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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Lines of Context:
t/data/testdata.crossmatch
 
1
cross_match 34_1_5_MSX1DF.seq msx1_ens2.fasta -alignments 
 
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cross_match version 0.990329
 
3
 
 
4
Run date:time  080103:101214
 
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Query file(s):  34_1_5_MSX1DF.seq
 
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Subject file(s):   msx1_ens2.fasta
 
7
Presumed sequence type: DNA
 
8
 
 
9
Pairwise comparison algorithm: banded Smith-Waterman
 
10
 
 
11
Score matrix (set by value of penalty: -2)
 
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    A   C   G   T   N   X
 
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A   1  -2  -2  -2   0  -3
 
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C  -2   1  -2  -2   0  -3
 
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G  -2  -2   1  -2   0  -3
 
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T  -2  -2  -2   1   0  -3
 
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N   0   0   0   0   0   0
 
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X  -3  -3  -3  -3   0  -3
 
19
 
 
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Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
 
21
Using complexity-adjusted scores. Assumed background frequencies:
 
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 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  
 
23
 
 
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minmatch: 14, maxmatch: 14, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
 
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vector_bound: 0
 
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word_raw: 0
 
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masklevel: 80
 
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Sequence file: 34_1_5_MSX1DF.seq    1 entries
 
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Residue counts:
 
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  A      123
 
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  C      148
 
33
  G      170
 
34
  N        1
 
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  T      161
 
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Total    603
 
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NO QUALITY FILE 34_1_5_MSX1DF.seq.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15.
 
39
Maximal single base matches (low complexity regions):
 
40
 
 
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 538  1.37 0.51 0.34  C:\Program       19   603 (0)    msx1_ens2     2824  3409 (3856)  
 
42
 
 
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  C:\Program          19 TCCCAA-CGTCTAAGACTGAGCCATTAA-GTGGACTCCAGGTGCCCAAGG 66
 
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                               -      i              -                     
 
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  msx1_ens2         2824 TCCCAAACGTCTAGGACTGAGCCATTAAAGTGGACTCCAGGTGCCCAAGG 2873
 
46
 
 
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  C:\Program          67 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 116
 
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  msx1_ens2         2874 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 2923
 
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  C:\Program         117 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 166
 
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  msx1_ens2         2924 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 2973
 
54
 
 
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  C:\Program         167 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 216
 
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  msx1_ens2         2974 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 3023
 
58
 
 
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  C:\Program         217 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 266
 
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  msx1_ens2         3024 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 3073
 
62
 
 
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  C:\Program         267 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 316
 
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  msx1_ens2         3074 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 3123
 
66
 
 
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  C:\Program         317 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 366
 
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  msx1_ens2         3124 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 3173
 
70
 
 
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  C:\Program         367 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 416
 
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  msx1_ens2         3174 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 3223
 
74
 
 
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  C:\Program         417 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTTTGACTCACATC 466
 
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                                                                -          
 
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  msx1_ens2         3224 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTT-GACTCACATC 3272
 
78
 
 
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  C:\Program         467 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTAGTCAT 516
 
80
                                                                     v  iv 
 
81
  msx1_ens2         3273 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTTGTTTT 3322
 
82
 
 
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  C:\Program         517 GTTTNTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 566
 
84
                             ?                                             
 
85
  msx1_ens2         3323 GTTTTTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 3372
 
86
 
 
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  C:\Program         567 ATACTTAGGGCAAAACCGCGGTGGTGAA-CATCTTCGA 603
 
88
                                  -       vvv        -         
 
89
  msx1_ens2         3373 ATACTTAGG-CAAAACCCGCGTGGTGAAACATCTTCGA 3409
 
90
 
 
91
Transitions / transversions = 0.40 (2 / 5)
 
92
Gap_init rate = 0.01 (5 / 586), avg. gap size = 1.00 (5 / 5)  
 
93
 
 
94
 
 
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1 matching entries (first file).
 
96
 
 
97
Discrepancy summary:
 
98
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)