work on generate-names tests

GMOD · Oct 9, 2012 · a377dab · a377dab
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diff --git a/tests/data/volvox_formatted_names/names/root.json b/tests/data/volvox_formatted_names/names/root.json
@@ -0,0 +1 @@
+[["ExampleFeatures","NameTest","snps","Motifs","Alignments","Genes","ReadingFrame","CDS","Transcript","Clones","EST"],null,["a",null,["gt",null,["221.",null,["3",[["agt221.3",10,"agt221.3","ctgA",7499,8000,null]]],["5",[["agt221.5",10,"agt221.5","ctgA",1049,7300,null]]]],["767.",null,["3",[["agt767.3",10,"agt767.3","ctgA",7999,9000,null]]],["5",[["agt767.5",10,"agt767.5","ctgA",1149,7200,null]]]],["830.",null,["3",[["agt830.3",10,"agt830.3","ctgA",5409,7503,null]]],["5",[["agt830.5",10,"agt830.5","ctgA",1049,3202,null]]]]],["pple",null,["1",[["Apple1",7,"Apple1","ctgA",9999,11500,null]]],["2",[["Apple2",6,"Apple2","ctgA",12999,17200,null],["Apple2",7,"Apple2","ctgA",12999,17200,null]]],["3",[["Apple3",6,"Apple3","ctgA",17399,23000,null],["Apple3",7,"Apple3","ctgA",17399,23000,null],["Apple3",8,"Apple3","ctgA",17399,23000,null]]]]],["b101.2",[["b101.2",9,"b101.2","ctgA",999,20000,null]]],["ctg",null,["a",[["ctgA",50001,"ctgA","seq/ctgA",0,50001,20000]]],["b",[["ctgB",6079,"ctgB","seq/ctgB",0,6079,20000]]]],["eden",[["EDEN",5,"EDEN","ctgA",1049,9000,null]],[".",null,["1",[["EDEN.1",6,"EDEN.1","ctgA",1049,9000,null]]],["2",[["EDEN.2",6,"EDEN.2","ctgA",1049,9000,null]]],["3",[["EDEN.3",6,"EDEN.3","ctgA",1299,9000,null]]]]],["f",null,["0",null,["1",[["f01",0,"f01","ctgA",44704,47713,null]]],["2",[["f02",0,"f02","ctgA",24561,28338,null]]],["3",[["f03",0,"f03","ctgA",36648,40440,null]]],["4",[["f04",0,"f04","ctgA",37241,38653,null]]],["5",[["f05",0,"f05","ctgB",4714,5968,null],["f05",0,"f05","ctgA",4714,5968,null]]],["6",[["f06",0,"f06","ctgB",3013,6130,null],["f06",0,"f06","ctgA",3013,6130,null]]],["7",[["f07",0,"f07","ctgB",1658,1984,null],["f07",0,"f07","ctgA",1658,1984,null]]],["8",[["f08",0,"f08","ctgA",13279,16394,null]]],["9",[["f09",0,"f09","ctgA",36033,38167,null]]]],["1",null,["0",[["f10",0,"f10","ctgA",15328,15533,null]]],["1",[["f11",0,"f11","ctgA",46989,48410,null]]],["2",[["f12",0,"f12","ctgA",49757,50000,null]]],["3",[["f13",0,"f13","ctgA",19156,22915,null]]],["4",[["f14",0,"f14","ctgA",23071,23185,null]]],["5",[["f15",0,"f15","ctgA",22131,24633,null]]]],["akesnp",[["FakeSNP",2,"FakeSNP","ctgA",999,1000,null]]]],["gene:hg",null,["a",[["Gene:hga",1,"Gene:hga","ctgA",1099,2000,null]]],["b",[["Gene:hgb",1,"Gene:hgb","ctgA",1599,3000,null]]]],["hg",null,["a",[["hga",0,"Remark:hga","ctgA",999,2000,null],["hga",1,"Gene:hga","ctgA",1099,2000,null],["hga",1,"Protein:HGA","ctgA",1199,1900,null]]],["b",[["hgb",1,"Gene:hgb","ctgA",1599,3000,null],["hgb",1,"Protein:HGB","ctgA",1799,2900,null]]]],["m",null,["0",null,["1",[["m01",3,"m01","ctgA",48252,48366,null]]],["2",[["m02",3,"m02","ctgA",28331,30033,null]]],["3",[["m03",3,"m03","ctgA",15395,16159,null]]],["4",[["m04",3,"m04","ctgA",33324,35791,null]]],["5",[["m05",3,"m05","ctgA",13800,14007,null]]],["6",[["m06",3,"m06","ctgA",30577,31748,null]]],["7",[["m07",3,"m07","ctgA",18047,18552,null]]],["8",[["m08",3,"m08","ctgA",17022,17675,null]]],["9",[["m09",3,"m09","ctgA",46011,48851,null]]]],["1",null,["0",[["m10",3,"m10","ctgA",28341,28447,null]]],["1",[["m11",3,"m11","ctgA",11910,15561,null]]],["2",[["m12",3,"m12","ctgA",21747,25612,null]]],["3",[["m13",3,"m13","ctgA",17666,17690,null]]],["4",[["m14",3,"m14","ctgA",14730,17239,null]]],["5",[["m15",3,"m15","ctgA",37496,40559,null]]]]],["protein:hg",null,["a",[["Protein:HGA",1,"Protein:HGA","ctgA",1199,1900,null]]],["b",[["Protein:HGB",1,"Protein:HGB","ctgA",1799,2900,null]]]],["remark:hga",[["Remark:hga",0,"Remark:hga","ctgA",999,2000,null]]],["seg",null,["0",null,["1",[["seg01",4,"seg01","ctgA",32328,32359,null]]],["2",[["seg02",4,"seg02","ctgA",26121,26126,null],["seg02",4,"seg02","ctgA",26496,26869,null],["seg02",4,"seg02","ctgA",27200,27325,null],["seg02",4,"seg02","ctgA",27371,27433,null],["seg02",4,"seg02","ctgA",27564,27565,null],["seg02",4,"seg02","ctgA",27812,28091,null],["seg02",4,"seg02","ctgA",28092,28201,null],["seg02",4,"seg02","ctgA",28328,28377,null],["seg02",4,"seg02","ctgA",28828,29194,null],["seg02",4,"seg02","ctgA",29516,29702,null],["seg02",4,"seg02","ctgA",29712,30061,null],["seg02",4,"seg02","ctgA",30328,30774,null],["seg02",4,"seg02","ctgA",30807,31306,null],["seg02",4,"seg02","ctgA",31515,31729,null],["seg02",4,"seg02","ctgA",31752,32154,null],["seg02",4,"seg02","ctgA",32594,32696,null],["seg02",4,"seg02","ctgA",32891,32901,null],["seg02",4,"seg02","ctgA",33126,33388,null],["seg02",4,"seg02","ctgA",33438,33443,null],["seg02",4,"seg02","ctgA",33758,34209,null],["seg02",4,"seg02","ctgA",34400,34466,null]]],["3",[["seg03",4,"seg03","ctgA",6884,7241,null],["seg03",4,"seg03","ctgA",7409,7737,null],["seg03",4,"seg03","ctgA",8054,8080,null],["seg03",4,"seg03","ctgA",8305,8999,null]]],["4",[["seg04",4,"seg04","ctgA",5232,5302,null],["seg04",4,"seg04","ctgA",5799,6101,null],["seg04",4,"seg04","ctgA",6441,6854,null],["seg04",4,"seg04","ctgA",7105,7211,null],["seg04",4,"seg04","ctgA",7694,8177,null],["seg04",4,"seg04","ctgA",8544,8783,null],["seg04",4,"seg04","ctgA",8868,8935,null],["seg04",4,"seg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diff --git a/tests/data/volvox_formatted_names/seq/refSeqs.json b/tests/data/volvox_formatted_names/seq/refSeqs.json
@@ -0,0 +1 @@
+[{"length":6079,"name":"ctgB","seqDir":"seq/ctgB","seqChunkSize":20000,"end":6079,"start":0},{"length":50001,"name":"ctgA","seqDir":"seq/ctgA","seqChunkSize":20000,"end":50001,"start":0}]
diff --git a/tests/perl_tests/generate-names.pl.t b/tests/perl_tests/generate-names.pl.t
@@ -1,26 +1,38 @@
 use strict;
 use warnings;
 
