTAATTTTTTTTTTGCG,100,128,GCGC,GCGC,0,1,CAAAAAAAAAATTAAAAAAAAAAAAGCG,28
-CTTTTTTTTTTTTAATTTTTTTTTTGCG,152,180,GCGC,GCGC,0,1,CAAAAAAAAAATTAAAAAAAAAAAAGCG,28
-CAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,152,194,GCGC,GCGC,1,0,CTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCG,42
-CTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCG,152,194,GCGC,GCGC,1,1,CAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,42
+GCGCAAAAAAAAAAGCGC,10,24,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,48,62,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,62,76,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCAAAAAAAAAAGCGC,180,194,GCGC,GCGC,0,0,GCGCTTTTTTTTTTGCGC,14
+GCGCTTTTTTTTTTGCGC,10,24,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,48,62,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,62,76,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCTTTTTTTTTTGCGC,180,194,GCGC,GCGC,0,1,GCGCAAAAAAAAAAGCGC,14
+GCGCAAAAAAAAAAGCGCAAAAAAAAAAGCGC,48,76,GCGC,GCGC,1,0,GCGCTTTTTTTTTTGCGCTTTTTTTTTTGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,100,128,GCGC,GCGC,0,0,GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,152,180,GCGC,GCGC,0,0,GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,28
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTGCGC,48,76,GCGC,GCGC,1,1,GCGCAAAAAAAAAAGCGCAAAAAAAAAAGCGC,28
+GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,100,128,GCGC,GCGC,0,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,28
+GCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,152,180,GCGC,GCGC,0,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGC,28
+GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,152,194,GCGC,GCGC,1,0,GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,42
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAATTTTTTTTTTGCGC,152,194,GCGC,GCGC,1,1,GCGCAAAAAAAAAATTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,42
diff --git a/test/test_data/genomes/hhai_msei_process_df_test.csv b/test/test_data/genomes/hhai_msei_process_df_test.csv
@@ -1,6 +1,6 @@
 seq,start,end,m1,m2,internal,reverse,revc,length
-CAAAAAAAAAAT,100,114,GCGC,TTAA,0,0,TAATTTTTTTTTTGCG,12
-CTTTTTTTTTTT,114,128,TTAA,GCGC,0,1,TAAAAAAAAAAAAGCG,12
-CAAAAAAAAAAT,152,166,GCGC,TTAA,0,0,TAATTTTTTTTTTGCG,12
-CTTTTTTTTTTT,166,180,TTAA,GCGC,0,1,TAAAAAAAAAAAAGCG,12
-CTTTTTTTTTTGCGCTTTTTTTTTTT,166,194,TTAA,GCGC,1,1,TAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,26
+GCGCAAAAAAAAAATTAA,100,114,GCGC,TTAA,0,0,TTAATTTTTTTTTTGCGC,12
+GCGCTTTTTTTTTTTTAA,114,128,TTAA,GCGC,0,1,TTAAAAAAAAAAAAGCGC,12
+GCGCAAAAAAAAAATTAA,152,166,GCGC,TTAA,0,0,TTAATTTTTTTTTTGCGC,12
+GCGCTTTTTTTTTTTTAA,166,180,TTAA,GCGC,0,1,TTAAAAAAAAAAAAGCGC,12
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAA,166,194,TTAA,GCGC,1,1,TTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,26
diff --git a/test/test_data/genomes/hhai_msei_raw_digest_test1.fasta.csv b/test/test_data/genomes/hhai_msei_raw_digest_test1.fasta.csv
@@ -1,6 +1,6 @@
 seq,start,end,m1,m2,internal,reverse,revc,length
-CAAAAAAAAAAT,100,114,GCGC,TTAA,0,0,TAATTTTTTTTTTGCG,12
-CTTTTTTTTTTT,114,128,TTAA,GCGC,0,1,TAAAAAAAAAAAAGCG,12
-CAAAAAAAAAAT,152,166,GCGC,TTAA,0,0,TAATTTTTTTTTTGCG,12
-CTTTTTTTTTTT,166,180,TTAA,GCGC,0,1,TAAAAAAAAAAAAGCG,12
-CTTTTTTTTTTGCGCTTTTTTTTTTT,166,194,TTAA,GCGC,1,1,TAAAAAAAAAAAAGCGCAAAAAAAAAAGCG,26
+GCGCAAAAAAAAAATTAA,100,114,GCGC,TTAA,0,0,TTAATTTTTTTTTTGCGC,12
+GCGCTTTTTTTTTTTTAA,114,128,TTAA,GCGC,0,1,TTAAAAAAAAAAAAGCGC,12
+GCGCAAAAAAAAAATTAA,152,166,GCGC,TTAA,0,0,TTAATTTTTTTTTTGCGC,12
+GCGCTTTTTTTTTTTTAA,166,180,TTAA,GCGC,0,1,TTAAAAAAAAAAAAGCGC,12
+GCGCTTTTTTTTTTGCGCTTTTTTTTTTTTAA,166,194,TTAA,GCGC,1,1,TTAAAAAAAAAAAAGCGCAAAAAAAAAAGCGC,26
diff --git a/test/test_readsynth.py b/test/test_readsynth.py
@@ -142,31 +142,11 @@ def test_get_adapters_1(self):
 
