fix docker tests

williamdlees · Jun 20, 2024 · 58d18d6 · 58d18d6
1 parent a252158
commit 58d18d6
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Showing 10 changed files with 237 additions and 245 deletions.
diff --git a/run_docker_tests b/run_docker_tests
@@ -1,6 +1,6 @@
 #!/bin/bash
-exit 0
-cd /digger/tests/human/IGH/verify
+
+cd /tests/human/IGH/verify
 
 bash -x run_digger.bat
 

diff --git a/tests/human/IGH/IMGT000035/IMGT000035.csv b/tests/human/IGH/IMGT000035/IMGT000035.csv
diff --git a/tests/human/IGH/verify/IMGT000035.csv b/tests/human/IGH/verify/IMGT000035.csv
diff --git a/tests/human/IGH/verify/IMGT000035_248000_270000.fasta b/tests/human/IGH/verify/IMGT000035_248000_270000.fasta
diff --git a/tests/human/IGH/verify/model_IMGT000035.csv b/tests/human/IGH/verify/model_IMGT000035.csv
diff --git a/tests/human/IGH/verify/run_digger.bat b/tests/human/IGH/verify/run_digger.bat
@@ -3,12 +3,7 @@ cd work
 extract_refs -L IGH "Homo sapiens"
 cat Homo_sapiens_IGHV.fasta Homo_sapiens_IGHD.fasta Homo_sapiens_IGHJ.fasta > Homo_sapiens_IGHVDJ.fasta
 
-parse_imgt_annotations --save_sequence IMGT000035.fasta "https://www.imgt.org/ligmdb/view?format=IMGT&id=BK063799" IMGT000035_genes.csv IGH
-
-head -n 1 IMGT000035.fasta >IMGT000035_trunc.fasta
-at_coords IMGT000035.fasta 1 15000 >>IMGT000035_trunc.fasta
-
-digger IMGT000035_trunc.fasta -keepwf -v_ref Homo_sapiens_IGHV.fasta -d_ref Homo_sapiens_IGHD.fasta -j_ref Homo_sapiens_IGHJ.fasta -v_ref_gapped Homo_sapiens_IGHV_gapped.fasta -ref imgt,Homo_sapiens_IGHVDJ.fasta -species human IMGT000035.csv
+digger ../IMGT000035_248000_270000.fasta -keepwf -v_ref Homo_sapiens_IGHV.fasta -d_ref Homo_sapiens_IGHD.fasta -j_ref Homo_sapiens_IGHJ.fasta -v_ref_gapped Homo_sapiens_IGHV_gapped.fasta -ref imgt,Homo_sapiens_IGHVDJ.fasta -species human IMGT000035.csv
 
 cp IMGT000035.csv ..
 

diff --git a/tests/human/TRB/IMGT000021/IMGT000021.csv b/tests/human/TRB/IMGT000021/IMGT000021.csv
diff --git a/tests/human/TRB/IMGT000021/comparison_results.csv b/tests/human/TRB/IMGT000021/comparison_results.csv
diff --git a/tests/human/TRB/IMGT000021/comparison_results.jpg b/tests/human/TRB/IMGT000021/comparison_results.jpg
diff --git a/tests/human/TRB/IMGT000021/comparison_results.txt b/tests/human/TRB/IMGT000021/comparison_results.txt
@@ -3,7 +3,6 @@
 type: V
 Functional sequences reported by digger but not by IMGT:
 158038,158323  imgt_match: TRBV5-3*02  imgt_func: ORF digger_match: TRBV5-3*02  digger_func: functional  notes: 
-405750,406039  imgt_match: TRBV21-1*02  imgt_func: pseudo digger_match: TRBV21-1*02  digger_func: functional  notes: 
 414833,415122  imgt_match: TRBV23-1*01  imgt_func: ORF digger_match: TRBV23-1*01  digger_func: functional  notes: 
 
 Functional sequences reported by IMGT but not by digger: