bio-maf 0.1.0-java

data/test/data/chr22_ieq.maf

@@ -0,0 +1,11 @@
+##maf version=1 scoring=autoMZ.v1
+a score=13668.000000
+s hg19.chr22              16054189 54 + 51304566 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGGT
+s ponAbe2.chrUn           13354616 54 + 72422247 TCTTTCAAACCCACAGTAATGGGGCTGACATCCTCTACCATATGCAAGAGAGGT
+q ponAbe2.chrUn                                  855489998999999899968899889893997969799999879999999989
+i ponAbe2.chrUn           C 0 C 0
+s panTro2.chrUn            7684562 54 + 58616431 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGAT
+q panTro2.chrUn                                  999999999999999999999999999999999999999999999999999999
+i panTro2.chrUn           C 0 C 0
+e turTru1.scaffold_109008    25049 1601 +    50103 I
+

data/test/data/chrY-1block.maf

@@ -0,0 +1,6 @@
+##maf version=1 scoring=autoMZ.v1
+a score=4443.000000
+s hg19.chrY              10501 107 + 59373566 GGACAGCCCGGAAAATGAGCTCCTCATCTCTAACCCAGTTCCCCTGTGGGGATTTAGGGGACCAGGGACAGCCCGTTGCATGAGCCCCTGGACTCTAACCCAGTTCC
+s tarSyr1.scaffold_53149  1869 107 +    12002 GGACAGCCCCACAGATGATCTCCTGTTCTGTAAACCAGTTCCCCTGGAGGGACTGAAGGAACCTGGGAGAGGCCCGCAGAGGGTCTCCTGGTTTGTAGGCCAGTTCC
+q tarSyr1.scaffold_53149                      99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+i tarSyr1.scaffold_53149 N 0 N 0

data/test/data/mm8_chr7_tiny.maf

@@ -0,0 +1,76 @@
+##maf version=1
+a score=10542.0
+s mm8.chr7                 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- 
+s rn4.chr1                136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- 
+s oryCun1.scaffold_199771     14021 43 -     75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- 
+s hg18.chr15               88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s panTro2.chr15            87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s rheMac2.chr7             69864714 28 + 169801366 -------GGGC--AAGTATGGA--AGGGAAGCCC--------------CAGAA- 
+s canFam2.chr3             56030570 39 +  94715083 AGGTTTAGGGCAGAGGGATGAAGGAGGAGAATCC--------------CTATG- 
+s dasNov1.scaffold_106893      7435 34 +      9831 GGAACGAGGGC--ATGTGTGG---AGGGGGCTGC--------------CCACA- 
+s loxAfr1.scaffold_8298       30264 38 +     78952 ATGATGAGGGG--AAGCGTGGAGGAGGGGAACCC--------------CTAGGA 
+s echTel1.scaffold_304651       594 37 -     10007 -TGCTATGGCT--TTGTGTCTAGGAGGGGAATCC--------------CCAGGA 
+
+a score=-33148.0
+s mm8.chr7                 80082368 103 + 145134094 TGAGAGGGCATGCT-GTGAAGGGACTGTGCT---CAGTTCAAGGCATAGTCCACTTCC--------CTTCCCTTGGTCATTCTGTTCGGTGTGTTTCCAGCAGATATGGAGAGT-------------------------------------C---- 
+s rn4.chr1                136011819  86 + 267910886 TGAGAGGGCATGTT-ATGAAGGCACTGTGCT--------------------CACTTTC--------CATCCCATGGTCATTCTGTTGAGTGTGTTCCCAGCAGATACGGAAAGT-------------------------------------C---- 
+s oryCun1.scaffold_199771     14064  74 -     75077 TAGGACTGCCTGGTGGGGGGGGCCCTGCACC--------------------TACTTCTGCAAGGCACGTCCCGCG----------TCTGTGCCTTCGCCGCA-----------T-------------------------------------C---- 
+s hg18.chr15               88557607 128 + 100338915 GGGGAAAGCCTGGT-TAAGGGGCCCTTCACCCCCCTCTCCAAGGCACATTCCCCTTTC--------TGTCCCTTTGTCGTTTCATTCACTCTACTCCCAGCATGGCTGGAGGGC---TTGTGG---CTGGCTCGTTTGG---------AGGC---- 
+s panTro2.chr15            87959864 116 + 100063422 GGGGAAAGCCTGGT-TAAGGGGCCCTTCACCCCCCTCTCCAAGGCACATTCCCCTTTC--------TGTCCCTTTGTCGTTTCATTCACTA------------GGCTAGAGGGC---TTGTGG---CTGGCTCGTTTGG---------AGGC---- 
+s rheMac2.chr7             69864742 107 + 169801366 GGAGAAAGCCTGGT-TAAGGGGCCCTTCA-----CTCTCCAAGGCACATTCCACTTTC--------TGTCCCTTTGTCATTCCATTCACTCTACTCCCCGCATGGCTAGAGGGC----------------------TGG---------AGGC---- 
+s canFam2.chr3             56030609 103 +  94715083 AGGGAATGCATGGTGTATGGGGGCCCCCGTC--------------------CACTTC---------TGTCCCGTTGCTATTTCCTTGACCATACTTCCAGTATGACTGGGGGAG---GTGCGG---TGGAGCAGGTTC------------------ 
