Correct POD errors

fortune9 · May 3, 2015 · 43a4822 · 43a4822
1 parent e9db198
commit 43a4822
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Showing 6 changed files with 156 additions and 101 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -1,130 +1,30 @@
-.git/COMMIT_EDITMSG
-.git/config
-.git/description
-.git/HEAD
-.git/hooks/applypatch-msg.sample
-.git/hooks/commit-msg.sample
-.git/hooks/post-commit.sample
-.git/hooks/post-receive.sample
-.git/hooks/post-update.sample
-.git/hooks/pre-applypatch.sample
-.git/hooks/pre-commit.sample
-.git/hooks/pre-rebase.sample
-.git/hooks/prepare-commit-msg.sample
-.git/hooks/update.sample
-.git/index
-.git/info/exclude
-.git/logs/HEAD
-.git/logs/refs/heads/master
-.git/objects/02/b1c1f4acea65587bdfcf098dc7ffc24f507d97
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-.git/refs/heads/master
-.gitignore
 bin/build_cai_param.pl
 bin/build_tai_param.pl
 bin/calculate_CUB.pl
-bin/tmp1
 Changes
 ignore.txt
 lib/Bio/CUA.pm
 lib/Bio/CUA/CodonTable.pm
 lib/Bio/CUA/CUB.pm
-lib/Bio/CUA/CUB/.Calculator.pm.swp
 lib/Bio/CUA/CUB/Calculator.pm
 lib/Bio/CUA/Seq.pm
 lib/Bio/CUA/SeqIO.pm
 lib/Bio/CUA/Summarizer.pm
 MANIFEST			This list of files
-MANIFEST.bak
-MANIFEST.SKIP
 README
 t/00-load.t
 t/01-seqio.t
 t/02-codontable.t
 t/03-summarizer.t
 t/04-builder.t
 t/05-calculator.t
-t/b_CAI_param.S2_top_200.b1000
-t/build_cai_param.v1.0.pl
-t/build_tai_param.pl
 t/cai.out
-t/CAI_param.S2_top_200
-t/CAI_param.S2_top_200.by_avg
-t/dmel_r5_apr2006.tAI_param
 t/dmel_r5_apr2006.tRNA_copy
 t/expected.tsv
-t/generate_expected_data.pl
-t/longest_cds.fa.filtered
-t/longest_cds.stat_summary.S2.bCAI_t200_b1000
 t/manifest.t
 t/pod-coverage.t
 t/pod.t
-t/S2_RPKM.tsv
-t/summarize_cds_stat.pl
 t/tai.out
 t/test.fa
-t/tmp1
-t/tmp2
-t/tmp_positive
 TODO
 xt/boilerplate.t
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
@@ -17,3 +17,7 @@ pm_to_blib
 Bio-CUA-*
 Bio-CUA-*.tar.gz
 .git/
+generate_expected_data.pl
+.bak
+.git*
+MANIFEST.SKIP
diff --git a/MANIFEST.bak b/MANIFEST.bak
@@ -0,0 +1,32 @@
+bin/build_cai_param.pl
+bin/build_tai_param.pl
+bin/calculate_CUB.pl
+Changes
+ignore.txt
+lib/Bio/CUA.pm
+lib/Bio/CUA/CodonTable.pm
+lib/Bio/CUA/CUB.pm
+lib/Bio/CUA/CUB/.Calculator.pm.swp
+lib/Bio/CUA/CUB/Calculator.pm
+lib/Bio/CUA/Seq.pm
+lib/Bio/CUA/SeqIO.pm
+lib/Bio/CUA/Summarizer.pm
+MANIFEST			This list of files
+MANIFEST.SKIP
+README
+t/00-load.t
+t/01-seqio.t
+t/02-codontable.t
+t/03-summarizer.t
+t/04-builder.t
+t/05-calculator.t
+t/cai.out
+t/dmel_r5_apr2006.tRNA_copy
+t/expected.tsv
+t/manifest.t
+t/pod-coverage.t
+t/pod.t
+t/tai.out
+t/test.fa
+TODO
+xt/boilerplate.t
diff --git a/bin/build_cai_param.pl b/bin/build_cai_param.pl
@@ -480,7 +480,7 @@ =head3 Auxiliary options
 If option C<--background> is activated, the 'background-normalization'
 method always uses the I<max> method to get final CAIs. 
 
