| Previous changeset 1:b79f6002b176 (2020-11-10) Next changeset 3:7adddc6015c1 (2023-04-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 9f522562ca2048b8bafa3404abf3f930f72f7f05 |
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modified:
interval2maf.py interval2maf.xml macros.xml test-data/interval2maf-out1.maf test-data/interval2maf-out2.maf test-data/interval2maf-out3.maf |
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added:
test-data/interval2maf-in.bed |
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| diff -r b79f6002b176 -r 1080e07a2233 interval2maf.py --- a/interval2maf.py Tue Nov 10 18:48:33 2020 +0000 +++ b/interval2maf.py Wed Nov 09 12:34:55 2022 +0000 |
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| @@ -31,7 +31,7 @@ import bx.align.maf import bx.intervals.io from bx.cookbook import doc_optparse -from galaxy.tools.util import maf_utilities +from galaxy.datatypes.util import maf_utilities def __main__(): |
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| diff -r b79f6002b176 -r 1080e07a2233 interval2maf.xml --- a/interval2maf.xml Tue Nov 10 18:48:33 2020 +0000 +++ b/interval2maf.xml Wed Nov 09 12:34:55 2022 +0000 |
| [ |
| @@ -1,11 +1,12 @@ -<tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1+galaxy0"> +<tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1+galaxy1" profile="21.05"> <description>given a set of genomic intervals</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <expand macro="requirements" /> - </requirements> + <xrefs> + <xref type="bio.tools">bx-python</xref> + </xrefs> + <expand macro="requirements" /> <command> <![CDATA[ #if $maf_source_type.maf_source == "cached" @@ -79,7 +80,7 @@ </outputs> <tests> <test> - <param name="input1" dbkey="hg38" value="interval2maf-in1.bed" /> + <param name="input1" dbkey="hg38" value="interval2maf-in.bed" /> <param name="maf_source" value="user" /> <param name="mafFile" dbkey="hg38" value="interval2maf-in1.maf" /> <param name="species" value="hg38,mm10,eulFla1" /> @@ -87,7 +88,7 @@ <output name="out_file1" file="interval2maf-out1.maf" /> </test> <test> - <param name="input1" dbkey="hg38" value="interval2maf-in2.bed"/> + <param name="input1" dbkey="hg38" value="interval2maf-in.bed"/> <param name="maf_source" value="cached"/> <param name="mafType" value="TEST"/> <param name="species" value="hg38,mm10,eulFla1" /> @@ -95,7 +96,7 @@ <output name="out_file1" file="interval2maf-out2.maf" /> </test> <test> - <param name="input1" dbkey="hg38" value="interval2maf-in3.bed"/> + <param name="input1" dbkey="hg38" value="interval2maf-in.bed"/> <param name="maf_source" value="cached"/> <param name="mafType" value="TEST"/> <param name="species" value="hg38,mm10,eulFla1" /> |
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| diff -r b79f6002b176 -r 1080e07a2233 macros.xml --- a/macros.xml Tue Nov 10 18:48:33 2020 +0000 +++ b/macros.xml Wed Nov 09 12:34:55 2022 +0000 |