+s loxAfr1.scaffold_8298       30302 144 +     78952 --TGGATGCCTGGT-TTAAGGATCC-GCTCACCCACTTCTGAGTCACGTTACACTTTC--------TGCCCCTTTGCCATTTCATTTATGGTACTCCCAACACCGGGGGAGGGTGCGCTTTGGTTCTTGAGCAGTTTGTGTATATAGGGGGCTGAG 
+s echTel1.scaffold_304651       631  67 -     10007 --TGGAGGGCTACT-TTAAGAAACC----CTCCCGTTTCTCAG-------------CC--------TGCTTC---------------------------------------------CTTTGGGTTTGAGGTACTTTGT----------------G 
+
+a score=87527.0
+s mm8.chr7                 80082471 121 + 145134094 CTG-AGC---------------CGCTGGCCCCTGGGCTTCCCCTCCAGCCTGGCTTGACTTTGTCTGAGGGACCCTGGGCAGC-TTGCCATCCA---------CCCAGGCTGAAGTGGAGGGGGTGTTGAGCTGCCACCTGGGACTT 
+s rn4.chr1                136011905 121 + 267910886 TCG-GAC---------------CGCTGGCACCCAGGCTTCCCCTCCAGCCTGGCCTGACTCTGTCTGAGGGACCCTGGGCAGC-TTGCCATCCA---------CGCAGGCAAAAGTGGAGGGGATGTTGAGCTGCCACCTGGAACTT 
+s oryCun1.scaffold_199771     14138 103 -     75077 CCGCAGT---------------GGATCCCACCTCGGCTGTAGCAGTAGGCCAACCAGG----GCCCGACAGGCGCCCGGCTGTGCTGGCTTCCA-CACCCTCTCCCAGGC---------------------CTGCCACCCAGGC--- 
+s hg18.chr15               88557735 127 + 100338915 CTG-GGCTGAACCAGGGACT--GGCTGGTCTATAGGTTTCCCCTCCAGCC-GGCTGCACTCTG----TAGTGCCCGAGGCAGG-TTTCCACCCC-----TTCTCCCAGGCGTAAGTGGG------ATTGAGTTGCCACCTGGGACTG 
+s panTro2.chr15            87959980 127 + 100063422 CTG-GGCTGAACCAGGGACT--GGCTGGTCTATAGGTTTCCCCTCCAGCC-GGCTGCACTCTG----TAGTGCCCGTGGCAGG-TTTCCACCCC-----TTCTCCCAGGCGTAAGTGGG------ATTGAGTTGCCACCTGGGACTG 
+s rheMac2.chr7             69864849 116 + 169801366 CTG-GGCTGAACCAGGGGCT--GGCTGGTCTGCAG----------------GGCTGCACTCTGTCTATAGTGCCCGAGGCAGG-TTTCCACCCC-----TTCTTCCAGTCGTAAGTGGG------GTTGAGCTGCCACCTGGGACTG 
+s bosTau2.scaffold2397        93191 110 +    117874 CTG-GGC---------------AGCTGGCGCCTCGGCTGCCCCTCCCACCTGGCT-------------GTGACCCTTGGCAAG-TCTCCCCGCCCCCCATGCCCCCAGGCCTGAGCAAG------GCTGAGCTGCCACCT-GGACTA 
+s canFam2.chr3             56030712 116 +  94715083 TCT-AGC---------------AGCTGGCGCCCCAGCTGTCCTTCCAACCTGGCTGTGCTCTGTCTACGTGACCTTTGGCAGA-TTGCCACTCC-------CTCCCAGGCCCGAGCAGG------GCCAAGCTGCCACCT-GGATGG 
+s loxAfr1.scaffold_8298       30446 129 +     78952 CTG-AAC-----CAGGGACTGCAGCTAGTGCCTGGGCCACCGCTCCAGCCTGGCTGTGCTCTGTCTACAGGACGCATGGCAAG-TTGCCACCCC----CCTCTCCCAGG-CTAGGTGGG------GCTAAGCTGCCACTTGAAACTT 
+s echTel1.scaffold_304651       698 101 -     10007 CTG-GAC-----CAGGAACTGCAGCT---------GCTGCCCCTCTAGCCTACCTGTGC---------------CTTGGCAGG-TTGCCAGCCC-------CTCCCAGGCCTAGGTGGG------GTGACGCTGCCTCCTGGGAC-- 
+
+a score=185399.0
+s mm8.chr7                 80082592 121 + 145134094 GTGCTTATCTCGGACTCTTGGCATTTCTGTTTCTGGACAGAACCCAAGGGTGGCTTCCCGCTTAGAGCTGTAGGTCCC----ACCCAGGTGGAAATG--CCCTCCGGTGCAGGCAGATAAGCTCTGG 
