Finished writing test files

fortune9 · May 1, 2015 · 1efa461 · 1efa461
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diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,4 @@ pod2htm*.tmp
 pm_to_blib
 Bio-CUA-*
 Bio-CUA-*.tar.gz
+.swp$
diff --git a/Changes b/Changes
@@ -1,5 +1,6 @@
 Revision history for Bio-CUA
 
-0.01    Date/time
-        First version, released on an unsuspecting world.
+1.01    Thu Apr 30 16:51:09 EDT 2015
+        First version, including methods to calculate codon usage bias
+		indice at both codon and sequence levels.
 
diff --git a/MANIFEST b/MANIFEST
@@ -1,11 +1,34 @@
+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/Builder.pm
 lib/Bio/CUA/CUB/Calculator.pm
+lib/Bio/CUA/Seq.pm
+lib/Bio/CUA/SeqIO.pm
+lib/Bio/CUA/Summarizer.pm
 Makefile.PL
 MANIFEST			This list of files
 README
 t/00-load.t
+t/b_CAI_param.S2_top_200.b1000
+t/build_cai_param.v1.0.pl
+t/build_tai_param.pl
+t/CAI_param.S2_top_200
+t/CAI_param.S2_top_200.by_avg
+t/dmel_r5_apr2006.tAI_param
+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/tmp1
+t/tmp2
+t/tmp_positive
+xt/boilerplate.t
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
@@ -0,0 +1,18 @@
+Makefile
+Makefile.old
+Build
+Build.bat
+META.*
+MYMETA.*
+.build/
+_build/
+cover_db/
+blib/
+inc/
+.lwpcookies
+.last_cover_stats
+nytprof.out
+pod2htm*.tmp
+pm_to_blib
+Bio-CUA-*
+Bio-CUA-*.tar.gz
diff --git a/Makefile.PL b/Makefile.PL
@@ -4,12 +4,16 @@ use warnings;
 use ExtUtils::MakeMaker;
 
 WriteMakefile(
-    NAME             => 'Bio::CUA::CUB::Builder',
+    NAME             => 'Bio::CUA',
     AUTHOR           => q{Zhenguo Zhang <zhangz.sci@gmail.com>},
-    VERSION_FROM     => 'lib/Bio/CUA/CUB/Builder.pm',
-    ABSTRACT_FROM    => 'lib/Bio/CUA/CUB/Builder.pm',
+    VERSION_FROM     => 'lib/Bio/CUA.pm',
+    ABSTRACT_FROM    => 'lib/Bio/CUA.pm',
     LICENSE          => 'gpl_3',
-    PL_FILES         => {},
+	#PL_FILES         => {'other.PL' => ''}, # files run during compilation 
+	EXE_FILES        => ["bin/build_cai_param.pl",
+	                     "bin/build_tai_param.pl",
+						 "bin/calculate_CUB.pl"
+	                    ], # files in bin directory
     MIN_PERL_VERSION => 5.006,
     CONFIGURE_REQUIRES => {
         'ExtUtils::MakeMaker' => 0,
@@ -20,7 +24,44 @@ WriteMakefile(
     PREREQ_PM => {
         #'ABC'              => 1.6,
         #'Foo::Bar::Module' => 5.0401,
+		'File::Sort'        => 1.01,
+		'File::Temp'        => 0,
+		'Fcntl'             => 0,
+		'parent'            => 0,
+		'Getopt::Long'      => 0,
+		'Carp'              => 0
     },
+
+	# add more information
+	META_MERGE  => {
+		resources => {
+			homepage => 'http://molevol.altervista.org/'
+		}
+	},
+
     dist  => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', },
     clean => { FILES => 'Bio-CUA-*' },
+	test  => { RECURSIVE_TEST_FILES => 1, # test directories in t recursively
+		# TESTS => 't/01-seqio.t'
+	},
+	# environment variables
+	macro => {
+#		'expected_file' => 't/expected.tsv' # expected results to compare
+	}
 );
+
+package MY; # other content MakeMaker can't produce
+
+sub postamble
+{
+	# The return will be directly write to makefile
+	my $postamble = <<POST;
+export expected_file = t/expected.tsv
+export seq_file = t/test.fa
+export tRNA_file = t/dmel_r5_apr2006.tRNA_copy
+POST
+
+	return $postamble;
+}
+
+# put subroutines here
diff --git a/README b/README
@@ -1,18 +1,35 @@
-Bio-CUA
+1. Bio-CUA
 
-The README is used to introduce the module and provide instructions on
-how to install the module, any machine dependencies it may have (for
-example C compilers and installed libraries) and any other information
-that should be provided before the module is installed.
+Version: 1.01
 
-A README file is required for CPAN modules since CPAN extracts the README
-file from a module distribution so that people browsing the archive
-can use it to get an idea of the module's uses. It is usually a good idea
-to provide version information here so that people can decide whether
-fixes for the module are worth downloading.
+2. Purpose
 
+The aim of this distribution is to provide comprehensive and flexible
+tools to analyze codon usage bias (CUB) and relevant problems.
 
-INSTALLATION
+One amino acid can be encoded by more than one synonymous codon, and
+synonymous codons are unevenly used. For example, some codons are used
+more often than other synonymous ones in highly expressed genes
+(I<Sharp and Li 1987>). To measure the unevenness of codon usage, multiple
+indices of codon usage bias have been developed, such as Fop
+(Frequency of optimal codons), CAI (Codon Adaptation Index), tAI (tRNA
+Adaptation Index), and ENC (Effective Number of Codons). The causes of
+CUB phenomena are complicated, including, mutational bias, selection
+on translational efficiency or accurancy. CUB is one fundamental concept
+in genetics.
+
+So far, no software exists to compute all the above CUB indices, and
+worse is that parameters of CUB calculations are often fixed in
+software, so one can only analyze genes in a limited list of species
+and one can not incorporate its own parameters such as sequences of
+highly expressed genes in a tissue.
+
+This package mainly solves these two problems. We also extend some
+methods, such as GC-content corrected ENC, background-data normalized
+CAI, etc. See the relevant methods in CUB classes for more details.
+
+
+3. INSTALLATION
 
 To install this module, run the following commands:
 
@@ -21,12 +38,15 @@ To install this module, run the following commands:
 	make test
 	make install
 
-SUPPORT AND DOCUMENTATION
+or install directly from CPAN as
+	cpan Bio::CUA
+
+4. SUPPORT AND DOCUMENTATION
 
 After installing, you can find documentation for this module with the
 perldoc command.
 
-    perldoc Bio::CUA::CUB::Builder
+    perldoc Bio::CUA
 
 You can also look for information at:
 
@@ -43,7 +63,7 @@ You can also look for information at:
         http://search.cpan.org/dist/Bio-CUA/
 
 
-LICENSE AND COPYRIGHT
+5. LICENSE AND COPYRIGHT
 
 Copyright (C) 2015 Zhenguo Zhang
 

diff --git a/TODO b/TODO
@@ -0,0 +1,3 @@
+I have the following in mind.
+
+1. add statistical methods to detect optimal codons.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		I have the following in mind.

		1. add statistical methods to detect optimal codons.