+use lib 'tests/perl_tests/lib';
 use JBlibs;
 
 use Test::More;
 
-use File::Temp;
 use File::Copy::Recursive 'dircopy';
+use File::Path qw( rmtree );
+use File::Temp;
 
-my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
-dircopy( 'tests/data/volvox_formatted_names', $tempdir );
+use FileSlurping qw( slurp slurp_tree );
 
+my $tempdir = new_volvox_sandbox();
 system $^X, 'bin/generate-names.pl', (
     '--out'   => "$tempdir",
     );
 ok( ! $?, 'generate-names.pl also ran ok on volvox test data' );
+is_deeply( slurp_tree($tempdir), slurp_tree('tests/data/volvox_formatted_names') );
 
-
+$tempdir = new_volvox_sandbox();
 system $^X, 'bin/generate-names.pl', (
-    '--out'   => "$tempdir",
-    '--tracks' => 'ExampleFeatures,NameTest'
+    '--dir'   => "$tempdir",
+    '--tracks' => 'ExampleFeatures,NameTest',
     );
 ok( ! $?, 'generate-names.pl also ran ok with the --tracks option' );
+cmp_ok( -s "$tempdir/names/root.json", '>', 1000, 'the root.json has some stuff in it' );
 
 done_testing;
+
+
+sub new_volvox_sandbox {
+    my $tempdir = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
+    dircopy( 'tests/data/volvox_formatted_names', $tempdir );
+    rmtree( "$tempdir/names" );
+    return $tempdir;
+}