+s rn4.chr1                136012026 121 + 267910886 GTGCTTATCTTGGCCTCTTGGCATTTCTGTATCTGGACAGAATCCAAGGGTGGCTTCCCGCTTAGAGCTGTAGGTCCC----ACCCAGGTGGAAATG--CCCTCCGGAGCAGGCAGATAAGCTCTGG 
+s oryCun1.scaffold_199771     14241 119 -     75077 ---CTTATCTCCGACTGCTGGCATTGCTGTGTCTGGGCAGAGGCCAAGGGCGGCCTCCCGCACAGACACTCGGGGCCC----GCCCAGGTAGAAGTG-CCCCTCCTGTGCAGGCAGATAAGCGCTGG 
+s hg18.chr15               88557862 119 + 100338915 AGGCTTATCTCTGACTCTTGGCATTTCTTTGTCTGGACAGATTCCAAGGGCGGTCTGCTGCCCAGACTTACAGGGCCT----GCCCAGGTGGAAACG--CTCTTT--TGCAGGTAGATAAGCACGGG 
+s panTro2.chr15            87960107 119 + 100063422 AGGCTTATCTCTGACTCTTGGCATTTCTTTGTCTGGACAGATTCCAAGGGCGGTCTGCTGCCCAGACTTACAGGGCCT----GCCCAGGTGGAAACG--CTCTTT--TGCAGGTAGATAAGCACGGG 
+s rheMac2.chr7             69864965 114 + 169801366 AGGCTTATCTCTGATCCTTGGCATTTCTGTGTCTGGACAGATTCCAAGGGCGGTCTGCTGCCCAGACTTACAGGGCCC----GCCCAGGTG-----G--CTCTTC--TGCAGGTAGATAAGCATGGG 
+s bosTau2.scaffold2397        93301 123 +    117874 AAGCTTATCTCTGACCTTTGGCATTCCTGTGTGTGGACAGATTGCAAGAGCAGCCTCT-GCCCAGGCTTACGGGGACCTGCTGCCTCGGTAGAAATG-CGCCTCCTCTGTAGGCAGATAAGCCCT-- 
+s canFam2.chr3             56030828 121 +  94715083 CAACTTATCTTTGACCTTCGGCATTTCTATATCTGGATGGATCCTAAGTGCAGCCTCCAGCCTAGACTTCCAGGACCC----ACCCTGGGA-AGATG-CCCCTCCTGTGTGGGCAGATAAATGTTGG 
+s echTel1.scaffold_304651       799 118 -     10007 ATGACAATCT--GACCTTTGACATT--TGTTTTAGGATAGGTTCCAAGTGAAGCCTCCTGCCTAGACTTCCTGATTCT-----CCCAGATAGAAGCGCCCCCTTCTTGGAAGACAGATAAGCGATAA 
+
+a score=30120.0
+s mm8.chr7                 80082713 54 + 145134094 CAA-------ACCAAAGGCAGCCTGT-GCTTCCAGAAAACCTT-GAGGGGTGCAAGAGATAAA 
+s rn4.chr1                136012147 54 + 267910886 CAA-------ACCAGAGGCAGCCTAC-GTTTCCAGAAAACCTT-GAGGGGTACAAGAGATAAA 
+s hg18.chr15               88557981 62 + 100338915 CAACCAGCTTATCTGAACCAGCCCTT-GCTTCCAGAGAACTATGGAAAAATCCAAAAGATAAG 
+s panTro2.chr15            87960226 62 + 100063422 CAACCAGCTTATCTGAACCAGCCCTT-GCTTCCAGAGAACTATGGAAAAATCCAAAAGATAAG 
+s rheMac2.chr7             69865079 62 + 169801366 CAACCAGCTTATCTGAACCAGCCCTC-GTTTCCAGGTAACTCTGGAAAAATCCAAAAGATGAG 
+s canFam2.chr3             56030949 40 +  94715083 -------CATATTTGACCCAGCCCTTGGCTTTCAGAAAACC------------ACAA----AG 
+s echTel1.scaffold_304651       917 55 -     10007 CAA-------ATTCCATCCCACCCTT-CGTTCTGGACGGGCTGGGAGGGGTACAAAAGATAAA 
+
+a score=58255.0
+s mm8.chr7              80082767 128 + 145134094 GGGGTGCAGGAGCTGTG----TGTCTTGATCTCCCAGA----GTCTTCGTGAGCCT-----------CACTTTTTGTCTTATCCCT---GTGATACACACAGG-AAGCCACAGTGAATTCAGTGGGTGTCAT---------ACAGAAGGGCCTCC-TGGAG- 
+s rn4.chr1             136012201 139 + 267910886 GGGGTACAGGAGCTGTG----TG-CTTGATGTCGCTGA----GCCTTCGTGAGGCTCCTGTGAGCTGCACTTTTTGTCTCGTCCCT---GTGATAGACACAAG-AAGCCACAGTGAATTCAGTGGGTATCAT---------ATGGAAGGGCCTCCTTGGAC- 
