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Change the package path

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coissac committed 2018-02-20 06:40:29 +11:00
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inst/extdata/termes.fasta
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inst/extdata/termes.tab
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id best_identity best_match clean:A01 clean:A02 clean:A03 clean:A04 clean:A05 clean:A06 clean:A07 clean:A08 clean:A09 clean:A10 clean:A11 clean:A11r clean:A12 clean:A13 clean:A14 clean:A15 clean:A16 clean:A16r clean:A17 clean:A18 clean:A19 head singleton internal family family_name genus genus_name sample:A01 sample:A02 sample:A03 sample:A04 sample:A05 sample:A06 sample:A07 sample:A08 sample:A09 sample:A10 sample:A11 sample:A11r sample:A12 sample:A13 sample:A14 sample:A15 sample:A16 sample:A16r sample:A17 sample:A18 sample:A19 occurrence order order_name scientific_name seqLength species species_list species_name taxid sequence Termites_00001 1.0 AF475002 h h s h h s i s h s NA h h NA s NA NA h h h NA 10 5 1 46569 Termitidae 187534 Cylindrotermes 26 14221 2 13 5 2 1 2 16 13 0 7 4 0 1 0 0 14 5 6 0 14338 7499 Isoptera Cylindrotermes parvignathus 68 187535 ['Cylindrotermes parvignathus'] Cylindrotermes parvignathus 187535 ttgtttctgagtgaatgatggattacattgttatttgttttattggattgttgatttttatattggca Termites_00002 0.392156862745 FJ456952 i s s s h s s s h h s h NA h s h h h s h h 10 9 1 NA NA NA NA 2 1 3 4 275 4 1 12 478 4 10 5425 0 9 4 5 185 1487 6 14492 83 22490 NA NA Coelomata 24 NA [] NA 33316 aaacagaaaaacgggcaggttaat Termites_00003 0.971014492754 DQ441638 s h NA s h s s s s h NA NA NA h NA s NA s h s s 5 10 0 46569 Termitidae NA NA 4 6 0 2 3 1 5 1 1 4 0 0 0 4 0 2 0 2 14079 2 1 14117 7499 Isoptera Apicotermitinae 69 NA ['Longustitermes manni', 'Anoplotermes janus', 'Coxotermes boukokoensis'] NA 92739 ttgtttctaagtggaatgatggattacattgttatttgtttacttggattgttaattttaatattgata Termites_00004 0.985294117647 DQ441638 NA NA h NA NA NA NA s NA NA h NA NA NA NA NA h s NA NA h 4 2 0 46569 Termitidae NA NA 0 0 7 0 0 0 0 4 0 0 19 0 0 0 0 0 9 1 0 0 8 48 7499 Isoptera Apicotermitinae 68 NA ['Anoplotermes banksi', 'Longustitermes manni', 'Coxotermes boukokoensis'] NA 92739 ttgtttctaagtggaatgatggattacactgttatttgtttattggattgttgattttaatattgata Termites_00005 1.0 DQ441682 h NA NA NA h NA NA NA h s s NA s h s NA s NA s NA NA 4 6 0 46569 Termitidae 377725 Cyrilliotermes 6 0 0 0 4 0 0 0 6 1 1 0 2 13795 1 0 1 0 2 0 0 13819 7499 Isoptera Cyrilliotermes angulariceps 71 377900 ['Cyrilliotermes angulariceps'] Cyrilliotermes angulariceps 377900 ttgtttctaagtggaatgatggattacattgttatttgtttgtggattgttggatttaaagggtatctgca Termites_00006 0.942857142857 DQ441775 h NA s NA NA h NA NA h NA s s NA NA h NA NA s s NA s 4 6 0 46569 Termitidae NA NA 6 0 2 0 0 3 0 0 3 0 2 1 0 0 5 0 0 1 1 0 1 25 7499 Isoptera Termitidae 69 NA ['Coatitermes kartaboensis', 'Termes comis', 'Obtusitermes sp. EC-1', 'Tuberculitermes bycanistes', 'Cavitermes tuberosus', 'Adaiphrotermes sp. CM2'] NA 46569 ttgtttctaagtggtgtgatggattacattgttatttgtttatttggattgttggttttgatattggca Termites_00007 1.0 DQ441651 NA NA NA NA NA NA NA NA NA NA NA NA NA i NA NA NA NA h s h 2 1 1 46569 Termitidae 377708 Atlantitermes 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 3 3 11 7499 Isoptera Atlantitermes cf. oculatissimus 67 377876 ['Atlantitermes cf. oculatissimus'] Atlantitermes cf. oculatissimus 377876 ttgtttctaagtggaatgatggattacattgttatttgtttttggattgttgattttaatattggca Termites_00008 0.95652173913 DQ441637 NA h NA NA NA NA NA NA NA h NA s NA NA s NA NA NA NA s NA 2 3 0 46569 Termitidae 62953 Anoplotermes 0 4 0 0 0 0 0 0 0 4 0 1 0 0 1 0 0 0 0 2 0 12 7499 Isoptera Anoplotermes 68 NA ['Anoplotermes sp. EC1', 'Anoplotermes cf. K'] NA 62953 ttgtttctaagtggaatgatggattacattggtatttgtttattggattgttggttttaatgttaaca Termites_00009 1.0 DQ441762 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 0 0 46569 Termitidae NA NA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7499 