From 52ed5d22eb5cdf22f7e47fcc0471b1c9be156915 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 5 Oct 2011 07:56:41 +0000
Subject: [PATCH] cleanup

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1539 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/test/test_AlignTwoSeq.pl | 641 ----------------------
 1 file changed, 641 deletions(-)
 delete mode 100755 code_perl/Maasha/test/test_AlignTwoSeq.pl

diff --git a/code_perl/Maasha/test/test_AlignTwoSeq.pl b/code_perl/Maasha/test/test_AlignTwoSeq.pl
deleted file mode 100755
index cd59552..0000000
--- a/code_perl/Maasha/test/test_AlignTwoSeq.pl
+++ /dev/null
@@ -1,641 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-use Test::More 'no_plan';
-use Data::Dumper;
-use Maasha::AlignTwoSeq;
-
-test_new_space();
-test_new_space_left();
-test_new_space_right();
-
-test_matches_select();
-
-test_word_size_calc();
-test_seq_index();
-test_seq_scan();
-test_matches_find();
-
-test_match_expand_forward_end_space();
-test_match_expand_forward_end_match();
-test_match_expand_backward_end_space();
-test_match_expand_backward_end_match();
-test_match_expand_end_space();
-test_match_expand_end_match();
-
-test_match_redundant_add();
-test_match_redundant();
-
-test_matches_filter();
-
-test_match_score_narrow();
-test_match_score_diag();
-test_match_score_len();
-test_match_score();
-
-test_align_two_seq();
-
-test_insert_indels();
-
-
-sub test_new_space
-{
-    my $space = { Q_SEQ => \"ATCG", S_SEQ => \"atcg" };
-    
-    Maasha::AlignTwoSeq::new_space( $space );
-
-    is( ${ $space->{ 'Q_SEQ' } }, "ATCG" );
-    is( ${ $space->{ 'S_SEQ' } }, "atcg" );
-    ok( $space->{ 'Q_MIN' } == 0 );
-    ok( $space->{ 'S_MIN' } == 0 );
-    ok( $space->{ 'Q_MAX' } == 3 );
-    ok( $space->{ 'S_MAX' } == 3 );
-}
-
-
-sub test_new_space_left
-{
-    my ( $best_match, $space, $new_space );
-
-    $best_match = {
-        Q_BEG => 2,
-        Q_END => 3,
-        S_BEG => 2,
-        S_END => 3,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    $new_space = Maasha::AlignTwoSeq::new_space_left( $best_match, $space );
-
-    ok( defined $new_space );
-    is( ${ $new_space->{ 'Q_SEQ' } }, "ATCG" );
-    is( ${ $new_space->{ 'S_SEQ' } }, "atcg" );
-    ok( $new_space->{ 'Q_MIN' } == 0 );
-    ok( $new_space->{ 'S_MIN' } == 0 );
-    ok( $new_space->{ 'Q_MAX' } == 1 );
-    ok( $new_space->{ 'S_MAX' } == 1 );
-}
-
-
-sub test_new_space_right
-{
-    my ( $best_match, $space, $new_space );
-
-    $best_match = {
-        Q_BEG => 0,
-        Q_END => 1,
-        S_BEG => 0,
-        S_END => 1,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    $new_space = Maasha::AlignTwoSeq::new_space_right( $best_match, $space );
-
-    ok( defined $new_space );
-    is( ${ $new_space->{ 'Q_SEQ' } }, "ATCG" );
-    is( ${ $new_space->{ 'S_SEQ' } }, "atcg" );
-    ok( $new_space->{ 'Q_MIN' } == 2 );
-    ok( $new_space->{ 'S_MIN' } == 2 );
-    ok( $new_space->{ 'Q_MAX' } == 3 );
-    ok( $new_space->{ 'S_MAX' } == 3 );
-}
-
-
-sub test_matches_select
-{
-    my ( $matches, $space );
-
-    $matches = [
-        { Q_BEG => 9,  S_BEG =>  9, Q_END => 10, S_END => 10 },
-        { Q_BEG => 10, S_BEG => 10, Q_END => 20, S_END => 20 },
-        { Q_BEG => 20, S_BEG => 20, Q_END => 21, S_END => 21 },
-    ];
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 10,
-        S_MIN => 10,
-        Q_MAX => 20,
-        S_MAX => 20,
-    };
-
-    Maasha::AlignTwoSeq::matches_select( $matches, $space );
-
-    ok( scalar @{ $matches } == 1 );
-}
-
-
-sub test_word_size_calc