+s hg18.chr15            88558043 143 + 100338915 AAGGGACCGCAG-TGTC----TGTCTTGGTCTCAC--------TCCTCTTGAGACTCCTGTGAT---CTTTATATGTCTCATTCCTCCCGTGACATGTATGAG-AAACTGCAGCTCATTGAGACGATGTCTCTGCTGCCTGACAGAAGGGCCTAC-TTGAG- 
+s panTro2.chr15         87960288 143 + 100063422 AAGGGACCGCAG-TGTC----TGTCTTGGTCTCAC--------TCCTCTTGAGACTCCTGTGAT---CTTTATATGTCTCATTCCTCCCGTGACATGTATGAG-AAACTGCAGCTCATTGAGACGATGTCTCTGCTGCCTGACAGAAGGGCCTAC-TTGAG- 
+s rheMac2.chr7          69865141 147 + 169801366 GAGGGACCACAG-TGTCTGTTTGTCCTGGTCTCAC--------TCCTCATGAGACTCCTGTGAT---CTTTGTATGTCTCATTCCTCCTGTGACATGTATGAG-AATGTACAGCTCAGTGAGATGATGTCTCTGCTGCCTGACAGAAGTGCCTAC-TTGAG- 
+s bosTau2.scaffold2397     93775 133 +    117874 GGACTGCAGTGGCCATT----TGCTCTGGCCTCACTGA----CTCCTTGTGAGCCCGCTGTGAG---TTTTGTTT---TCATTATCCCCAT------TATGAGAAAACTCCAGTTTGGTGAGATGGCATCTACCCTGCCCT--------ACAAAC-ATGgtg 
+s canFam2.chr3          56030989 153 +  94715083 GGGATGTGGAAGACGTT----TGCCCTCGTCTCACAGACTCCCTCCTTGTAAGGCTGCTGGGAG---TCATATTTTGCTCATTATCCCTGCGGTATGTATGAG-AAGCCAAAGGTCAGTGAGCTGGAGTTTGCACTGCCCTCCAGAGGGACCGAC-ATGgtg 
+
+a score=2607.0
+s mm8.chr7              80082895 114 + 145134094 CTTCTCAGAGTGTAGT-----------CCTTGGGCTACC-TCCTCCTAAGTCACTGGG-----------------------AGCTGGTCA-AGAGG------CTCAGACCAGCAGTTTCAGAATCTCTTGGGAGGGCCT--------GGAGTCCGGGTGATGTT 
+s rn4.chr1             136012340 112 + 267910886 CTTCTCAGA--GTAGT-----------CCTTGGGCCACC-TCCTTCTAAGTTACTGAG-----------------------AGCTGGTCA-AGAGG------CTCAGACCAGCAGTTTCAGAATCTCTTGGGAGGGCCT--------GGAGTCAAGGTACTGTT 
+s rheMac2.chr7          69865323 119 + 169801366 CTTCTTGTTGACTAGTGTCACCCCCACCCGAGGGCTTCCTTCCTCATTTGCTGCCAGGTGTAAAGCTGAGCTTC-------agctgggcgcagtgg------ctcacacccataatcctagca--ttttgggag------------------------------ 
+s bosTau2.scaffold2397     93908 136 +    117874 cttctcaaagtgtgct-----------ccatgagcctcc-tacttcagaatcccctgg---------gagattcaaaaccttgcatgttc-tcaggccccatcacgggccagcatcgtcagagtcttcagggtcagctcgtggatctagagtgtaggt------ 
+s canFam2.chr3          56031142 126 +  94715083 cttttcagagggtggt-----------ccctgggcctcc-cactttggaattgcctgg---------gag-ctcatagaattgcccgttg-tcagg--ccatcccagggcagtggcagcag-gcctctagggcaggcct------------ttcaggtgacttt 
+
+a score=8132.0
+s mm8.chr7  80083009 147 + 145134094 TAGGGAGGTTGGCATTGGTGCTGGAACTTTCCTTGGCCCCCCAATTTATCGAAGTACTAAGGGTTGGAAGTCTCTGGAGCTGCAGGAGTT--GAGTTTGAGAAAAGGCTCTTGGTGGTTTAAAGAGA----------------GGTTTCAACTGC--------------------------CTCTGGCCTC 
+s rn4.chr1 136012452 190 + 267910886 TAGGGAGATTGGGATTGGTACTGGAACTTTCCTTGGCCTCCCAGTGTATT-CAGTACTAAGGGTTGGAAGTCTCGGGTGCTACAAGAATTAAGAGTTTGAGAAGAGGCTCTTGGTAGTTTAGAAAGAGAGAAGGACATCTTTGGGTTTCGACTACCTGTGGTGGCAGTGTCAGAATTCAGGCTCTGGCCTC 
+

