Fix the error of MANIFEST (missing some files)

fortune9 · May 14, 2015 · 0fb1fd0 · 0fb1fd0
1 parent 2c1815c
commit 0fb1fd0
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diff --git a/MANIFEST b/MANIFEST
@@ -7,9 +7,11 @@ lib/Bio/CUA.pm
 lib/Bio/CUA/CodonTable.pm
 lib/Bio/CUA/CUB.pm
 lib/Bio/CUA/CUB/Calculator.pm
+lib/Bio/CUA/CUB/Builder.pm
 lib/Bio/CUA/Seq.pm
 lib/Bio/CUA/SeqIO.pm
 lib/Bio/CUA/Summarizer.pm
+LICENSE
 MANIFEST			This list of files
 README
 t/00-load.t
@@ -28,3 +30,4 @@ t/tai.out
 t/test.fa
 TODO
 xt/boilerplate.t
+Makefile.PL
diff --git a/lib/Bio/CUA.pm b/lib/Bio/CUA.pm
@@ -14,16 +14,17 @@ my $sep = "\t";
 
 =head1 NAME
 
-Bio::CUA - the root class for the whole distribution of
-L<http://search.cpan.org/dist/Bio-CUA/>
+Bio::CUA - Codon Usage Analyzer.
 
 =head1 VERSION
 
 Version 1.01
 
 =head1 SYNOPSIS
 
-This class provides some routine methods used by all classs in the
+This is the root class for the whole distribution of
+L<http://search.cpan.org/dist/Bio-CUA/>,
+providing some routine methods used by all classs in the
 distribution L<http://search.cpan.org/dist/Bio-CUA/>. Users should not use this class
 directly. Please start with its child classes such as
 L<Bio::CUA::Summarizer>, L<Bio::CUA::CUB::Builder>.