-{
-    ok( Maasha::AlignTwoSeq::word_size_calc( { Q_MIN => 0, S_MIN => 0, Q_MAX => 1, S_MAX => 1 } ) == 1 );
-    ok( Maasha::AlignTwoSeq::word_size_calc( { Q_MIN => 0, S_MIN => 0, Q_MAX => 200, S_MAX => 200 } ) == 10 + 1 );
-}
-
-
-sub test_seq_index
-{
-    my ( $space, $word_size, $index );
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    $word_size = 2;
-    
-    $index = Maasha::AlignTwoSeq::seq_index( $space, $word_size );
-
-    ok( scalar keys %{ $index } == 3 );
-    ok( exists $index->{ 'AT' } );
-    ok( exists $index->{ 'TC' } );
-    ok( exists $index->{ 'CG' } );
-    ok( $index->{ 'AT' }->[ 0 ] == 0 );
-    ok( $index->{ 'TC' }->[ 0 ] == 1 );
-    ok( $index->{ 'CG' }->[ 0 ] == 2 );
-}
-
-
-sub test_seq_scan
-{
-    my ( $space, $word_size, $index, $matches );
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    $word_size = 2;
-    
-    $index   = Maasha::AlignTwoSeq::seq_index( $space, $word_size );
-    $matches = Maasha::AlignTwoSeq::seq_scan( $index, $space, $word_size );
-
-    ok( scalar @{ $matches } == 1 );
-    ok( $matches->[ 0 ]->{ 'Q_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'S_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'Q_END' } == 3 );
-    ok( $matches->[ 0 ]->{ 'S_END' } == 3 );
-    ok( $matches->[ 0 ]->{ 'LEN' }   == 4 );
-    ok( $matches->[ 0 ]->{ 'SCORE' } == 0 );
-}
-
-
-sub test_matches_find
-{
-    my ( $space, $matches );
-
-    $space = { Q_SEQ => \"ATCG", S_SEQ => \"ATCG", Q_MIN => 0, S_MIN => 0, Q_MAX => 3, S_MAX => 3 };
-
-    $matches = Maasha::AlignTwoSeq::matches_find( $space );
-
-    ok( scalar @{ $matches } == 1 );
-    ok( $matches->[ 0 ]->{ 'Q_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'S_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'Q_END' } == 3 );
-    ok( $matches->[ 0 ]->{ 'S_END' } == 3 );
-    ok( $matches->[ 0 ]->{ 'LEN' }   == 4 );
-
-    $space = { Q_SEQ => \"ATXXGAT", S_SEQ => \"ATCGAT", Q_MIN => 0, S_MIN => 0, Q_MAX => 6, S_MAX => 5 };
-
-    $matches = Maasha::AlignTwoSeq::matches_find( $space );
-
-    ok( scalar @{ $matches } == 4 );
-    ok( $matches->[ 0 ]->{ 'Q_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'S_BEG' } == 0 );
-    ok( $matches->[ 0 ]->{ 'Q_END' } == 1 );
-    ok( $matches->[ 0 ]->{ 'S_END' } == 1 );
-    ok( $matches->[ 0 ]->{ 'LEN' }   == 2 );
-    ok( $matches->[ 1 ]->{ 'Q_BEG' } == 5 );
-    ok( $matches->[ 1 ]->{ 'S_BEG' } == 0 );
-    ok( $matches->[ 1 ]->{ 'Q_END' } == 6 );
-    ok( $matches->[ 1 ]->{ 'S_END' } == 1 );
-    ok( $matches->[ 1 ]->{ 'LEN' }   == 2 );
-    ok( $matches->[ 2 ]->{ 'Q_BEG' } == 4 );
-    ok( $matches->[ 2 ]->{ 'S_BEG' } == 3 );
-    ok( $matches->[ 2 ]->{ 'Q_END' } == 6 );
-    ok( $matches->[ 2 ]->{ 'S_END' } == 5 );
-    ok( $matches->[ 2 ]->{ 'LEN' }   == 3 );
-    ok( $matches->[ 3 ]->{ 'Q_BEG' } == 0 );
-    ok( $matches->[ 3 ]->{ 'S_BEG' } == 4 );
-    ok( $matches->[ 3 ]->{ 'Q_END' } == 1 );
-    ok( $matches->[ 3 ]->{ 'S_END' } == 5 );
-    ok( $matches->[ 3 ]->{ 'LEN' }   == 2 );
-}
-
-sub test_match_expand_forward_end_space
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 1,
-        Q_END => 2,
-        S_BEG => 1,
-        S_END => 2,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    Maasha::AlignTwoSeq::match_expand_forward( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 1 );
-    ok( $match->{ 'S_BEG' } == 1 );
-    ok( $match->{ 'Q_END' } == 3 );
-    ok( $match->{ 'S_END' } == 3 );
-    ok( $match->{ 'LEN' }   == 3 );
-}
-
-
-sub test_match_expand_forward_end_match