data/test/data/mm8_mod_a.maf

@@ -0,0 +1,7 @@
+##maf version=1
+a score=10542.0
+s mm8.chr7                 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- 
+s rn4.chr1                136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- 
+s oryCun1.scaffold_199771     14021 43 -     75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- 
+s hg18.chr15               88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s hg181.chr15            87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 

data/test/data/mm8_single.maf

@@ -0,0 +1,13 @@
+##maf version=1
+a score=10542.0
+s mm8.chr7                 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- 
+s rn4.chr1                136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- 
+s oryCun1.scaffold_199771     14021 43 -     75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- 
+s hg18.chr15               88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s panTro2.chr15            87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s rheMac2.chr7             69864714 28 + 169801366 -------GGGC--AAGTATGGA--AGGGAAGCCC--------------CAGAA- 
+s canFam2.chr3             56030570 39 +  94715083 AGGTTTAGGGCAGAGGGATGAAGGAGGAGAATCC--------------CTATG- 
+s dasNov1.scaffold_106893      7435 34 +      9831 GGAACGAGGGC--ATGTGTGG---AGGGGGCTGC--------------CCACA- 
+s loxAfr1.scaffold_8298       30264 38 +     78952 ATGATGAGGGG--AAGCGTGGAGGAGGGGAACCC--------------CTAGGA 
+s echTel1.scaffold_304651       594 37 -     10007 -TGCTATGGCT--TTGTGTCTAGGAGGGGAATCC--------------CCAGGA 
+

data/test/data/mm8_subset_a.maf

@@ -0,0 +1,23 @@
+##maf version=1
+a score=10542.0
+s mm8.chr7                 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- 
+s rn4.chr1                136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- 
+s oryCun1.scaffold_199771     14021 43 -     75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- 
+s hg18.chr15               88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s panTro2.chr15            87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+s rheMac2.chr7             69864714 28 + 169801366 -------GGGC--AAGTATGGA--AGGGAAGCCC--------------CAGAA- 
+s canFam2.chr3             56030570 39 +  94715083 AGGTTTAGGGCAGAGGGATGAAGGAGGAGAATCC--------------CTATG- 
+s dasNov1.scaffold_106893      7435 34 +      9831 GGAACGAGGGC--ATGTGTGG---AGGGGGCTGC--------------CCACA- 
+s loxAfr1.scaffold_8298       30264 38 +     78952 ATGATGAGGGG--AAGCGTGGAGGAGGGGAACCC--------------CTAGGA 
+s echTel1.scaffold_304651       594 37 -     10007 -TGCTATGGCT--TTGTGTCTAGGAGGGGAATCC--------------CCAGGA 
+
+a score=-33148.0
+s mm8.chr7                 80082368 103 + 145134094 TGAGAGGGCATGCT-GTGAAGGGACTGTGCT---CAGTTCAAGGCATAGTCCACTTCC--------CTTCCCTTGGTCATTCTGTTCGGTGTGTTTCCAGCAGATATGGAGAGT-------------------------------------C---- 
+s rn4.chr1                136011819  86 + 267910886 TGAGAGGGCATGTT-ATGAAGGCACTGTGCT--------------------CACTTTC--------CATCCCATGGTCATTCTGTTGAGTGTGTTCCCAGCAGATACGGAAAGT-------------------------------------C---- 
+s oryCun1.scaffold_199771     14064  74 -     75077 TAGGACTGCCTGGTGGGGGGGGCCCTGCACC--------------------TACTTCTGCAAGGCACGTCCCGCG----------TCTGTGCCTTCGCCGCA-----------T-------------------------------------C---- 
+s hg18.chr15               88557607 128 + 100338915 GGGGAAAGCCTGGT-TAAGGGGCCCTTCACCCCCCTCTCCAAGGCACATTCCCCTTTC--------TGTCCCTTTGTCGTTTCATTCACTCTACTCCCAGCATGGCTGGAGGGC---TTGTGG---CTGGCTCGTTTGG---------AGGC---- 
+s panTro2.chr15            87959864 116 + 100063422 GGGGAAAGCCTGGT-TAAGGGGCCCTTCACCCCCCTCTCCAAGGCACATTCCCCTTTC--------TGTCCCTTTGTCGTTTCATTCACTA------------GGCTAGAGGGC---TTGTGG---CTGGCTCGTTTGG---------AGGC---- 
+s rheMac2.chr7             69864742 107 + 169801366 GGAGAAAGCCTGGT-TAAGGGGCCCTTCA-----CTCTCCAAGGCACATTCCACTTTC--------TGTCCCTTTGTCATTCCATTCACTCTACTCCCCGCATGGCTAGAGGGC----------------------TGG---------AGGC---- 
+s canFam2.chr3             56030609 103 +  94715083 AGGGAATGCATGGTGTATGGGGGCCCCCGTC--------------------CACTTC---------TGTCCCGTTGCTATTTCCTTGACCATACTTCCAGTATGACTGGGGGAG---GTGCGG---TGGAGCAGGTTC------------------ 
+s loxAfr1.scaffold_8298       30302 144 +     78952 --TGGATGCCTGGT-TTAAGGATCC-GCTCACCCACTTCTGAGTCACGTTACACTTTC--------TGCCCCTTTGCCATTTCATTTATGGTACTCCCAACACCGGGGGAGGGTGCGCTTTGGTTCTTGAGCAGTTTGTGTATATAGGGGGCTGAG 
+s echTel1.scaffold_304651       631  67 -     10007 --TGGAGGGCTACT-TTAAGAAACC----CTCCCGTTTCTCAG-------------CC--------TGCTTC---------------------------------------------CTTTGGGTTTGAGGTACTTTGT----------------G 