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| @@ -1,7 +1,10 @@ <macros> <xml name="requirements"> - <requirement type="package" version="0.8.9">bx-python</requirement> - <yield /> + <requirements> + <requirement type="package" version="0.8.9">bx-python</requirement> + <requirement type="package" version="22.1.1">galaxy-data</requirement> + <yield /> + </requirements> </xml> <xml name="citations"> <citations> |
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| diff -r b79f6002b176 -r 1080e07a2233 test-data/interval2maf-in.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf-in.bed Wed Nov 09 12:34:55 2022 +0000 |
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| @@ -0,0 +1,43 @@ +chr22 17108306 17109820 NM_001289905.1_cds_11_0_chr22_17108307_f 0 + +chr22 17119390 17121127 NM_031890.4_cds_0_0_chr22_17119391_r 0 - +chr22 17817310 17819129 NM_015241.3_cds_6_0_chr22_17817311_r 0 - +chr22 18846931 18848320 XM_017029167.2_cds_0_0_chr22_18846932_f 0 + +chr22 18918315 18918491 NM_001195226.2_cds_3_0_chr22_18918316_r 0 - +chr22 21030830 21031812 NM_004173.3_cds_3_0_chr22_21030831_r 0 - +chr22 21634684 21635266 NM_152612.3_cds_3_0_chr22_21634685_f 0 + +chr22 21634684 21635644 NM_001331066.1_cds_3_0_chr22_21634685_f 0 + +chr22 22514001 22515630 NM_080740.5_cds_0_0_chr22_22514002_r 0 - +chr22 22646311 22646521 XM_005261815.3_cds_1_0_chr22_22646312_f 0 + +chr22 23394179 23394792 XM_017029168.1_cds_3_0_chr22_23394180_f 0 + +chr22 23394222 23394792 XM_017029169.1_cds_2_0_chr22_23394223_f 0 + +chr22 23573265 23573585 NM_001369906.1_cds_0_0_chr22_23573266_r 0 - +chr22 26026444 26027678 NM_001318245.2_cds_42_0_chr22_26026445_f 0 + +chr22 27796762 27800543 NM_002430.3_cds_1_0_chr22_27796763_r 0 - +chr22 27982220 27983851 NM_001145418.1_cds_0_0_chr22_27982221_r 0 - +chr22 29441541 29442122 NM_021026.2_cds_1_0_chr22_29441542_f 0 + +chr22 29488848 29490703 NM_021076.4_cds_3_0_chr22_29488849_f 0 + +chr22 31712082 31717291 NM_173566.3_cds_5_0_chr22_31712083_r 0 - +chr22 32190771 32191352 NM_001098527.3_cds_0_0_chr22_32190772_r 0 - +chr22 32358071 32358444 NM_001098535.1_cds_0_0_chr22_32358072_f 0 + +chr22 32358153 32358611 XM_017028534.1_cds_1_0_chr22_32358154_f 0 + +chr22 32358158 32358444 NM_006604.2_cds_1_0_chr22_32358159_f 0 + +chr22 35726210 35727194 NM_030642.1_cds_2_0_chr22_35726211_f 0 + +chr22 35726271 35727194 XM_006724321.4_cds_3_0_chr22_35726272_f 0 + +chr22 35726284 35727194 XM_017028945.2_cds_2_0_chr22_35726285_f 0 + +chr22 36141199 36142058 NM_145640.2_cds_0_0_chr22_36141200_r 0 - +chr22 36191074 36191842 XM_024452274.1_cds_0_0_chr22_36191075_r 0 - +chr22 36265150 36266033 NM_001136540.1_cds_5_0_chr22_36265151_f 0 + +chr22 36937376 36938502 NM_000395.3_cds_13_0_chr22_36937377_f 0 + +chr22 37206546 37207803 NM_001051.5_cds_0_0_chr22_37206547_r 0 - +chr22 37655271 37655684 NM_018957.5_cds_17_0_chr22_37655272_f 0 + +chr22 37723184 37726503 NM_001039141.3_cds_6_0_chr22_37723185_f 0 + +chr22 38080839 38081679 NM_013356.2_cds_1_0_chr22_38080840_r 0 - +chr22 42141151 42141396 NM_001348386.3_cds_2_0_chr22_42141152_r 0 - +chr22 42209650 42215305 NM_005650.3_cds_4_0_chr22_42209651_r 0 - +chr22 42692889 42693951 NM_001318038.2_cds_0_0_chr22_42692890_r 0 - +chr22 46256560 46263322 NM_006071.2_cds_0_0_chr22_46256561_r 0 - +chr22 46363995 46364251 NM_014246.3_cds_1_0_chr22_46363996_r 0 - +chr22 46533626 46537170 NM_014246.3_cds_34_0_chr22_46533627_r 0 - +chr22 49883662 49887178 NM_014838.3_cds_1_0_chr22_49883663_f 0 + +chr22 50433133 50434498 XM_017029177.1_cds_0_0_chr22_50433134_r 0 - +chr22 50546243 50549951 NM_138433.5_cds_0_0_chr22_50546244_f 0 + |