-=iem -o/--out-file
+=item -o/--out-file
 
 file to store the result. Default is standard output, usually screen.
 

diff --git a/t/cai.out b/t/cai.out
@@ -0,0 +1,59 @@
+CCG	0.878306878306878
+ACA	0.469767441860465
+GTT	0.330316742081448
+AGG	0.310810810810811
+TGT	0.23
+CGT	0.371621621621622
+GCA	0.274336283185841
+AGC	1
+ACT	0.288372093023256
+GAT	0.892857142857143
+ATC	1
+TGC	1
+CAC	1
+CCA	0.587301587301587
+TCA	0.254612546125461
+CTC	0.386058981233244
+AAA	0.398576512455516
+ACG	0.744186046511628
+CCT	0.407407407407407
+CTT	0.142091152815013
+TTG	0.329758713136729
+AAT	0.604477611940298
+ATA	0.284518828451883
+GAG	1
+ATT	0.414225941422594
+CCC	1
+CGA	0.364864864864865
+GTA	0.194570135746606
+TCC	0.845018450184502
+TAT	0.537634408602151
+GAC	1
+TCT	0.191881918819188
+CGC	1
+AAC	1
+GAA	0.394927536231884
+GCT	0.309734513274336
+CAT	0.537688442211055
+CAA	0.380352644836272
+CAG	1
+CTA	0.190348525469169
+GGG	0.174657534246575
+ACC	1
+GCG	0.47787610619469
+TCG	0.712177121771218
+TAC	1
+AGA	0.243243243243243
+TTA	0.0857908847184987
+GGT	0.335616438356164
+CTG	1
+GTC	0.565610859728507
+TTC	1
+GGC	1
+TTT	0.450261780104712
+GTG	1
+GCC	1
+CGG	0.540540540540541
+AGT	0.450184501845018
+GGA	0.537671232876712
+AAG	1
diff --git a/t/tai.out b/t/tai.out
@@ -0,0 +1,60 @@
+ATC	0.309751434034417
+ACT	0.430210325047801
+GAT	0.394837476099426
+TGC	0.334608030592734
+AGC	0.286806883365201
+CAC	0.239005736137667
+TGG	0.397705544933078
+TCA	0.095640535372849
+CCA	0.239039196940727
+CTC	0.17208413001912
+ACG	0.235181644359465
+AAA	0.286806883365201
+TTG	0.252390057361377
+CTT	0.239005736137667
+CCT	0.334608030592734
+ATA	0.0956453154875717
+AAT	0.338432122370937
+CCG	0.315487571701721
+AGG	0.189292543021033
+GTT	0.286806883365201
+ACA	0.286849904397706
+TGT	0.197418738049713
+GCA	0.09565965583174
+CGT	0.478011472275335
+GCG	0.173996175908222
+TCG	0.221797323135755
+AGA	0.1434034416826
+TAC	0.430210325047801
+CTG	0.413001912045889
+TTA	0.191204588910134
+GGT	0.394837476099426
+TTC	0.382409177820268
+GGC	0.669216061185469
+GTC	0.206500956022945
+GCC	0.413001912045889
+GTG	0.365200764818356
+TTT	0.225621414913958
+AGT	0.169216061185469
+CGG	0.152963671128107
+AAG	0.713193116634799
+GGA	0.286806883365201
+CCC	0.240917782026769
+ATT	0.430210325047801
+GAG	1
+GTA	0.0956309751434034
+CGA	0.478059273422562
+TAT	0.253824091778203
+GAC	0.669216061185469
+TCC	0.275334608030593
+GAA	0.286806883365201
+AAC	0.573613766730402
+TCT	0.382409177820268
+CGC	0.344168260038241
+GCT	0.573613766730402
+CAG	0.443594646271511
+CAA	0.191204588910134
+CAT	0.141013384321224
+CTA	0.0956261950286807
+GGG	0.0917782026768642
+ACC	0.309751434034417