data/test/data/t1-bad1.maf

@@ -0,0 +1,15 @@
+##maf version=1 scoring=humor.v4
+# humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
+# /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
+
+a score=0.128
+s human_hoxa 100  8 + 100257 ACA-TTACT
+s horse_hoxa 120  9 -  98892 ACAATTGCT
+s fugu_hoxa   88  7  + 90788 ACA--TGCT
+
+
+a score=0.071
+s human_unc 9077 8 + 10998 ACAGTATT
+# Comment
+s horse_unc 4555 6 -  5099 ACA--ATT
+s fugu_unc  4000 4 +  4038 AC----TT

data/test/data/t1.fasta

@@ -0,0 +1,12 @@
+>human_hoxa:100-108
+ACA-TTACT
+>horse_hoxa:120-129
+ACAATTGCT
+>fugu_hoxa:88-95
+ACA--TGCT
+>human_unc:9077-9085
+ACAGTATT
+>horse_unc:4555-4561
+ACA--ATT
+>fugu_unc:4000-4004
+AC----TT

data/test/data/t1.maf

@@ -0,0 +1,15 @@
+##maf version=1 scoring=humor.v4
+# humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
+# /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
+
+a score=0.128
+s human_hoxa 100  8 + 100257 ACA-TTACT
+s horse_hoxa 120  9 -  98892 ACAATTGCT
+s fugu_hoxa   88  7  + 90788 ACA--TGCT
+
+
+a score=0.071
+s human_unc 9077 8 + 10998 ACAGTATT
+# Comment
+s horse_unc 4555 6 -  5099 ACA--ATT
+s fugu_unc  4000 4 +  4038 AC----TT

data/test/data/t1a.maf

@@ -0,0 +1,17 @@
+##maf version=1 scoring=humor.v4
+# humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
+# /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
+
+a score=0.128
+s human_hoxa 100  8 + 100257 ACA-TTACT
+s horse_hoxa 120  9 -  98892 ACAATTGCT
+s fugu_hoxa   88  7  + 90788 ACA--TGCT
+
+
+a score=0.071
+s human_unc 9077 8 + 10998 ACAGTATT
+# Comment
+s horse_unc 4555 6 -  5099 ACA--ATT
+s fugu_unc  4000 4 +  4038 AC----TT
+
+##eof maf

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-maf'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-maf.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioMaf < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

data/travis-ci/install_kc

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+## NOTE: I am aware that this shell script is horrible.
+
+cd /tmp
+wget http://fallabs.com/kyotocabinet/pkg/kyotocabinet-1.2.76.tar.gz
+tar xzf kyotocabinet-1.2.76.tar.gz
+cd kyotocabinet-1.2.76
+./configure && make && make install
+grep -q local /etc/ld.so.conf
+if [ $? -ne 0 ]; then
+  echo "/usr/local/lib" >> /etc/ld.so.conf && ldconfig
+fi

data/travis-ci/install_kc_java

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+## NOTE: I am aware that this shell script is horrible.
+
+export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-i386
+
+cd /tmp
+wget http://fallabs.com/kyotocabinet/javapkg/kyotocabinet-java-1.24.tar.gz
+tar xzf kyotocabinet-java-1.24.tar.gz
+cd kyotocabinet-java-1.24
+./configure && make && make install
+cp -Rf /usr/local/lib/libjkyotocabinet.so* /usr/lib/jni/
+ldconfig

