merging hmm updates

jmeppley · Jan 31, 2018 · 88994dc · 88994dc
2 parents 6ef35eb + e61157e
commit 88994dc
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Showing 7 changed files with 121,842 additions and 434 deletions.
diff --git a/.gitignore b/.gitignore
@@ -63,3 +63,5 @@ target/
 *.local
 *.sge
 *.slurm
+.tst.*
+.batch_launcher
diff --git a/LICENSE b/LICENSE
diff --git a/batch_launcher.py b/batch_launcher.py
diff --git a/test_data/bats/hmmer.bats b/test_data/bats/hmmer.bats
@@ -0,0 +1,16 @@
+#!/usr/bin/env bats
+
+@test "Testing HMM db split" {
+    run ./batch_launcher.py -X local -N 5 -- hmmsearch --tblout test_data/.tst.genes.v.pfam.tbl --cpu 2 test_data/pfams.100.hmm test_data/genes.faa
+    [ "$status" = 0 ]
+    run diff <(grep -v "^#" test_data/.tst.genes.v.pfam.tbl) <(grep -v "^#" test_data/genes.v.pfam.tbl)
+    [ "$status" = 0 ]
+}
+
+@test "Testing HMM db split with keep" {
+    run ./batch_launcher.py -X local -N 5 -K -- hmmsearch --tblout test_data/.tst.genes.v.pfam.tbl --cpu 2 test_data/pfams.100.hmm test_data/genes.faa
+    [ "$status" = 0 ]
+    run diff <(grep -v "^#" test_data/.tst.genes.v.pfam.tbl) <(grep -v "^#" test_data/genes.v.pfam.tbl)
+    [ "$status" = 0 ]
+}
+
diff --git a/test_data/genes.faa b/test_data/genes.faa
diff --git a/test_data/genes.v.pfam.tbl b/test_data/genes.v.pfam.tbl
diff --git a/test_data/pfams.100.hmm b/test_data/pfams.100.hmm
-Original file line number
+Diff line change
@@ Expand Up / @@ -63,3 +63,5 @@ target/ @@
     *.local
     *.sge
     *.slurm
+    .tst.*
+    .batch_launcher