add a little test for biodb-to-json.pl

GMOD · Feb 8, 2012 · dbf047b · dbf047b
1 parent 921da3f
commit dbf047b
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Showing 7 changed files with 55 additions and 0 deletions.
diff --git a/tests/data/volvox_formatted_refseqs/refSeqs.json b/tests/data/volvox_formatted_refseqs/refSeqs.json
@@ -0,0 +1,18 @@
+[
+   {
+      "length" : 66,
+      "name" : "ctgB",
+      "seqDir" : "seq/ctgB",
+      "seqChunkSize" : 20000,
+      "end" : 66,
+      "start" : 0
+   },
+   {
+      "length" : 50002,
+      "name" : "ctgA",
+      "seqDir" : "seq/ctgA",
+      "seqChunkSize" : 20000,
+      "end" : 50002,
+      "start" : 0
+   }
+]
diff --git a/tests/data/volvox_formatted_refseqs/seq/ctgA/0.txt b/tests/data/volvox_formatted_refseqs/seq/ctgA/0.txt
diff --git a/tests/data/volvox_formatted_refseqs/seq/ctgA/1.txt b/tests/data/volvox_formatted_refseqs/seq/ctgA/1.txt
diff --git a/tests/data/volvox_formatted_refseqs/seq/ctgA/2.txt b/tests/data/volvox_formatted_refseqs/seq/ctgA/2.txt
@@ -0,0 +1 @@
+ggcgtggaggcatagggccggagtgttcccgtaccaattacgagctaagaccgcctgtccagccctggtgattacgtagtaagctcggtacaagcctgtaattagcttccgggtggcggacattcgttcatattgccagtcacggcagaggccgcgctagctaggccagccccgatgaaacacgtgctagttttctatcgtgcctaaggatcgatggctatcgcggcattgttaacttatcaagcagccgaatcggcgatagtggacacaacatgaacacgctaagctctgagtgccagactctaccgcggcgaatcctaggccctgctggggctcccccacagagcagtaatggtcttctgcggccgcgtgcattcaatccgcgctggtcaatgcgttccatcgtgccttaagcggggcagtgtgataagacaattttgggggtttcatggagatatcttcagaaacctcgcgaggtgcgtttagataccacacgcgcggcggtcttttcacacaattcagtccgcggccggtaacctaactttgcttatcaatacataatcctcccaaatgtacggtttcgaaggagatacctctcccctgttagactctaggttttgcagtgctacctagagatcacaccagcattaaaccaaggtatcagcatcgtaacatggggaggcacgcgcttggcggtaagtacccgccacgattactctgtttcatagcgccaacgcccgtatagtgtgcttttaacgtcctcagaaatcaccgactgatcagtatggcgacatcggagggaggttggcgaaatgttgcttttatagatcgttaaaacctatcgttggcgcgtatcgcctccatagaacttcttactcacctagtctgatcccgggactggtcgaaatggagacgacgtagcttgagatctggatcgatcgactgatatcacacttaaatatgatcagattttactacggtcgatctccatatatctatcccagcacttgatacctcctgtccagccgactgcttggaccctagcacgcgatattagagggcgcgttgtagctcaaagtaaccagtgggacgacccgagtgaggttaccgctggcacgtaagggtgacatgactcccccagaaacactgaatttgtctagcagtacatcataatctgagaacatttagcgaagacgagaacaagctgtctcaatggacgtaggacgagaggaatgtgacggttataatacgcgacctctatgtgtctattaaatccctacgggccgtagcgagcaagctcgggatctttagtagcggatcgggtcttctacatggcgcaccaggtttgatatttcgagctagagttgctctaaagaaacgctcttgcttgggaaagtgacctggggtacgacgaagacacgggcctggttgcataccgtctcaccttcattcatcgagcgcgatagcgtagcattatccagcacgggaggcacctggcatgggcgtgaaatacaatccgaagagcagcatgaaaaaaaaatgagcggtcgtgacccgagggtgcgtccctccgaacgttgttcgttgccaaggtaagggacccacgccaagcatggttagggaagcgtgaccgacacaacatagaggacaatctcaatatgccttctgggtatcacctgggtgtgtagcagtgctactgttacaagtcgcgccatctgcgacgtcgttcgtccctattccctcctaaaggccccgactctgaaaaaacctacaatcctagacacgttgtggcccagcacaacgcgtctgctatacagcaagtcattcgtcgaatggggcaacacgtataagaaggccgtgattccaagggcacatggcgggtctctcaatgatctacgacgtgacgcaaacggggaaaggctggaccgttgtccggtaggcgatccatcataaaaggcgtctggttctgtggttattgtgtacacgtttgaaatatctgactgtagaacgatggaggtctctacgtagctctgcacgattccctcgggctcacgttcatggcaaggcgacatcacatgaacagggttgggtaacagccatctctgaagcattcccccagctcgcacggctcctttacccgctactacgtcatgcactggctagagacccaccaactattgtgcaagtaaagaccataaaattttggagctgtagcgaaagcgagttgctgcgatggttagaccaacattgggtcaaactattctaatccggctaggctcattaagcatcgcagattgccgatactaatgctaacgagcgatgaatgggcctcttcgagacgcgtccgtacctgcgaatatcaaccatgaaccctaatctggaaagtttgatgccgctgtgatagccactcctgtgtcgcgacggcaacgtaatgtacgtgcttggtttgagctctaaacataccttcgttagagttggtcagaggaggatattgtcatagcgctacaaccagcgccaaaggatagctccgtggctggtcggacgcgctagaatctaggcagaacacgtgcggcttcttgcactctgacgctcacgcattggactttggcggtcatctggttctcataagtccgaatcacagtagataaagatccgcgtgataagatatgcctacgtacttaagtagcaccctctgttcttggcgatcctatcattgcgggttctatacatatgttgatccaaccatcggccgccgggccgtcgtaggatctaatggccaacacatcaatcaaatcactcgcgaggacgcggaggtcccgtccataggtgtgtatgttggtacgcagcacctaatctggtctggtcaagcaactggcttgttccagtatataatctcagatagactgccctgaaagtagacaatgataaatatgtaagagcggggaaatcccatcgtcgactgtgttgcggacgattagcttgcaaagagaggtgtgagcggctgtcttaaattatggactcctcgcttccgtcgaacgtctgactagagaatctcttggaggtacacacgaacgtaggttcctcacagtatgtggcatggacaccggacaggtcacttgtatttatccattgaacgtgatatagtgtgtcgagtcgttatacaatacatactccaagcgtactccctttgggtaacgggtttgggtacatattaccatggtgtggaccgatttgtaaccctataagcgttccgggtactttaccatcgcggatgcgatcgcggatctacctatgtcagcgacatactgcccgtccaaaagtgattcagtatgtgttaatcagcgtattgcatcatcagtcattgagagtggaccgttctcgaagagcaagattcctgaccctttccactgggccatccagtacacccaattatatgcagacgaaaagctccatacatatataatacctcttcacaccgtgtgcagagaccaacttgatcgatattgtactcactcgtacggaataattagaagggcccgactgtcgagaccgttagcatttgcattatcgcggtgagcgtatagaaacaattataggctttgctgcgatcgcagtgtctgggacagagtctcctagacctagatcagcttaaaacaatgattgtaggtaatgtgcgttgccgtcgggccacacctttcagttcggttacaccgactcagaattatcttctatcgggaccctcaaactgataatggggtcaaatggtggtggtcccgtctttctgcagtgctttgtgagcagaatagctctcgagcgctccagtacgcctgagtatggctgcgcccaccaattggcgccgttaatgcgtggcgacacaagagaaccagtccacataagttatgcccttaagaagatcaccgggtttgcgccatcctgattcaggtaacggacgtccgtgtacacgaaccatactaatgagttctacatcgctccaacgcgtcttgaaccctatcgacaattacaaatgcaaagtattagttgggtcagtgcgtagcttatccaagggctgcagtaagtcgtccccatgacagacggacggcataagggccaaaaattccgccgcattagctgttaataatgccatccagaaccggacagtctcgatatataacttacggctgcgaactggcccttatgaattacatccacgtgctagttaacaggacggatcgcccggactaattgccgatcggccgtcccattctccgtacgatgtactgaacccaggcgtgtgaatgggtatgtcaacgtttacccatcgaccctgcctatagacctgagtttcattccagttgagcgtagaatgggatgagcagctttgcttgaggtgcgatattcgggagacctggtcagcaggattgatggttttatagtgctggattccctgctgaaattctctcttctgccgcatgtgaagaaggccttgcttcccttccacatgattgtaagatttcctaaggcctcccagctgcgtggaactgtgagtcaattaaacctctttcctttataaattacccagtctcaggtatttccttatcgtggtatgagaacggattaatacagttgtgtaagccagctccttataataaatctctctccctctctctgcctctcatctatgtatgtatgtatctgtcatctatctcctataagttgtttcttttgagaactctgactaacatagacattaaataaacaatttgtatactgaataattatataactactgcttgggggtgtggttgtgttgtgtggtgagggggtgtagaaatgtctaggggttgatctagcctaacaccttccagatgaccctaggttctggcctttccccaaagagtcctggtctactcagtcatctcccacaatttggccatcttcttgggtgctcaggacaataaatgacccagccagatcctctagagtcgacctgcaggcatgcaagcttggcgtaatcatggtcatagctgtttgctgtgtgaaattgttatgcgctcacattgcacacaacatacgagccggaagcatacagtgtagagcctggggtggcgtatgagtgagctaactcacattaatttgcgtttgcgctcactgccgcttttcagtcggggaaactgtcgtgacagctgcatttaatgatcggtcatcgcgcggggagatgcggttttgcgtattgtgccgcaggtggttatttctctcaacagtgagacgggcacagctgattgccctcaccggctgggctgagagagttgcagcaagcgtacacgcggggtttgcccagcagggcgaaattcctgttgtgatgtggattccgaatcgggcaaatgccctataaatcaaagcatagtccgagatagggtttgagtgtgttcagttttgggacagaggtcactataaagaacgttgactgcacgtcaagggcgagaaacgtcatcaggcgattgcactacgtgacatcaccaatcagttttttgggtcaggtgcgtgagacttatcggaactaaaggagcccgttttagcttcggggaaacgcgaagtgtcggaagaaggaaaacgaagagcgggtatcgcggaatgtacgtgctgagcgaaaccaacgcgcgttacggtcaagcgtgtatgtgttttggaggtaagtttccctgataaagcggaacaggggctatgtgtttacgggggtcgcatggagtacaagggggcaggacaagatttgcgcgacatggttttttttaaattgcgggagatggttggctgtcccgatgagattagaacctgcttttgttttagtttcggttcggtcagttcggactttggattggttttgttgggtatttaagaagggtgtttgtgggatgtttttttttgggtcgagcatcactggactatgtgtgtcctgcgtatcgtggcggggcctcgaacttagaggtaggacgattccgatgcaacaaccttatgctttactccaagcgatggtgaggcaaccttgtacagaagtgcaaccgccattgtggctgggtcggcccaaggaacggatattctcctgggtactgacaacccaggtctactgggttctatcgacggtacagtcaagcctcgagtttactgtctcccacttaagtccgctctgggcattaatgagtctgtggggtatcaagggtcacccaacgaagtagctagtcccgttgtacatttcgcgcgttacctagggagcacggtgagctacgagggtgtagctgcacacagcacggtatataggaacgcaaacatagtagtatgtccctatgcataacagggagaagtgactctccgacggtcatttatcccagactctcctcgctccctactaattgttctatatacaatcggagtaaattggtacctctctgacaacataggggggttgaagtttatgccacgcagtctgttacacttttgccggggaattgtgtagaccatgactcaaggtggtggtgcgagttactctactatctactgcttctcattacacatctcttggcttacaggccccagttatcagttacgaggctgccttaagagaaggccaacattcatgatcagatccccgcacacgggatgatagtctgagatctgccggacgctcgtctgctacaagtgtgggttgagcatagggtaagcctaagggctcgtaatggtacttcgcgatgtttattcgatatgagctacaaggtataacgttgccttcaccatttcggctcacgactcttacctcgcctcaccgctagacaccctgaccaaccgttagggtactgacaaccgatcaggcgactcctaaaggacctctcagcctcccagacatgaggtccgctcgcatgctgttcagcgagtccatatcaggaacagcaacgagacaaggcgagagcaacactagacttggagacataccaccacatctgtttactcttgattcaggaagacctgtggtaactgggcgacgcgtgcgtttatccgtcttccaatctccacagaatctgctccgtcagagggatgtatgactaacgcactgattttttgttcagtaaccgggcgcggattacggggcgtattccaggggtacattcaacgggaccccaaggaaaagttcggggtatttaaggaggcggtccaactctcggacttattgggcgacgtaatgataagcacacctctgctcatacagtgcacgaagaccggcattgttcaaacacagccgtccattccgcgactattgtcctgtgtacaggtgcctcgggtcccaaatccagcttatacccaaaactctcccggacttttttcgtccttgcaggaggaaaggacctgactccacgtttattaggggatcgttgggcccggacaatcgtgtattcaacataataaatgggttctagtttaaagccggaggtgacggtggattatggactagaggtaaacatttccggcgtaggtcagaaagaatatagaccctaaatttacgcaaaacgtgcacacgattgtaggtggagtcgtattaggaactcagggcgggtggaacgagtgtgttttaggcttaccatgaaccgtcgcgcggaaaatgatgacagaatggacggtgcttttttgcggggccaacaaaactcgcttatgttcgccattggatgtaagtaccgctatactacgcagcgaccccttacgacattgttgatttccaatgctttcatggaggtttgtgagcggtcgctaggaatcttcctccagcgagtagccagctggccactagttagcaaccagagttcatatgagctccagtaacacgaaggtacataaggaacgcaagcaagttcgggactacatagaacttggggtgcgtctaagccggggatcttaatagacaagaggccatcgtatgggtcaaatttcatgtttcgtcagatgccctatccgtggacacctaaatcaagcatcatatcctaatgctatttgctctcgctttggtatgattcatatgcagccctgtccgtaaaatgacgggccagaggatacctgtcactacctatttcagattaccactgttcgaaaccttgctctgaaatcgatcttcgtagagtgttcgttaatcgccgcgtgaattatataatcccccaaggagtacccttcgtcggtgcagtctacgtaactttcccaggttagcccccatctaatcgacgtacgtgagggggctacgggagatcgcacaagccgaagcatttctgctctgtttcgttacaactggaatcctcatcacgcagcgctaccggatgccatccctagtcatccccgcgagtttaaccagtcgagatggctcgaaccgtgtttcgaaggctggctattgaaccagttataaagcaggggcgactgtccgtcggacttcgatataaactatcacaaatttggcataagtatatacagccaagaaggctcagataggcacacgcacccaaatagtgaccgcctacgttcaggttgcccggcaacgaagcgcgcttgctccattaatccactatcagaggtaacgaccctctttcaccgtagctgcccccatgtcggggcaacagtttcccaccgataacgtgttctgtctagtacgtgaaacggattggctaacccctgtcagcctaattagatgacatcctcgtacctctagagaaggtgaggagaccgctggaacataagtaaacagtttaccaaacaatgatcatacatataacagaaaggagagatgcccggtggggtcgaagatacagctgtggttgatatctgcaacggccaggctgtcatgaagatcacgcgcacgaagctatttatgaaagatacccatgccggggcggcagcggtacctagtcctaaataccgacacgtagcaacgcgtcccctgaggcccaccctagtcaagggaacttaaaatatacgctgactttgtctaccaatcatcttcgattaacaccggcatactaagtctaccctggacccagcaatgagaaaaacttttccgaatgatcattgtgagtttacagagattaggaacaccaaaaaaatttacgtacgtccggttacccctgtgtgacccttggccacaaaccgtaaggtgcagcatgggcgttgagtccagggtttgtgacaccagacatgaataccctgtggcgggttgttagcatgttattcggatccgatttcagagggtccgttgataccgggcagtacaagacaccccacaccactgaggtggtacgtccgccagtctgctccctacgttatgcaaaattccttccccggcgttcttgcctgtactactcctaaagggccgtgaaatccgacgttgctgctccgtctcgggacacccacacaacagctacggaaaatcgtgaggatgcacaagggtcttgcattgttgatctatacagctcttcgcacggtgtgctactgttttccacaatgggcaaggggcgtgtaggtcttatgtaggagtaccccgtgatctggctataccttgctatctattccaccaaaatagccggggtcttatagttttattccggatctatcaagtgacaagtccatggggtaaacggtaagtttcgtacgctgggcggtgatccccgcttataaacgagcaaaccgccaaagcaaccattgccgggcttccagctagtaaatgttgggtgtcaatcgtgcatgtgactacttacccacaaagggacgcttgaagcgcctgaactcgtcacgtcatgcctagctcccggttgaaacacgaagacgcgtgaacctatctttgcttactattcgcctcctttaagaggcttcttgatgtggctctgcgacatggacagtagtagttgtacctgggtatgttagtgaaattacaagtacctcaaaaacgaattacgtgtatagagattatgtcactccgtcac>
diff --git a/tests/data/volvox_formatted_refseqs/seq/ctgB/0.txt b/tests/data/volvox_formatted_refseqs/seq/ctgB/0.txt
@@ -0,0 +1 @@
+ACTGATCGATGATGACTGACTAGTAGAACATGCTAGCTACGTGCATGCTCGACATGCATCATCAGC
diff --git a/tests/data/volvox_formatted_refseqs/trackList.json b/tests/data/volvox_formatted_refseqs/trackList.json
@@ -0,0 +1,14 @@
+{
+   "tracks" : [
+      {
+         "config" : {
+            "chunkSize" : 20000,
+            "urlTemplate" : "seq/{refseq}/"
+         },
+         "type" : "SequenceTrack",
+         "label" : "DNA",
+         "key" : "DNA"
+      }
+   ],
+   "formatVersion" : 1
+}
diff --git a/tests/perl_tests/biodb-to-json.pl.t b/tests/perl_tests/biodb-to-json.pl.t
@@ -0,0 +1,19 @@
+use strict;
+use warnings;
+
+use Test::More;
+use File::Temp;
+use File::Copy::Recursive 'dircopy';
+
+my $tempdir = File::Temp->newdir;
+dircopy( 'tests/data/volvox_formatted_refseqs', $tempdir );
+
+diag "writing output to $tempdir";
+system $^X, 'bin/biodb-to-json.pl', (
+    #'-q',
+    '--conf'  => 'sample_data/raw/volvox.json',
+    '--out'   => "$tempdir",
+  );
+ok( ! $?, 'biodb-to-json.pl ran ok' );
+
+done_testing;