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| diff -r b79f6002b176 -r 1080e07a2233 test-data/interval2maf-out1.maf --- a/test-data/interval2maf-out1.maf Tue Nov 10 18:48:33 2020 +0000 +++ b/test-data/interval2maf-out1.maf Wed Nov 09 12:34:55 2022 +0000 |
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| b'@@ -1,4 +1,3724 @@\n ##maf version=1\n+a score=13157571.0\n+s hg38.chr22 17108306 359 + 50818468 ATGGCCTGCCTGCGGCTGACCTGATCCCCCCACCGCTGAAGCCCAGGAAGGTCTGGATCATCTACTCAGCCGACCACCCCCTCTACGTGGACGTGGTCCTGAAATTCGCCCAGTTCCTGCTCACCGCCTGCGGCACGGAAGTGGCCCTGGACCTGCTGGAAGAGCAGGCCATCTCGGAGGCAGGAGTCATGACCTGGGTGGGCCGTCAGAAGCAGGAGATGGTGGAGAGCAACTCTAAGATCATCGTCCTGTGCTCCCGCGGCACGCGCGCCAAGTGGCAGGCGCTCCTGGGCCGGGGGGCGCCTG---TGCGGCTGCGCTGCGACCACGGAAAGCCCGTGGGGGACCTGTTCACTGCAGCC \n+s eulFla1.LGHW01008773v1 31653 362 + 91162 ATGTCCTGCCTGCAGCTGACCTGAGCCCCCCGCCCCTGAAGCCAAGGAAGGTCTGGATCGTCTACTCGGCCGACCACCCTCTCTATGTGGATGTCGTCCTAAAATTCGCCCAGTTCCTGCTCACCGTCTGTGGCACTGAAGTAGCCCTCGACCTGCTGGAGGAACAGGTCATCTCGGAGGTGGGGGTCATGACCTGGGTAGGCCGCCAGAAGCAGGAAATGGTGGAGAGCAGCTCCAAAATCATCATCCTGTGCTCCCGAGGTACCCAGGCCAAGTGGCAGGCTATCCTTGGCTGGGAGGAGCCCGCCGTCCAGCTGCGGTGTGACCGCAGGAAGCCCGCTGGGGACCTGTTCACGGCGGCC \n+i eulFla1.LGHW01008773v1 I 155 C 0 \n+s mm10.chr6 120480982 362 + 149736546 GCATCTTGCCCGTAGCAGACCTGACTCCCCCACCCCTGAGGCCCAGGAAGGTCTGGATCGTCTACTCGGCCGACCACCCCCTCTATGTGGAGGTGGTCCTAAAGTTCGCCCAGTTCCTGATCACTGCCTGTGGCACTGAAGTAGCCCTTGACCTCCTGGAAGAGCAGGTTATCTCTGAGGTGGGGGTCATGACCTGGGTGAGCCGACAGAAGCAGGAGATGGTGGAGAGCAACTCCAAAATCATCATCCTGTGTTCCCGAGGCACCCAAGCAAAGTGGAAAGCTATCTTGGGTTGGGCTGAGCCTGCTGTCCAGCTACGGTGTGACCACTGGAAGCCTGCTGGGGACCTTTTCACTGCAGCC \n+i mm10.chr6 C 0 C 0 \n+\n+a score=13157571.0\n+s hg38.chr22 17108306 359 + 50818468 ATGGCCTGCCTGCGGCTGACCTGATCCCCCCACCGCTGAAGCCCAGGAAGGTCTGGATCATCTACTCAGCCGACCACCCCCTCTACGTGGACGTGGTCCTGAAATTCGCCCAGTTCCTGCTCACCGCCTGCGGCACGGAAGTGGCCCTGGACCTGCTGGAAGAGCAGGCCATCTCGGAGGCAGGAGTCATGACCTGGGTGGGCCGTCAGAAGCAGGAGATGGTGGAGAGCAACTCTAAGATCATCGTCCTGTGCTCCCGCGGCACGCGCGCCAAGTGGCAGGCGCTCCTGGGCCGGGGGGCGCCTG---TGCGGCTGCGCTGCGACCACGGAAAGCCCGTGGGGGACCTGTTCACTGCAGCC \n+s eulFla1.LGHW01008773v1 31653 362 + 91162 ATGTCCTGCCTGCAGCTGACCTGAGCCCCCCGCCCCTGAAGCCAAGGAAGGTCTGGATCGTCTACTCGGCCGACCACCCTCTCTATGTGGATGTCGTCCTAAAATTCGCCCAGTTCCTGCTCACCGTCTGTGGCACTGAAGTAGCCCTCGACCTGCTGGAGGAACAGGTCATCTCGGAGGTGGGGGTCATGACCTGGGTAGGCCGCCAGAAGCAGGAAATGGTGGAGAGCAGCTCCAAAATCATCATCCTGTGCTCCCGAGGTACCCAGGCCAAGTGGCAGGCTATCCTTGGCTGGGAGGAGCCCGCCGTCCAGCTGCGGTGTGACCGCAGGAAGCCCGCTGGGGACCTGTTCACGGCGGCC \n+i eulFla1.LGHW01008773v1 I 155 C 0 \n+s mm10.chr6 120480982 362 + 149736546 