Add extra test for flanking sequence extraction

boasvdp · Feb 18, 2022 · 895e4ca · 895e4ca
1 parent 8d10a44
commit 895e4ca
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Showing 4 changed files with 40 additions and 3 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -51,8 +51,11 @@ jobs:
          python extract_genes_abricate.py -a test/input/test.tsv -g test/genomes -o test/out_genecluster -s .fasta --genecluster
          cmp test/correct/correct_genecluster.fasta test/out_genecluster/input_ncbi.out
          # Testing with flanking sequences
-         python extract_genes_abricate.py -a test/input/flanking.tsv -g test/genomes -o test/out_flanking --flanking --flanking-bp 5
-         cmp test/correct/correct_flanking.out test/out_flanking/flanking_blaCTX-M-15.out
+         python extract_genes_abricate.py -a test/input/flanking.tsv -g test/genomes -o test/out_flanking_5bp --flanking --flanking-bp 5
+         cmp test/correct/correct_flanking_5bp.out test/out_flanking_5bp/flanking_blaCTX-M-15.out
+         # Testing with flanking sequences which run off the contig end
+         python extract_genes_abricate.py -a test/input/flanking.tsv -g test/genomes -o test/out_flanking_15bp --flanking --flanking-bp 15
+         cmp test/correct/correct_flanking_15bp.out test/out_flanking_15bp/flanking_blaCTX-M-15.out
       - name: Tests with combined ABRicate files from multiple genomes
         run: |
          # Normal gene extraction should work for files with multiple genomes

diff --git a/test/correct/correct_flanking_15bp.out b/test/correct/correct_flanking_15bp.out
@@ -0,0 +1,17 @@
+>flanking_blaCTX-M-15
+GGGGGGGGGGATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGT
+CACGCTGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACT
+TGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGA
+TAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGT
+GATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCG
+AGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAA
+TGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGC
+GATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACA
+GCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCC
+GGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGAC
+GCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAA
+TACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAA
+AACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCG
+TGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCG
+CGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCCCCCCCCCCC
+C
diff --git a/test/correct/correct_flanking_5bp.out b/test/correct/correct_flanking_5bp.out
@@ -0,0 +1,16 @@
+>flanking_blaCTX-M-15
+GGGGGATGGTTAAAAAATCACTGCGCCAGTTCACGCTGATGGCGACGGCAACCGTCACGC
+TGTTGTTAGGAAGTGTGCCGCTGTATGCGCAAACGGCGGACGTACAGCAAAAACTTGCCG
+AATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATT
+CGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGG
+CCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTG
+AGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGA
+CGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGA
+ATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGG
+GAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCG
+ATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGG
+GTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCA
+CCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAAAACCG
+GCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCGTGCGC
+CGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCGATG
+TATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCC
diff --git a/test/genomes/flanking.fasta b/test/genomes/flanking.fasta
@@ -13,4 +13,5 @@ GCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAA
 TACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAA
 AACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCG
 TGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCG
-CGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCCCCCCC
+CGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCCCCCCCCCCC
+CCCCCC