diff --git a/t/cai.out b/t/cai.out
@@ -1,59 +1,59 @@
-CCA	0.587301587301587
-CTG	1
-AAT	0.604477611940298
-CCT	0.407407407407407
-GAT	0.892857142857143
-TAC	1
-ACA	0.469767441860465
-TTA	0.0857908847184987
-CGA	0.364864864864865
 GAG	1
-ATC	1
-CTC	0.386058981233244
-ATA	0.284518828451883
-CCC	1
-CTT	0.142091152815013
-CAG	1
-TTC	1
-GTC	0.565610859728507
-TCT	0.191881918819188
 ACG	0.744186046511628
-ACC	1
-TGT	0.23
-CTA	0.190348525469169
+CAC	1
+CGG	0.540540540540541
 CAA	0.380352644836272
-GCG	0.47787610619469
-TAT	0.537634408602151
-TTT	0.450261780104712
-TGC	1
+CTG	1
+ATC	1
 ATT	0.414225941422594
-GGT	0.335616438356164
-GTA	0.194570135746606
-GGG	0.174657534246575
-AGT	0.450184501845018
-AGG	0.310810810810811
-TCA	0.254612546125461
+CCC	1
+TAC	1
 GCT	0.309734513274336
-AAC	1
-GTT	0.330316742081448
-AAG	1
-AGA	0.243243243243243
-TCC	0.845018450184502
-CGT	0.371621621621622
-CGC	1
-CGG	0.540540540540541
-GGC	1
-AGC	1
 CAT	0.537688442211055
-GGA	0.537671232876712
-GAC	1
+TTC	1
+AAA	0.398576512455516
+TCA	0.254612546125461
+GAA	0.394927536231884
+AAC	1
 CCG	0.878306878306878
+CTC	0.386058981233244
+TAT	0.537634408602151
+AGT	0.450184501845018
+GGA	0.537671232876712
+AGC	1
 GTG	1
 GCC	1
+AGA	0.243243243243243
+GCG	0.47787610619469
+ACC	1
+ATA	0.284518828451883
+GTT	0.330316742081448
+TTA	0.0857908847184987
 TTG	0.329758713136729
-GAA	0.394927536231884
+CGT	0.371621621621622
+CTA	0.190348525469169
+CTT	0.142091152815013
+GGT	0.335616438356164
 TCG	0.712177121771218
+TGT	0.23
+GGG	0.174657534246575
+GTA	0.194570135746606
+GTC	0.565610859728507
+TGC	1
+AGG	0.310810810810811
+AAT	0.604477611940298
+GGC	1
+CAG	1
+TCC	0.845018450184502
+TTT	0.450261780104712
+TCT	0.191881918819188
+CGA	0.364864864864865
+CCT	0.407407407407407
+CGC	1
+GAT	0.892857142857143
 GCA	0.274336283185841
-CAC	1
-AAA	0.398576512455516
+AAG	1
+CCA	0.587301587301587
+ACA	0.469767441860465
 ACT	0.288372093023256
+GAC	1
diff --git a/t/tai.out b/t/tai.out
@@ -1,60 +1,60 @@
-ATC	0.309751434034417
+TCA	0.095640535372849
+AAA	0.286806883365201
+AAC	0.573613766730402
+GAA	0.286806883365201
 CTC	0.17208413001912
-ATA	0.0956453154875717
-CCC	0.240917782026769
-CTT	0.239005736137667
-ACG	0.235181644359465
-GTC	0.206500956022945
-CAG	0.443594646271511
-TCT	0.382409177820268
-TTC	0.382409177820268
+CCG	0.315487571701721
+AGC	0.286806883365201
+TAT	0.253824091778203
+GGA	0.286806883365201
+AGT	0.169216061185469
+GTG	0.365200764818356
+GCC	0.413001912045889
+AGA	0.1434034416826
+GCG	0.173996175908222
 ACC	0.309751434034417
-TGT	0.197418738049713
-CCA	0.239039196940727
-AAT	0.338432122370937
+ACG	0.235181644359465
+GAG	1
+CAC	0.239005736137667
+CGG	0.152963671128107
+CAA	0.191204588910134
 CTG	0.413001912045889
+ATC	0.309751434034417
+ATT	0.430210325047801
+CCC	0.240917782026769
+TAC	0.430210325047801
+GCT	0.573613766730402
+CAT	0.141013384321224
+TTC	0.382409177820268
+TTT	0.225621414913958
+CGA	0.478059273422562
+TCT	0.382409177820268
+CGC	0.344168260038241
 CCT	0.334608030592734
 GAT	0.394837476099426
+CCA	0.239039196940727
+AAG	0.713193116634799
+GCA	0.09565965583174
 ACA	0.286849904397706
+ACT	0.430210325047801
+GAC	0.669216061185469
+ATA	0.0956453154875717
+GTT	0.286806883365201
 TTA	0.191204588910134
-TAC	0.430210325047801
-TGG	0.397705544933078
-CGA	0.478059273422562
-GAG	1
+CGT	0.478011472275335
+TTG	0.252390057361377
+CTT	0.239005736137667
+CTA	0.0956261950286807
 GGT	0.394837476099426
+TCG	0.221797323135755
 GTA	0.0956309751434034
 GGG	0.0917782026768642
-AGT	0.169216061185469
-AGG	0.189292543021033
-TCA	0.095640535372849
-CTA	0.0956261950286807
-CAA	0.191204588910134
-GCG	0.173996175908222
-TAT	0.253824091778203
-TTT	0.225621414913958
+TGT	0.197418738049713
+TGG	0.397705544933078
+GTC	0.206500956022945
 TGC	0.334608030592734
-ATT	0.430210325047801
+AGG	0.189292543021033
+AAT	0.338432122370937
+CAG	0.443594646271511
 TCC	0.275334608030593
-CGT	0.478011472275335
-CGG	0.152963671128107
-CGC	0.344168260038241
 GGC	0.669216061185469
-AGC	0.286806883365201
-GCT	0.573613766730402
-AAC	0.573613766730402
-GTT	0.286806883365201
-AAG	0.713193116634799
-AGA	0.1434034416826
-TTG	0.252390057361377
-GCA	0.09565965583174
-TCG	0.221797323135755
-GAA	0.286806883365201
-CAC	0.239005736137667
-ACT	0.430210325047801
-AAA	0.286806883365201
-CAT	0.141013384321224
-GGA	0.286806883365201
-CCG	0.315487571701721
-GAC	0.669216061185469
-GTG	0.365200764818356
-GCC	0.413001912045889