check plotting density plots for a signal-to-read alignment

hiruna72 · Nov 17, 2024 · 6b7a401 · 6b7a401
1 parent dc4c987
commit 6b7a401
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diff --git a/src/calculate_offsets.py b/src/calculate_offsets.py
@@ -162,6 +162,8 @@ def calculate_offsets(args, sig_move_offset, output_pdf, s5):
                     fasta_seq = fasta_seq.replace('N', 'T')
                 elif 'U' in fasta_seq:
                     fasta_seq = fasta_seq.replace('U', 'T')
+            if not ('T' in fasta_seq and 'A' in fasta_seq and 'C' in fasta_seq and 'G' in fasta_seq):
+                continue
             if args.rna:
                 fasta_seq = fasta_seq[::-1]
 

diff --git a/test/data/raw/calculate_offsets/calculate_offset_dataset/read_density_plot.pdf b/test/data/raw/calculate_offsets/calculate_offset_dataset/read_density_plot.pdf
diff --git a/test/data/raw/calculate_offsets/calculate_offset_dataset/readlist.txt b/test/data/raw/calculate_offsets/calculate_offset_dataset/readlist.txt
@@ -0,0 +1,10 @@
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+81e012b2-c897-4821-976b-47aafabd054d
+4e1ffff1-46a9-437c-ada0-f4840e5c66c0
+1aa08fb6-8ca1-418e-86c4-c225b12fb19d
+ce0cfbdb-0175-48ec-8d1a-c799e7dfc4c1
+b5be7cec-222a-4948-87b0-8171d6a41a7e
+fd0074eb-780f-46c5-a8b1-1bfa254c55bc
+cec6a34b-270e-4d3e-8632-81ec7d53f95a
+9d12ebf3-59d2-415d-8e16-f4ae7fe2efc6
+e7291b90-d8cc-4305-bab8-2e2696831423
diff --git a/test/data/raw/calculate_offsets/calculate_offset_dataset/reads.blow5 b/test/data/raw/calculate_offsets/calculate_offset_dataset/reads.blow5
diff --git a/test/data/raw/calculate_offsets/calculate_offset_dataset/reads.fastq b/test/data/raw/calculate_offsets/calculate_offset_dataset/reads.fastq
diff --git a/test/data/raw/calculate_offsets/calculate_offset_dataset/reform.paf b/test/data/raw/calculate_offsets/calculate_offset_dataset/reform.paf