GCATCTTGCCCGTAGCAGACCTGACTCCCCCACCCCTGAGGCCCAGGAAGGTCTGGATCGTCTACTCGGCCGACCACCCCCTCTATGTGGAGGTGGTCCTAAAGTTCGCCCAGTTCCTGATCACTGCCTGTGGCACTGAAGTAGCCCTTGACCTCCTGGAAGAGCAGGTTATCTCTGAGGTGGGGGTCATGACCTGGGTGAGCCGACAGAAGCAGGAGATGGTGGAGAGCAACTCCAAAATCATCATCCTGTGTTCCCGAGGCACCCAAGCAAAGTGGAAAGCTATCTTGGGTTGGGCTGAGCCTGCTGTCCAGCTACGGTGTGACCACTGGAAGCCTGCTGGGGACCTTTTCACTGCAGCC \n+i mm10.chr6 C 0 C 0 '..b' \n+s mm10.chr15 89387721 762 + 104043685 GACAGGGAGCGCATCCTGAACCTGCGGACGTGCCAGGGCCAGACAGTGCTGGGGGTCCTCGTGCTACCCAGCCTTTATCAGGTGAGCCGCTCGGGGCTCACGAGGGGCCCTCCCAGCGAGGAAGCTCCTGCAGCCAGGTCTGAGCACTTGCATCTTCACACATACCTCCATGTATTCAACCCACAAGAGAATGTGTGGTGGCCCCTGACTCAAGTACCAGAGGAGGTCCCCCTTCGGGGCTGTGGCCTCTGCACTATGCATAACTATCTGTTTCTGGCAGGCGGCATCAGGGGTTCTGGTGCCAAGGCTGTCTGCTCCAACAAGGTGTTCTGCTACAACCCTCTGACCAATATTTGGAGCCAGATTCGGCCCATGCAGCAAGCCCGGGCCCAGCTCAAGCTGGTGGCCCTGGATGGAATGCTTTATGCCATTGGTGGCGAGTGCCTATACAGCATGGAGCGCTATGACCCACGCACAGATACCTGGACCTTGAGAGCATCCCTCCCTGAGGGCACCTTTCCCGTGGCCCACGAGGCTGTGGTCTGCCGAGGAGAGATCTACGTCACAGGGGGTCATCTCTTTTACCGCCTGCTCAGATACAGCCCCATGAAAGACTCATGGGATGAGTGTCCCTACAGCGCCAGCCACCGACGCTCCAGTGATATGGTGGCGCTAGGGGGCTTCCTATACCGCTTTGACTTGTTGCGGGGTGTGGGTGCTGCGGTGATGCGCTACAACACAGTGACCGGCTCCTGGAGCCGG \n+i mm10.chr15 C 0 C 0 \n+\n+a score=2630763.0\n+s hg38.chr22 50549726 80 + 50818468 GctgcctccctgcccctgcccgcccccgccccactgcactgcaccaccctgGGCAACACCATTTACTGCCTCAACCCCCA \n+s eulFla1.LGHW01001310v1 112657 80 - 301835 GCCGCCTCCCTGCCCCTGCCGGCCCCCACCCCGCTCCGCTGCACGGTGCTGGGAAACACCATTTACTGCCTCAACCCCCA \n+i eulFla1.LGHW01001310v1 C 0 C 0 \n+s mm10.chr15 89388483 80 + 104043685 GCAGCCTCCCTGCCACTGTCTGACCCCGCCCCACTCCACTGCACGGTATTGGGCAACACCATTTACTGTCTCAACCACCA \n+i mm10.chr15 C 0 C 0 \n+\n+a score=5390823.0\n+s hg38.chr22 50549806 145 + 50818468 GGTCACTGCCACCTTCACGGTCTCTGGGGGGACTGCCCAGTTCCAGGCCAAGGAGCTGCAGCCCTTCCCCTTGGGGAGCACCGGGGTCCTCAGTCCATTCATCCTGACTCTGCCCCCTGAGGACCGGCTGCAGACCTCACTCTGA \n+s eulFla1.LGHW01001310v1 112737 145 - 301835 GGTCACCGCCACCTTTACAGTCTCTGAGGGGACTGCTCAGTTCCAGGCCACGGAGCTGCAGCCCTTCCCTCTGGGAAGCAGGGGCGTCCTCTGTCCCTTCATCCTGACTCTGCCCTGCGAGGGCCGGCGGCAGACCTCGCTGTGA \n+i eulFla1.LGHW01001310v1 C 0 C 0 \n+s mm10.chr15 89388563 145 + 104043685 GGTCACGGCTACCTTCACAGTTTCGGAGGGGACCGCCCTGTTTCAGGCCAAGGAGCTGCAGCCCTTCCCACTGGGAAGTAAGGGGGTCCTCTATCCGTTCACTCTGACTCTGCCCCCTAAGACCTGGTTGCAGACCACAATCTGA \n+i mm10.chr15 C 0 C 0 \n+\n' |
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| diff -r b79f6002b176 -r 1080e07a2233 test-data/interval2maf-out2.maf --- a/test-data/interval2maf-out2.maf Tue Nov 10 18:48:33 2020 +0000 +++ b/test-data/interval2maf-out2.maf Wed Nov 09 12:34:55 2022 +0000 |
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| b'@@ -217,14 +217,6 @@\n s hg38.chr22 31899977 176 - 50818468 GATGCCTATGACAATGTGACCCTGGACGTGGAGCTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTGCGGGGCGCATACCTGGCCCAGGAGCGAGCCCGTGCGGCAGAGATCGGCTATGAGGACCCCATCAACCCCACGTACGAGGCCACCAACGCCATGTACCACAG \n s mm10.chr16 80131351 176 - 98207768 GATGCCTATGACAATGTGACCTTGGATATGGAACTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTACGTGGTGCATACATGGCCCAAGAGCGTGTCAGGGCAGCAGAGATCGGTTATGAGGACCCCATCAACCCTACATATGAAGCCACCAATGCTATGTACCACAG \n \n-a score=3722810.0\n-s hg38.chr22 31899977 176 - 50818468 GATGCCTATGACAATGTGACCCTGGACGTGGAGCTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTGCGGGGCGCATACCTGGCCCAGGAGCGAGCCCGTGCGGCAGAGATCGGCTATGAGGACCCCATCAACCCCACGTACGAGGCCACCAACGCCATGTACCACAG \n-s mm10.chr16 80131351 176 - 98207768 GATGCCTATGACAATGTGACCTTGGATATGGAACTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTACGTGGTGCATACATGGCCCAAGAGCGTGTCAGGGCAGCAGAGATCGGTTATGAGGACCCCATCAACCCTACATATGAAGCCACCAATGCTATGTACCACAG \n-\n-a score=3722810.0\n-s hg38.chr22 31899977 176 - 50818468 GATGCCTATGACAATGTGACCCTGGACGTGGAGCTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTGCGGGGCGCATACCTGGCCCAGGAGCGAGCCCGTGCGGCAGAGATCGGCTATGAGGACCCCATCAACCCCACGTACGAGGCCACCAACGCCATGTACCACAG \n-s mm10.chr16 80131351 176 - 98207768 GATGCCTATGACAATGTGACCTTGGATATGGAACTGGCTCGCCGTGAGGGCTGGTGTTTTGGGGCCAAGCTGGTACGTGGTGCATACATGGCCCAAGAGCGTGTCAGGGCAGCAGAGATCGGTTATGAGGACCCCATCAACCCTACATATGAAGCCACCAATGCTATGTACCACAG \n-\n a score=8099880.0\n s hg38.chr22 29787438 200 - 50818468 CCAGAACCCACGGCGGTCTGTGCCTCTGGCCATCGCCATCTCGCTTGCCATTGCAGCTGGTGCCTACATCCTTGTCTCCACCGTGCTAACCCTCATGGTGCCCTGGCACAGCCTGGACCCCGACTCAGCGCTTGCAGATGCCTTCTACCAGCGGGGCTACAGGTGGGCTGGCTTCATCGTGGCAGCTGGCTCCATCTGCG \n s eulFla1.LGHW01008912v1 36347 200 + 74594 TCAGAACCCAAGGCGGGCCGTGCCCGTGGCCATTGCCATCGCGCTTAGCCTGGCTGCAAGTGCCTACATCCTTGTCTCCACTGTGCTGACCCTCATGGTGCCCTGGTACAGCCTGGAGCCTGACTCGGCGCTCGCCGATGCCTTCTACCGGCGGGGCTACAGCTGGGCTGGCTTCATCGTGGCCACCGGCTCCATCTGCG \n@@ -350,6 +342,100 @@\n i mm10.chr16 C 0 C 0 \n \n a score=6521322.0\n+s hg38.chr22 21635217 49 + 50818468 CTCCCCCTCCATGTCTAGTGC---CCAGGTGGCCACCAGATTCAAACTCAAG \n+s eulFla1.LGHW01001899v1 119076 49 + 262521 CTCCCCCTCCACGTCTAATGC---CCAGATCGCCACCAAATTCAGGCTCAAG \n+s mm10.chr16 81066123 46 - 98207768 ------CTCCCCACCTAATGCAGTCCAGATGGCTACCAGATTCAGGCTCAAG \n+\n+a score=31953654.0\n+s hg38.chr22 21634684 360 + 50818468 AAAGGCCTCAGTCAGTCCTGCTCCCAGAGGGACTCCCTGCTGTGGGATTCGCTGGGTAGCCAGACCAGCTTTCAGTGGACACAGGAGCAGCCCTTGTCCTGGTTCTCAGGGCTGCTGGGCTCAAGCTCTGGCGTGCCTGAAGCATCAGAGCCGAGGCCTGGAGAACAGGAGCCAATCTTCCGCAAGCGAGAGTTCAATAAGGAGATCAAGTCATTACTGAGCCAGCTGGAGTCCCTCGACCTGCCTGGCTACTGTCCGCTCCGTGAGCCCCATCGCACGCTGAACTTCCTGGCTGACCACCGCCTCTTCCCTGCCCTGCAAAGCGTGGTCAGCCAGGCTGTGGATAAGCTCCGTGGCGCC \n+s eulFla1.LGHW01001899v1 118501 357 + 262521 AAAGGCCTGAGTCAGTCCTGCTCCC---AGGACTCCCTGCTGTGGGACTCGCTGGGCAGCCAGACCAGCAGCCAGTGGACCCAGGAGCAGCCCCTGTCGTGGTTCTCAGGGCTGCTGGACTCAAGTTCAGGCACACCGGAAGCGTCAGTGCTGGGGCCTAGAGAGCGCGAGCTGATCTTCCTCAAGCCGGAGTTCAACAAGGACATCAAGTCGCTACTGAACCAGCCGACATCCTTCAACCCGCCTGGCTACTGTTCACTCCGGCAGCCCCATCGCACCCTGGACTTCCTGGCCAAGCACCACCTCTTCCCCGCCCTGCAGGGTGTGGTCAGCCAGGCTGTGGACAAGCTCAGTGGCGCC \n+i eulFla1.LGHW01001899v1 C 0 C 0 \n+s mm10.chr16 81065566 360 - 98207768 AAAATCCTGAATCAATCCTGCTCCCAGAGGGATTCCCTGCTGTGGGACTCACTGGGCAGCCAAACCAGCAGTCAGTGGACCCGGGAGCAGCCCCTGTCTTGGTTCTCTGGGCTATTGGGCTCCAGTCCAGCCACCCCTGAAACTTCAGAGTTGGGACTTGGAGAACAGGAGATGATTTTCCTCAAACAAAAGTTAAACAAGGAGATGAAGTCACTGCTGAACCAGCCAAGACCCTTCAACCTGCCTACCTATTGTCCACTCAGGGAACCCCATCATACCCTGGACTTCCTAGCTAAGCATCGTCTCTTTCCTGCCCTGCAGCGTGTGGTCAGCCAGGCTGTAGACAAGCTCA'..b'GCTGGGCCTGGTGCTGCTCGTGGAGGCCGTGGCCGTGCTCATCGGACCGCCCTCCGCCG \n+s mm10.chr15 24791713 98 - 104043685 GCTCATGGCAACCGTGGGTGCACCCCGCTTCCCTAGTGCATTGGGCCTAGTGCTGCTCGTGGAGGCCGTGGCTGTGCTCATAGGACCGCCCTCTGCCG \n+\n+a score=1184954.0\n+s hg38.chr22 12737495 36 - 50818468 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s eulFla1.LGHW01006107v1 634009 36 + 657376 CTCCTACGGCATGGTGGGCGCGCTGCAGTTCGAGGT \n+s mm10.chr15 24791677 36 - 104043685 GTCCTACGGCATGGTGGGCGCACTGCAGTTTGAGGT \n+\n+a score=4109169.0\n+s hg38.chr22 12737373 122 - 50818468 CTGCGGCCGCACGTCCCGTATCTGTTCAGCCTGGCCCTGCTGGCCAATGGGCTCACAGACCTGAGCAGCGCACGCGCGCGCTCCTACGGCGCCCTCGTCGCCTTCTGCGTCGCCTTCGGCCT \n+s eulFla1.LGHW01006107v1 633887 122 + 657376 CTGCGACCGCGGGTGCCCTATCTCTTCAGCCTGGCCCTGCTGGCCAACGGGCTCACGGACCTGAGCAGTGCGCGCGCGCGCTCCTACGGAGCCCTCGTCGCCTTCTGCATCGCCTTCGGCCT \n+s mm10.chr15 24791555 122 - 104043685 CTGAGACCCCACGTCCCCTACCTCTTCAGCCTGGCCCTGTTGGCCAATGGGCTCACGGACCTGATTAGCGCGCGTGCGCGCTCCTACGGGACCCTCGTTGCTTTCTGCATTGCCTTCGGCCT \n+\n+a score=8150994.0\n+s hg38.chr22 12737111 262 - 50818468 GCAGCTGCGCGAGGCATCCCCCAGGGTCCGGCCC--CGCCGGCGCCTGCTGGACTTGGCAGTGTGCACCGACCGCGCCTTCGCCGTGTACGCCGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTCCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCCGACACCGACGCCGCCTTCCTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCGCGCCCGGCGTGCGGCGCCCTGGCGGGCCTGGCGCGT \n+s eulFla1.LGHW01006107v1 633625 262 + 657376 gcgcgtgcgcgaggcgCCCCCTGGCGGCCGCACC--CGCCGGCGGCTGCTGGACGTGGCTGTGTGTGCCGACCGCGCCTTCGTGGTGTACGCGGTCACCAAGTTCCTGATGGCGCTCGGGCTCTTCGTGCCCGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGACGCCGCCTTCCTGTTATCCATCGTGGGCTTCGTAGACATCGTGGCGCGGCCAGCGTGCGGCGCCCTGGCGGGCCTGGCGCGC \n+s mm10.chr15 24791316 239 - 104043685 -------------------------GCCCGGCTCGCCGCCGGCGGCTGCTGGACGTGGCAGTGTGCACCGACCGTGCTTTCGTGGTGTACGTGGTCACCAAGTTCCTGATGGCACTCGGGCTCTTTGTGCCGGCCATCCTGCTGGTGAACTACGCCAAGGACGCGGGCGTGCCTGACGCCGAGGCCGCCTTCTTGCTGTCCATCGTGGGCTTCGTGGACATCGTGGCACGACCGGCGTGCGGTGCTTTGGCGGGTCTGGGGCGC \n+\n+a score=373719.0\n+s hg38.chr22 12737090 21 - 50818468 GGAGGCTGACGGTGCGGGGCT \n+s eulFla1.LGHW01006107v1 633604 21 + 657376 ggaggcggagggcgaggggct \n+s mm10.chr15 24791310 6 - 104043685 --------ACGGTG------- \n+\n+a score=149374.0\n+s hg38.chr22 12737084 6 - 50818468 CGAGGC \n+s eulFla1.LGHW01006107v1 633592 6 + 657376 Agaggc \n+\n+a score=172154.0\n+s hg38.chr22 12737070 14 - 50818468 GGGGACGCTCCGGG \n+s eulFla1.LGHW01006107v1 633578 14 + 657376 ggggACTCTGCGGG \n+s mm10.chr15 24791305 5 - 104043685 ------GCCCC--- \n+\n+a score=5393236.0\n+s hg38.chr22 12736861 209 - 50818468 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGCGCTGTCGCCGCTCGGCCAGCAGCTGCTGGAGCGCTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCCTGCGGGGCTGTCATGAGGCCGCCGCCCGGGCCGGGCCCGCGACCG------CGCAGGGACAGCGCCGGCGACCGCGCC \n+s eulFla1.LGHW01006107v1 633363 215 + 657376 TGGCCAACGGGCTGGCGGCGGCGGGCAGCCCCGTGTTCCTGTCCGTGCTGTCGCCTCTCGGCCAGCAGCTGCTCGAGCACTTCGGCTGGCGCGGCGGCTTCCTGCTGCTCGGCGGGCTCCTGCTGCACTGCTGCGCGTGCGGAGCCGTCATGCggccgccgccggggccggggccggggccaccgccgcgcggggccggcgcccgggacctggcg \n+s mm10.chr15 24791115 190 - 104043685 TGGCCAACGGGCTGGCAGCGGCGGGCAGTCCCGTGTTTCTGTCCATGCTGTCGCCGCTCGGGCAGCTGCTGGGGGAGCGCTTCGGCTGGCGTGGCGGCTTCCTGCTGTTTGGCGGCCTCCTGCTGCACTGTTGCGCCTGTGGGGCAGTCATGCGTCCGCCCCCTGGACC---CCCG---CCG------CGCAGAGACCCCTC------------- \n+\n+a score=810987.0\n+s hg38.chr22 12736835 26 - 50818468 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s eulFla1.LGHW01006107v1 633337 26 + 657376 GCTGTACTTCGAGCGGCGGCGGCCTC \n+s mm10.chr15 24791089 26 - 104043685 ACTCTACTTCGAGCGGCGACGGCCCC \n+\n+a score=2187734.0\n+s hg38.chr22 12736789 46 - 50818468 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s eulFla1.LGHW01006107v1 633291 46 + 657376 GCCTGGGCCTGGCCCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+s mm10.chr15 24791043 46 - 104043685 GCCTGGGCCTAGCTCTCAACTTCCAGCCGTCGCTCATCATGCTGGG \n+\n' |
| b |
| diff -r b79f6002b176 -r 1080e07a2233 test-data/interval2maf-out3.maf --- a/test-data/interval2maf-out3.maf Tue Nov 10 18:48:33 2020 +0000 +++ b/test-data/interval2maf-out3.maf Wed Nov 09 12:34:55 2022 +0000 |
| b |
| b'@@ -1,411 +1,1618 @@\n ##maf version=1\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=196573.0\n-s hg38.chr22 18627690 7 - 50818468 CAAATAA \n-\n-a score=6623803.0\n-s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n-\n-a score=6623803.0\n-s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n-\n-a score=6623803.0\n-s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n-\n-a score=6623803.0\n-s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n-\n-a score=6623803.0\n-s hg38.chr22 18627116 574 - 50818468 TGGATATGACCTTGGATGCCAACACAGCCAACAACTTCCTCCTCATTTCTGACGACCTCAGGAGCGTCCGAAGTGGGCGCATCAGACAGAATCGGCAAGACCTTGCCGAGAGATTTGACGTGTCCGTTTGCATCCTGGGCTCCCCTCGCTTTACCTGTGGCCGCCACTGCTGGGAGGTGGACGTGGGAACAAGCACAGAATGGGACCTGGGAGTCTGCAGAGAATCTGTTCACCGCAAAGGGAGGATCCAGCTGACCACAGAGCTTGGATTCTGGACTGTGAGTTTGAGGGATGGAGGCCGCCTCTCTGCCACCACGGTGCCGCTGACTTTCCTCTTCGTAGACCGCAAGTTACAGCGAGTGGGGATTTTTCTGGATATGGGCATGCAGAACGTTTCCTTTTTTGATGCTGAAAGTGGTTCCCATGTCTATACATTCAGGAGCGTATCTGCTGAGGAGCCATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTTGAGCATCTGTCCTTTGATGAACTCAGGCACTACTGATGCTCCAGTCCGTCCTGGGGAGGC \n-\n-a sco'..b'AGAACGCCTCCTCGGCCTGGCCCCTGAATGCCACCCTGGGAAACGTGTCGGTGGGCCCAAGCCCGGCAGGGCTGGCCGTCAGTGGCGTTTTGATCCCACTGGTCTACCTGGTGGTGTGCGTGGTGGGCCTGCTGGGCAACTCGCTGGTCATCTACGTGGTCCTGAGGCACACGACCAGCCCGTCGGTCACCAATGTCTACATCCTCAACCTGGCGCTGGCTGATGAGCTCTTCATGCTGGGGCTGCCCTTCCTGGCTGCCCAGAACGCTCTGTCCTACTGGCCCTTTGGCTCCCTCATGTGCCGCCTGGTCATGGCCGTGGACGGCATCAACCAGTTCACAAGCATCTTCTGTCTCACCGTCA \n-s mm10.chr15 25503156 396 - 104043685 ATCCTTCATCTGAGCCTACGACCTTGGACCCTGGGAACGCATCCTCGACCTGGCCCCTGGATACCACCCTGGGGAACACATCCGCTGGCGCTAGCCTGACAGGCCTGGCTGTCAGTGGCATCTTGATCTCTCTGGTGTACCTGGTGGTGTGCGTGGTGGGTTTGCTGGGCAACTCGCTGGTGATCTACGTGGTCCTGCGGCACACGTCCAGCCCATCAGTGACCAGTGTCTATATCCTCAACCTGGCTCTGGCTGATGAGCTCTTCATGCTAGGGCTACCCTTCCTGGCTGCTCAGAACGCCCTGTCCTACTGGCCCTTCGGATCTCTCATGTGCCGTCTGGTCATGGCCGTGGATGGCATCAACCAGTTCACCAGCATCTTCTGCCTCACCGTCA \n-\n-a score=14491711.0\n-s hg38.chr22 