Mercurial > repos > peterjc > seq_primer_clip
changeset 0:945053d79e60 draft
Uploaded v0.0.8, first public release
| author | peterjc |
|---|---|
| date | Mon, 29 Apr 2013 06:11:00 -0400 |
| parents | |
| children | 8c02a91a8680 |
| files | test-data/primers/MID4_GLZRM4E04_rnd30.fasta test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30.sff test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff test-data/primers/dop_primers.fasta tools/primers/seq_primer_clip.py tools/primers/seq_primer_clip.txt tools/primers/seq_primer_clip.xml |
| diffstat | 13 files changed, 1094 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fasta Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,60 @@ +>GLZRM4E04IPVGX +CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT +>GLZRM4E04JAY4Z +CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG +>GLZRM4E04I0CYE +TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I2NA7 +CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04IK8WX +GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG +>GLZRM4E04I22QH +CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04IVVFA +GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG +>GLZRM4E04ILU3V +CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG +>GLZRM4E04I3ZJ6 +CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04JVL8Q +CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT +>GLZRM4E04IOQ36 +CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG +>GLZRM4E04IEFNO +CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04J4HNG +CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT +>GLZRM4E04JC544 +CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,120 @@ +@GLZRM4E04IPVGX +CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +FIIIIIIIIHHHIDDDIIIIIIIIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +IIIIGCBCF=422211:882<<9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIIIIIIIF;;;;HFDDEHHHIIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +IIIIIIIIIIIIIIIIIIII666IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +IIIIIH???GDGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129 +@GLZRM4E04ITXFU +CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT ++ +IIIIGDD===@@3111DD@><<DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 +@GLZRM4E04JAY4Z +CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +FIIIIIIIIIIHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +IIIIIIIIIIIIIGGGIIII;;;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ++ +IIHIIIIE@111177?@88<AA88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII +@GLZRM4E04I0CYE +TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT ++ +HHHIIHIIIIIIIIIIIIIIIIIIIIIIIIIHHHHHHHHHHFFFFFFFFFFFFCC666::ADDBA?888866,,,,,.,,, +@GLZRM4E04I2NA7 +CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ++ +FGDBAA??==21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, +@GLZRM4E04I5BWJ +CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ++ +FIIIIIIIIIIIIHHHHHHIIIIIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,- +@GLZRM4E04IK8WX +GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG ++ +IIIIIIIIIIIIIIH??;;;HIIICCGIIIIIIH????IIIIIIIIII?666HIIIIII +@GLZRM4E04I22QH +CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +444:<:34466,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04IVVFA +GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG ++ +HHIICCBBIIIIIIIIIHHHIIIIIIIIGGGIIIIIIIH6666IIIAAIIIIH;;;IHHHHIIBBCCIIIIIIIIIIIIII +@GLZRM4E04ILU3V +CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +DDDDFECADBBA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ++ +IIIIIIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@@@ICCHHDDDDHII +@GLZRM4E04I3ZJ6 +CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG ++ +CCGIIIIIIAAAAIFH;;;IIIIIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII +@GLZRM4E04I3UBT +CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA ++ +GGGIIIIIGG9999GGHHHIIIIIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIII???IIGG;;;HIIIIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 +CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ++ +:8875782222..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=<////71?<<=<5566BGGGGGEEDDDDD@<;766EE??6779IIIFFFIIHHHIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIICCAAIIFFIIIIIIIIBBBIIIIIIFFFHHIHHHHHFBBBIIIIIIII>>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III<D776<<GGGGEEB6555@BBBIIIIIIIIIIIIIIIIIIIIII@@@@BDAADBAA +@GLZRM4E04J4EK3 +CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG ++ +IIIIIIII>>>>8888DIIIIIHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH +@GLZRM4E04IK96G +CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA ++ +FIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12, +@GLZRM4E04JVL8Q +CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT ++ +../42236,,,9:2116../4---3;666?>:>>44...<:9,,,--17,,,,--,,,,,116?44449@A=<<44440..672222../00998?AAAABB=5333=====<<4466AA981118>@:?444>>===>>;;0...:00000..0@<===;;?:AAAA=36333BAAAAB9;==FFFFFF666EFDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGF:::DD?FIGGGGIDDFGDDD??==DD:66DDDGDDDDA???=444=>?88///?000<889?AAAD???DDDDDIDDDIIIDD====D:DBA>>??89//---88:86888==DD???>D>>>D:88888>DDDDBBBDDDD33333DD7777D>>>?33331::,:8875222220444::::/:9:99766622226::::98:5:77600..,,, +@GLZRM4E04IOQ36 +CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT ++ +HHHGCD@B?0-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998 +@GLZRM4E04JBJJ1 +CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ++ +IIIIIIH?;;;@>IIBD@@EII555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII +@GLZRM4E04IEFNO +CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA ++ +IIIIIIIIIIIIIIIIIIIE666EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 +@GLZRM4E04JOT5I +CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ++ +IIIIIIIII=999E144445CCCIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII +@GLZRM4E04J4HNG +CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT ++ +FFHHHHHHFF888??