From 895e4caec9511ae1261be8c6bd267cd0a8828eaa Mon Sep 17 00:00:00 2001
From: boasvdp <boasvdp@gmail.com>
Date: Fri, 18 Feb 2022 12:20:42 +0100
Subject: [PATCH] Add extra test for flanking sequence extraction

---
 .github/workflows/main.yml             |  7 +++++--
 test/correct/correct_flanking_15bp.out | 17 +++++++++++++++++
 test/correct/correct_flanking_5bp.out  | 16 ++++++++++++++++
 test/genomes/flanking.fasta            |  3 ++-
 4 files changed, 40 insertions(+), 3 deletions(-)
 create mode 100644 test/correct/correct_flanking_15bp.out
 create mode 100644 test/correct/correct_flanking_5bp.out

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ece9453..b1b5063 100644
--- 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
new file mode 100644
index 0000000..d997166
--- /dev/null
+++ 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
new file mode 100644
index 0000000..6dd26d0
--- /dev/null
+++ 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
index c71212e..45b2c11 100644
--- a/test/genomes/flanking.fasta
+++ b/test/genomes/flanking.fasta
@@ -13,4 +13,5 @@ GCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAA
 TACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCTGGGTTGTGGGGGATAA
 AACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAAGATCG
 TGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCG
-CGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCCCCCCC
+CGATGTATTAGCGTCGGCGGCTAAAATCGTCACCGACGGTTTGTAACCCCCCCCCCCCCC
+CCCCCC