data/travis-ci/report_errors

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+cat $HOME/builds/csw/bioruby-maf/hs*.log 2>/dev/null
+exit 0

metadata

@@ -0,0 +1,182 @@
+--- !ruby/object:Gem::Specification
+name: bio-maf
+version: !ruby/object:Gem::Version
+  prerelease:
+  version: 0.1.0
+platform: java
+authors:
+- Clayton Wheeler
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2012-06-29 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-bigbio
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+    none: false
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: bio-genomic-interval
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+    none: false
+  prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: kyotocabinet-java
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+    none: false
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+    none: false
+  prerelease: false
+  type: :runtime
+description: Multiple Alignment Format parser for BioRuby.
+email: cswh@umich.edu
+executables:
+- maf_count
+- maf_dump_blocks
+- maf_extract_ranges_count
+- maf_index
+- maf_parse_bench
+- maf_to_fasta
+- maf_write
+- random_ranges
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- .document
+- .simplecov
+- .travis.yml
+- .yardopts
+- DEVELOPMENT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- benchmarks/dispatch_bench
+- benchmarks/iter_bench
+- benchmarks/read_bench
+- benchmarks/sort_bench
+- benchmarks/split_bench
+- bin/maf_count
+- bin/maf_dump_blocks
+- bin/maf_extract_ranges_count
+- bin/maf_index
+- bin/maf_parse_bench
+- bin/maf_to_fasta
+- bin/maf_write
+- bin/random_ranges
+- features/maf-indexing.feature
+- features/maf-output.feature
+- features/maf-parsing.feature
+- features/maf-querying.feature
+- features/maf-to-fasta.feature
+- features/step_definitions/convert_steps.rb
+- features/step_definitions/index_steps.rb
+- features/step_definitions/output_steps.rb
+- features/step_definitions/parse_steps.rb
+- features/step_definitions/query_steps.rb
+- features/step_definitions/ucsc_bin_steps.rb
+- features/support/env.rb
+- features/ucsc-bins.feature
+- lib/bio-maf.rb
+- lib/bio-maf/maf.rb
+- lib/bio/maf.rb
+- lib/bio/maf/index.rb
+- lib/bio/maf/parser.rb
+- lib/bio/maf/struct.rb
+- lib/bio/maf/writer.rb
+- lib/bio/ucsc.rb
+- lib/bio/ucsc/genomic-interval-bin.rb
+- lib/bio/ucsc/ucsc_bin.rb
+- man/.gitignore
+- man/maf_index.1
+- man/maf_index.1.markdown
+- man/maf_index.1.ronn
+- man/maf_to_fasta.1
+- man/maf_to_fasta.1.ronn
+- spec/bio/maf/index_spec.rb
+- spec/bio/maf/parser_spec.rb
+- spec/bio/maf/struct_spec.rb
+- spec/spec_helper.rb
+- test/data/big-block.maf
+- test/data/chr22_ieq.maf
+- test/data/chrY-1block.maf
+- test/data/empty
+- test/data/empty.db
+- test/data/mm8_chr7_tiny.kct
+- test/data/mm8_chr7_tiny.maf
+- test/data/mm8_mod_a.maf
+- test/data/mm8_single.maf
+- test/data/mm8_subset_a.maf
+- test/data/t1-bad1.maf
+- test/data/t1.fasta
+- test/data/t1.maf
+- test/data/t1a.maf
+- test/helper.rb
+- test/test_bio-maf.rb
+- travis-ci/install_kc
+- travis-ci/install_kc_java
+- travis-ci/report_errors
+homepage: http://github.com/csw/bioruby-maf
+licenses:
+- MIT
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      segments:
+      - 0
+      hash: 2
+      version: '0'
+  none: false
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+  none: false
+requirements: []
+rubyforge_project:
+rubygems_version: 1.8.24
+signing_key:
+specification_version: 3
+summary: MAF parser for BioRuby
+test_files: []
+...