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 1,
-        Q_END => 2,
-        S_BEG => 1,
-        S_END => 2,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCGXX",
-        S_SEQ => \"atcgnn",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 6,
-        S_MAX => 6,
-    };
-
-    Maasha::AlignTwoSeq::match_expand_forward( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 1 );
-    ok( $match->{ 'S_BEG' } == 1 );
-    ok( $match->{ 'Q_END' } == 3 );
-    ok( $match->{ 'S_END' } == 3 );
-    ok( $match->{ 'LEN' }   == 3 );
-}
-
-
-sub test_match_expand_backward_end_space
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 1,
-        Q_END => 2,
-        S_BEG => 1,
-        S_END => 2,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    Maasha::AlignTwoSeq::match_expand_backward( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 0 );
-    ok( $match->{ 'S_BEG' } == 0 );
-    ok( $match->{ 'Q_END' } == 2 );
-    ok( $match->{ 'S_END' } == 2 );
-    ok( $match->{ 'LEN' }   == 3 );
-}
-
-
-sub test_match_expand_backward_end_match
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 2,
-        Q_END => 3,
-        S_BEG => 2,
-        S_END => 3,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"XATCG",
-        S_SEQ => \"natcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 4,
-        S_MAX => 4,
-    };
-
-    Maasha::AlignTwoSeq::match_expand_backward( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 1 );
-    ok( $match->{ 'S_BEG' } == 1 );
-    ok( $match->{ 'Q_END' } == 3 );
-    ok( $match->{ 'S_END' } == 3 );
-    ok( $match->{ 'LEN' }   == 3 );
-}
-
-
-sub test_match_expand_end_space
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 1,
-        Q_END => 2,
-        S_BEG => 1,
-        S_END => 2,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"ATCG",
-        S_SEQ => \"atcg",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 3,
-        S_MAX => 3,
-    };
-
-    Maasha::AlignTwoSeq::match_expand( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 0 );
-    ok( $match->{ 'S_BEG' } == 0 );
-    ok( $match->{ 'Q_END' } == 3 );
-    ok( $match->{ 'S_END' } == 3 );
-    ok( $match->{ 'LEN' }   == 4 );
-}
-
-
-sub test_match_expand_end_match
-{
-    my ( $match, $space );
-
-    $match = {
-        Q_BEG => 2,
-        Q_END => 3,
-        S_BEG => 2,
-        S_END => 3,
-        SCORE => 0,
-        LEN   => 2,
-    };
-
-    $space = {
-        Q_SEQ => \"XATCGX",
-        S_SEQ => \"natcgn",
-        Q_MIN => 0,
-        S_MIN => 0,
-        Q_MAX => 6,
-        S_MAX => 6,
-    };
-
-    Maasha::AlignTwoSeq::match_expand( $match, $space );
-
-    ok( $match->{ 'Q_BEG' } == 1 );
-    ok( $match->{ 'S_BEG' } == 1 );
-    ok( $match->{ 'Q_END' } == 4 );
-    ok( $match->{ 'S_END' } == 4 );
-    ok( $match->{ 'LEN' }   == 4 );
-}
-
-
-sub test_match_redundant_add
-{
-    my ( $redundant );
-
-    $redundant = {};
-
-    Maasha::AlignTwoSeq::match_redundant_add( { Q_BEG => 10, Q_END => 20, S_BEG => 110, S_END => 120 }, $redundant );
-    Maasha::AlignTwoSeq::match_redundant_add( { Q_BEG => 15, Q_END => 25, S_BEG => 210, S_END => 220 }, $redundant );
-
-    ok( scalar keys %{ $redundant } == 16 );
-}
-
-
-sub test_match_redundant
-{
-    my ( $redundant );
-
-    $redundant = {};
-
-    Maasha::AlignTwoSeq::match_redundant_add( { Q_BEG => 10, Q_END => 20, S_BEG => 110, S_END => 120 }, $redundant );
-    Maasha::AlignTwoSeq::match_redundant_add( { Q_BEG => 15, Q_END => 25, S_BEG => 210, S_END => 220 }, $redundant );
-