     def test_create_adapters_1(self):
         args = Variables()
-        args.motif_dt1 = {'GCGC': 3}
-        args.motif_dt2 = {'TTAA': 1}
-        args.m1 = ['GCG/C']
-        args.m2 = ['T/TAA']
-        a1 = [['AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGCG',
-               'CCTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT',
-               'rs1']]
-        a2 = [['CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT',
-               'TAACTGTCTCTTATACACATCTCCGAGCCCACGAGACATCTCGTATGCCGTCTTCTGCTTG',
-               'rs2']]
-        args.a1, args.a2 = rs.create_adapters(args)
-        self.assertEqual(args.a1, a1)
-        self.assertEqual(args.a2, a2)
-
-    def test_create_adapters_2(self):
-        args = Variables()
-        args.motif_dt1 = {'GAATTC': 1}
-        args.motif_dt2 = {'TTAA': 1}
-        args.m1 = ['G/AATTC']
-        args.m2 = ['T/TAA']
-        a1 = [['AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGG',
-               'AATTCCTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT',
+        a1 = [['AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG',
+               'CTGTCTCTTATACACATCTGACGCTGCCGACGAGTGTAGATCTCGGTGGTCGCCGTATCATT',
                'rs1']]
-        a2 = [['CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT',
-               'TAACTGTCTCTTATACACATCTCCGAGCCCACGAGACATCTCGTATGCCGTCTTCTGCTTG',
+        a2 = [['CAAGCAGAAGACGGCATACGAGATGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG',
+               'CTGTCTCTTATACACATCTCCGAGCCCACGAGACATCTCGTATGCCGTCTTCTGCTTG',
                'rs2']]
         args.a1, args.a2 = rs.create_adapters(args)
         self.assertEqual(args.a1, a1)

diff --git a/vignettes/helius/run_readsynth.sh b/vignettes/helius/run_readsynth.sh
@@ -1,3 +1,5 @@
+mkdir ecori_msei_10M_output
+
 python3 ../../readsynth.py \
   -g abundances.csv \
   -o ecori_msei_10M_output/ \

diff --git a/vignettes/small_test/run_readsynth.sh b/vignettes/small_test/run_readsynth.sh
@@ -1,3 +1,5 @@
+mkdir small_ecori_msei_1M_output
+
 python3 ../../readsynth.py \
   -g abundances.csv \
   -o small_ecori_msei_1M_output/ \

diff --git a/vignettes/small_test/run_readsynth_error.sh b/vignettes/small_test/run_readsynth_error.sh
@@ -1,3 +1,5 @@
+mkdir small_ecori_msei_1M_error_output
+
 python3 ../readsynth/readsynth.py \
   -g abundances.csv \
   -o small_ecori_msei_1M_error_output/ \