=A6998><44344888877=:433624 +@GLZRM4E04JC544 +CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC ++ +IIIIHIHIC4------//<=IIIIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,50 @@ +>GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT +>GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG +>GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG +>GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04IOQ36 +TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG +>GLZRM4E04IEFNO +GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,100 @@ +@GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129 +@GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT ++ +DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7 +@GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG ++ +88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII +@GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ++ +21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, +@GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ++ +IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,- +@GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +6,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG ++ +CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@@@ICCHHDDDDHII +@GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG ++ +IIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII +@GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA ++ +IIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT ++ +2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=<////71?<<=<5566BGGGGGEEDDDDD@<;766EE??6779IIIFFFIIHHHIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIICCAAIIFFIIIIIIIIBBBIIIIIIFFFHHIHHHHHFBBBIIIIIIII>>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III<D776<<GGGGEEB6555@BBBIIIIIIIIIIIIIIIIIIIIII@@@@BDAADBAA +@GLZRM4E04J4EK3 +TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG ++ +IHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH +@GLZRM4E04IK96G +TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA ++ +IIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12, +@GLZRM4E04IOQ36 +TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT ++ +-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998 +@GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG ++ +555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII +@GLZRM4E04IEFNO +GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA ++ +6EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87 +@GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG ++ +CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII +@GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC ++ +IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,50 @@ +>GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT +>GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG +>GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC +>GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG +>GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA +>GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC +>GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC +>GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG +>GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG +>GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA +>GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC +>GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC +>GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG +>GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC +>GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG +>GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA +>GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG +>GLZRM4E04JFA38 +GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT +>GLZRM4E04J4EK3 +TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG +>GLZRM4E04IK96G +TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA +>GLZRM4E04IOQ36 +TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT +>GLZRM4E04JBJJ1 +AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG +>GLZRM4E04IEFNO +GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA +>GLZRM4E04JOT5I +GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG +>GLZRM4E04JC544 +ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,100 @@ +@GLZRM4E04IPVGX +AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT ++ +IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1 +@GLZRM4E04I9EJK +TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG ++ +9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII +@GLZRM4E04JHW0A +AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC ++ +IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,, +@GLZRM4E04IBNFY +GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG ++ +6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII +@GLZRM4E04IKCQP +GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA ++ +DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129 +@GLZRM4E04ITXFU +CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC ++ +DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>88 +@GLZRM4E04JAY4Z +GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC ++ +IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81 +@GLZRM4E04H9M21 +CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG ++ +;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII +@GLZRM4E04IQDP5 +TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG ++ +88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CC +@GLZRM4E04I2NA7 +TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA ++ +21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113, +@GLZRM4E04I5BWJ +TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC ++ +IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,- +@GLZRM4E04I22QH +CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC ++ +6,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232----- +@GLZRM4E04ILU3V +CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG ++ +BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0 +@GLZRM4E04IDVJT +GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC ++ +CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@ +@GLZRM4E04I3ZJ6 +ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG ++ +IIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII +@GLZRM4E04I3UBT +AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA ++ +IIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,, +@GLZRM4E04H59S1 +TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG ++ +IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC +@GLZRM4E04JFA38 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/primers/dop_primers.fasta Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,16 @@ +>DOP_start +CCGACTCGAG +>DOP1 +CCGACTCGAGNNNNNNATGTGG +>DOP2 +CCGACTCGAGATGNNNNNNTG +>DOP3 +CCGACTCGAGNNNNNNAAATGC +>DOP4 +CCGACTCGAGNNNNNNTTTACG +>DOP5 +CCGACTCGAGNNNNNNTTCAGG +>DOP6 +CCGACTCGAGNNNNNNAAGTCC +>DOP7 +CCGACTCGAGANNNNNNTCTGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.py Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,358 @@ +#!