-    ok( Maasha::AlignTwoSeq::match_redundant( { Q_BEG => 10, Q_END => 20, S_BEG => 110, S_END => 120 }, $redundant ) );
-    ok( not Maasha::AlignTwoSeq::match_redundant( { Q_BEG => 1, Q_END => 2, S_BEG => 110, S_END => 120 }, $redundant ) );
-}
-
-
-sub test_matches_filter
-{
-    ok( 0 );
-}
-
-
-sub test_match_score_narrow
-{
-    ok( 0 );
-}
-
-
-sub test_match_score_diag
-{
-    ok( 0 );
-}
-
-
-sub test_match_score_len
-{
-    ok( 0 );
-}
-
-
-sub test_match_score
-{
-    ok( 0 );
-}
-
-
-sub test_align_two_seq
-{
-    my ( $space, $matches );
-
-    $space = {
-        Q_SEQ => \"ATXCG",
-        S_SEQ => \"ATCG",
-    };
-
-    $matches = Maasha::AlignTwoSeq::align_two_seq( $space, [] );
-
-#    print Dumper( $matches );
-
-    ok( 0 );
-}
-
-
-sub test_insert_indels
-{
-    my ( $matches, $q_seq, $s_seq );
-
-    $matches = [
-        { Q_BEG => 1, S_BEG => 1, Q_END => 4, S_END => 4 }
-    ];
-
-    $q_seq = "XATCG";
-    $s_seq = "PATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "XATCG" );
-    is( $s_seq, "PATCG" );
-
-    $matches = [
-        { Q_BEG => 0, S_BEG => 1, Q_END => 3, S_END => 4 }
-    ];
-
-    $q_seq = "ATCG";
-    $s_seq = "PATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "-ATCG" );
-    is( $s_seq, "PATCG" );
-
-    $matches = [
-        { Q_BEG => 1, S_BEG => 0, Q_END => 4, S_END => 3 }
-    ];
-
-    $q_seq = "XATCG";
-    $s_seq = "ATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "XATCG" );
-    is( $s_seq, "-ATCG" );
-
-    $matches = [
-        { Q_BEG => 0, S_BEG => 0, Q_END => 3, S_END => 3 },
-        { Q_BEG => 6, S_BEG => 6, Q_END => 9, S_END => 9 },
-    ];
-
-    $q_seq = "ATCGXXATCG";
-    $s_seq = "ATCGNNATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "ATCGXXATCG" );
-    is( $s_seq, "ATCGNNATCG" );
-
-    $matches = [
-        { Q_BEG => 0, S_BEG => 0, Q_END => 3, S_END => 3 },
-        { Q_BEG => 6, S_BEG => 4, Q_END => 9, S_END => 7 },
-    ];
-
-    $q_seq = "ATCGXXATCG";
-    $s_seq = "ATCGATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "ATCGXXATCG" );
-    is( $s_seq, "ATCG--ATCG" );
-
-    $matches = [
-        { Q_BEG => 0, S_BEG => 1, Q_END => 2, S_END => 3 },
-        { Q_BEG => 5, S_BEG => 4, Q_END => 8, S_END => 7 },
-    ];
-
-    $q_seq = "TCGXXATCG";
-    $s_seq = "ATCGATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "-TCGXXATCG" );
-    is( $s_seq, "ATCG--ATCG" );
-
-    $matches = [
-        { Q_BEG => 1, S_BEG => 0, Q_END => 3, S_END => 2 },
-        { Q_BEG => 6, S_BEG => 3, Q_END => 9, S_END => 6 },
-    ];
-
-    $q_seq = "ATCGXXATCG";
-    $s_seq = "TCGATCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "ATCGXXATCG" );
-    is( $s_seq, "-TCG--ATCG" );
-
-    $matches = [
-        { Q_BEG => 1, Q_END =>  3, S_BEG => 0, S_END => 2 },
-        { Q_BEG => 6, Q_END =>  7, S_BEG => 3, S_END => 4 },
-        { Q_BEG => 9, Q_END => 10, S_BEG => 7, S_END => 8 },
-    ];
-
-    $q_seq = "ATCGXXATACG";
-    $s_seq = "TCGATNTCG";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "ATCGXXAT-ACG" );
-    #             |||  ||  ||
-    is( $s_seq, "-TCG--ATNTCG" );
-
-    $matches = [
-        { Q_BEG => 1, Q_END =>  3, S_BEG => 0, S_END => 2 },
-        { Q_BEG => 6, Q_END =>  7, S_BEG => 3, S_END => 4 },
-        { Q_BEG => 9, Q_END => 10, S_BEG => 7, S_END => 8 },
-    ];
-
-    $q_seq = "ATCGXXATACG";
-    $s_seq = "TCGATNTCGXX";
-
-    Maasha::AlignTwoSeq::insert_indels( $matches, \$q_seq, \$s_seq );
-
-    is( $q_seq, "ATCGXXAT-ACG--" );
-    #             |||  ||  ||
-    is( $s_seq, "-TCG--ATNTCGXX" );
-}
-- 
2.39.2