13610678 396 - 50818468 ATCCATCATCGGTGTCCACGACCTCAGAACCTGAGAATGCCTCCTCGGCCTGGCCCCCAGATGCCACCCTGGGCAACGTGTCGGCGGGCCCAAGCCCGGCAGGGCTGGCCGTCAGTGGCGTTCTGATCCCCCTGGTCTACCTGGTGGTGTGCGTGGTGGGCCTGCTGGGTAACTCGCTGGTCATCTATGTGGTCCTGCGGCACACGGCCAGCCCTTCAGTCACCAACGTCTACATCCTCAACCTGGCGCTGGCCGACGAGCTCTTCATGCTGGGGCTGCCCTTCCTGGCCGCCCAGAACGCCCTGTCCTACTGGCCCTTCGGCTCCCTCATGTGCCGCCTGGTCATGGCGGTGGATGGCATCAACCAGTTCACCAGCATATTCTGCCTGACTGTCA \n-s eulFla1.LGHW01004134v1 54887 396 - 294365 ATCCTTCATTGGTGCCCACGACCCCGGAACCCGAGAACGCCTCCTCGGCCTGGCCCCTGAATGCCACCCTGGGAAACGTGTCGGTGGGCCCAAGCCCGGCAGGGCTGGCCGTCAGTGGCGTTTTGATCCCACTGGTCTACCTGGTGGTGTGCGTGGTGGGCCTGCTGGGCAACTCGCTGGTCATCTACGTGGTCCTGAGGCACACGACCAGCCCGTCGGTCACCAATGTCTACATCCTCAACCTGGCGCTGGCTGATGAGCTCTTCATGCTGGGGCTGCCCTTCCTGGCTGCCCAGAACGCTCTGTCCTACTGGCCCTTTGGCTCCCTCATGTGCCGCCTGGTCATGGCCGTGGACGGCATCAACCAGTTCACAAGCATCTTCTGTCTCACCGTCA \n-s mm10.chr15 25503156 396 - 104043685 ATCCTTCATCTGAGCCTACGACCTTGGACCCTGGGAACGCATCCTCGACCTGGCCCCTGGATACCACCCTGGGGAACACATCCGCTGGCGCTAGCCTGACAGGCCTGGCTGTCAGTGGCATCTTGATCTCTCTGGTGTACCTGGTGGTGTGCGTGGTGGGTTTGCTGGGCAACTCGCTGGTGATCTACGTGGTCCTGCGGCACACGTCCAGCCCATCAGTGACCAGTGTCTATATCCTCAACCTGGCTCTGGCTGATGAGCTCTTCATGCTAGGGCTACCCTTCCTGGCTGCTCAGAACGCCCTGTCCTACTGGCCCTTCGGATCTCTCATGTGCCGTCTGGTCATGGCCGTGGATGGCATCAACCAGTTCACCAGCATCTTCTGCCTCACCGTCA \n-\n-a score=2714701.0\n-s hg38.chr22 13610665 13 - 50818468 ATGGACATGCTT----C \n-s eulFla1.LGHW01004134v1 54871 13 - 294365 ATGGACACCCCTG---- \n-s mm10.chr15 25503140 16 - 104043685 ATGGCCACTGTTACCT- \n-\n-a score=2714701.0\n-s hg38.chr22 13610665 13 - 50818468 ATGGACATGCTT----C \n-s eulFla1.LGHW01004134v1 54871 13 - 294365 ATGGACACCCCTG---- \n-s mm10.chr15 25503140 16 - 104043685 ATGGCCACTGTTACCT- \n-\n a score=22922130.0\n s hg38.chr22 13611339 583 - 50818468 CTACCTGCTCATCGTGGTGAAGGTGCGCTCAGCTGGGCGCCGGGTGTGGGCACCCTCGTG------------------------CCAGCGGCGGCGGCGCTCCGAACGCAGGGTCACGCGCATGGTGGTGGCCGTGGTGGCGCTCTTCGTGCTCTGCTGGATGCCCTTCTACGTGCTCAACATCGTCAACGTGGTGTGCCCACTGCCCGAGGAGCCTGCCTTCTTTGGGCTCTACTTCCTGGTGGTGGCGCTGCCCTATGCCAACAGCTGTGCCAACCCCATCCTTTATGGCTTCCTCTCCTACCGCTTCAAGCAGGGCTTCCGCAGGGTCCTGCTGCGGCCCTCCCGCCGTGTGCGCAGCCAGGAGCCCACTGTGGGGCCCCCGGAGAAGACTga---ggaggaggatgaggaggaggaggatggggaggagagcagggaggggggcaag------gggaaggagATGAACGGCCGGGTCAGCCAGATCACGCAGCCTGGCACCAGCGGGCAGGAGCGGCCGCCCAGCAGAGTGGCCAGCAAGGAGCAGCAGCTCCTACCCCAAGAGGCTTCCACTGGGGAGAAGTCCAGCACGATGCGCATCAGCTACCTGTAG \n s eulFla1.LGHW01004134v1 55548 580 - 294365 CTACCTGCTCATTGTGGTGAAGGTGCGCTCGGCTGGGCGGCGGGTGTGGGCACCCTCGTG------------------------CCAGCGGCGACGGAACTCTGAGCGCAGGGTCACACGCATGGTGGTGGCCGTGGTGGCGCTCTTCGTCCTCTGCTGGATGCCCTTCTACGTGCTCAACATTGTCAACGTGGTGTGCCCGCTGCCCGAGGAGCCTGCCTTCTTCGGCCTCTACTTCCTGGTGGTGGCGCTGCCTTATGCCAACAGCTGTGCCAACCCCATCCTCTACGGCTTCCTCTCCTACCGCTTCAAGCAGGGCTTCCGCAGGGTCCTGCTGCGGCCTTCCCGCCGTGTGTGCAACCAGGAGCCCACTGTGGGGCCTCCAGAGAAGACCga---ggaggaggacggggaagagga---tggggaggagggaggggcgcaggggaag------gggaaggaggagAATAGCCGGCTCAGCCAGATCACACAGCCTGGCAGCAGCGGGCAGGAGCGGCCGCCCAGCAGAGCGGCTGGCAAGGAGCGGCAGTTCCTGCCCCAGGAGCCCTCAGCTGGGGAGAAGTCCAGCACGCTGCACATCAGCTACCTGTAG \n' |