Isoptera Nasutitermitinae 67 NA [] NA 62941 ttgtttttaagtggaatgatggattacattgttatttgtttatggattgtcggttttaatattggca Termites_00010 0.985294117647 AF475002 NA i NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA s i s 0 2 2 46569 Termitidae 187534 Cylindrotermes 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 1 11 7499 Isoptera Cylindrotermes parvignathus 68 187535 ['Cylindrotermes parvignathus'] Cylindrotermes parvignathus 187535 ttgtttctgagtgaatgatggattatattgttatttgttttattggattgttgatttttatattggca Termites_00011 0.411764705882 FJ456952 h NA NA s NA NA NA s NA NA s h s s s NA s NA NA NA h 3 7 0 NA NA NA NA 2485 0 0 2 0 0 0 3 0 0 1 4 1 1 2 0 2 0 0 0 16 2517 NA NA Coelomata 27 NA [] NA 33316 agcaaacagaagaacgggcaggttaat Termites_00012 0.387096774194 AF324511 NA NA NA NA NA NA NA NA s s NA NA s s s NA s NA NA NA NA 0 6 0 NA NA NA NA 0 0 0 0 0 0 0 0 1 1 0 0 1 1 1 0 1 0 0 0 0 6 NA NA Coelomata 27 NA [] NA 33316 tcgtatggaaaaattcgaatcattcct Termites_00013 1.0 DQ441671 NA NA NA NA NA NA NA NA NA s NA NA h NA NA s NA NA NA NA NA 1 2 0 46569 Termitidae 62946 Cornitermes 0 0 0 0 0 0 0 0 0 1 0 0 3 0 0 1 0 0 0 0 0 5 7499 Isoptera Cornitermes pugnax 67 377892 ['Cornitermes pugnax'] Cornitermes pugnax 377892 ttgtttctaagtgaatgatggattacattattatttgtttatggattatttggtttaaatattgata Termites_00014 0.352941176471 FJ456952 NA NA NA NA s NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 1 0 NLine truncated
inst/extdata/termes_ngsfilt.txt
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termes_data A01 acacacac:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01A; serie=01; coordX=5; coordY=5;
termes_data A02 acagcaca:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01B; serie=01; coordX=10; coordY=5;
termes_data A03 gtgtacat:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01C; serie=01; coordX=15; coordY=5;
termes_data A04 tatgtcag:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01D; serie=01; coordX=20; coordY=5;
termes_data A05 tagtcgca:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01E; serie=01; coordX=25; coordY=5;
termes_data A06 tactatac:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01F; serie=01; coordX=30; coordY=5;
termes_data A07 actagatc:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01G; serie=01; coordX=35; coordY=5;
termes_data A08 gatcgcga:acacacac ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_01H; serie=01; coordX=40; coordY=5;
termes_data A09 acacacac:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02A; serie=01; coordX=45; coordY=5;
termes_data A10 acagcaca:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02B; serie=01; coordX=50; coordY=5;
termes_data A11 gtgtacat:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02C; serie=01; coordX=55; coordY=5;
termes_data A12 tatgtcag:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02D; serie=01; coordX=60; coordY=5;
termes_data A13 tagtcgca:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02E; serie=02; coordX=65; coordY=5;
termes_data A14 tactatac:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02F; serie=02; coordX=70; coordY=5;
termes_data A15 actagatc:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02G; serie=02; coordX=75; coordY=5;
termes_data A16 gatcgcga:acagcaca ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_02H; serie=02; coordX=80; coordY=5;
termes_data A17 acacacac:gtgtacat ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_03A; serie=02; coordX=85; coordY=5;
termes_data A18 acagcaca:gtgtacat ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_03B; serie=02; coordX=90; coordY=5;
termes_data A19 gtgtacat:gtgtacat ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=01_03C; serie=02; coordX=95; coordY=5;
termes_data A11r tcagtgtc:gtcgtaga ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=04_10B; serie=01; coordX=55; coordY=5;
termes_data A16r actctgct:gtcgtaga ATTTCAGGTCAAGGTGCAGC TACAACCAAATCCAATTTCA F @ position=04_10C; serie=02; coordX=80; coordY=5;