/usr/bin/env python +"""Looks for the given primer sequences and clips matching SFF reads. + +Takes eight command line options, input read filename, input read format, +input primer FASTA filename, type of primers (forward, reverse or reverse- +complement), number of mismatches (currently only 0, 1 and 2 are supported), +minimum length to keep a read (after primer trimming), should primer-less +reads be kept (boolean), and finally the output sequence filename. + +Both the primer and read sequences can contain IUPAC ambiguity codes like N. + +This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not +supported. + +The mismatch parameter does not consider gapped alignemnts, however the +special case of missing bases at the very start or end of the read is handled. +e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG... +if one or more mismatches are allowed. + +This can also be used for stripping off (and optionally filtering on) barcodes. + +Note that only the trim/clip values in the SFF file are changed, not the flow +information of the full read sequence. + +This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved. +See accompanying text file for licence details (MIT/BSD style). + +This is version 0.0.8 of the script. Currently it uses Python's regular +expression engine for finding the primers, which for my needs is fast enough. +""" +import sys +import re +from galaxy_utils.sequence.fasta import fastaReader, fastaWriter +from galaxy_utils.sequence.fastq import fastqReader, fastqWriter + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.5" + sys.exit(0) + +def stop_err(msg, err=1): + sys.stderr.write(msg) + sys.exit(err) + +try: + from Bio.Seq import reverse_complement + from Bio.SeqIO.SffIO import SffIterator, SffWriter +except ImportError: + stop_err("Requires Biopython 1.54 or later") +try: + from Bio.SeqIO.SffIO import ReadRocheXmlManifest +except ImportError: + #Prior to Biopython 1.56 this was a private function + from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest + +#Parse Command Line +try: + in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:] +except ValueError: + stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) + +if in_file == primer_fasta: + stop_err("Same file given as both primer sequences and sequences to clip!") +if in_file == out_file: + stop_err("Same file given as both sequences to clip and output!") +if primer_fasta == out_file: + stop_err("Same file given as both primer sequences and output!") + +try: + mm = int(mm) +except ValueError: + stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm) +if mm < 0: + stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm) +if mm not in [0,1,2]: + raise NotImplementedError + +try: + min_len = int(min_len) +except ValueError: + stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len) +if min_len < 0: + stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len) + + +if keep_negatives.lower() in ["true", "yes", "on"]: + keep_negatives = True +elif keep_negatives.lower() in ["false", "no", "off"]: + keep_negatives = False +else: + stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives) + + +if primer_type.lower() == "forward": + forward = True + rc = False +elif primer_type.lower() == "reverse": + forward = False + rc = False +elif primer_type.lower() == "reverse-complement": + forward = False + rc = True +else: + stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type) + + +ambiguous_dna_values = { + "A": "A", + "C": "C", + "G": "G", + "T": "T", + "M": "ACM", + "R": "AGR", + "W": "ATW", + "S": "CGS", + "Y": "CTY", + "K": "GTK", + "V": "ACGMRSV", + "H": "ACTMWYH", + "D": "AGTRWKD", + "B": "CGTSYKB", + "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC] + "N": ".", + } + +ambiguous_dna_re = {} +for letter, values in ambiguous_dna_values.iteritems(): + if len(values) == 1: + ambiguous_dna_re[letter] = values + else: + ambiguous_dna_re[letter] = "[%s]" % values + + +def make_reg_ex(seq): + return "".join(ambiguous_dna_re[letter] for letter in seq) + +def make_reg_ex_mm(seq, mm): + if mm > 2: + raise NotImplementedError("At most 2 mismatches allowed!") + seq = seq.upper() + yield make_reg_ex(seq) + for i in range(1,mm+1): + #Missing first/last i bases at very start/end of sequence + for reg in make_reg_ex_mm(seq[i:], mm-i): + yield "^" + reg + for reg in make_reg_ex_mm(seq[:-i], mm-i): + yield "$" + reg + if mm >= 1: + for i,letter in enumerate(seq): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + pattern = seq[:i] + "N" + seq[i+1:] + assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ + % (pattern, len(pattern), seq, len(seq)) + yield make_reg_ex(pattern) + if mm >=2: + for i,letter in enumerate(seq): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + for k,letter in enumerate(seq[i+1:]): + #We'll use a set to remove any duplicate patterns + #if letter not in "NX": + pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:] + assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \ + % (pattern, len(pattern), seq, len(seq)) + yield make_reg_ex(pattern) + +def load_primers_as_re(primer_fasta, mm, rc=False): + #Read primer file and record all specified sequences + primers = set() + in_handle = open(primer_fasta, "rU") + reader = fastaReader(in_handle) + count = 0 + for record in reader: + if rc: + seq = reverse_complement(record.sequence) + else: + seq = record.sequence + #primers.add(re.compile(make_reg_ex(seq))) + count += 1 + for pattern in make_reg_ex_mm(seq, mm): + primers.add(pattern) + in_handle.close() + #Use set to avoid duplicates, sort to have longest first + #(so more specific primers found before less specific ones) + primers = sorted(set(primers), key=lambda p: -len(p)) + return count, re.compile("|".join(primers)) #make one monster re! + + + +#Read primer file and record all specified sequences +count, primer = load_primers_as_re(primer_fasta, mm, rc) +print "%i primer sequences" % count + +short_neg = 0 +short_clipped = 0 +clipped = 0 +negs = 0 + +if seq_format.lower()=="sff": + #SFF is different because we just change the trim points + if forward: + def process(records): + global short_clipped, short_neg, clipped, negs + for record in records: + left_clip = record.annotations["clip_qual_left"] + right_clip = record.annotations["clip_qual_right"] + seq = str(record.seq)[left_clip:right_clip].upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + #so move the left clip along + if len(seq) - result.end() >= min_len: + record.annotations["clip_qual_left"] = left_clip + result.end() + clipped += 1 + yield record + else: + short_clipped += 1 + elif keep_negatives: + if len(seq) >= min_len: + negs += 1 + yield record + else: + short_neg += 1 + else: + def process(records): + global short_clipped, short_neg, clipped, negs + for record in records: + left_clip = record.annotations["clip_qual_left"] + right_clip = record.annotations["clip_qual_right"] + seq = str(record.seq)[left_clip:right_clip].upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + #so move the right clip back + new_len = result.start() + if new_len >= min_len: + record.annotations["clip_qual_right"] = left_clip + new_len + clipped += 1 + yield record + else: + short_clipped += 1 + elif keep_negatives: + if len(seq) >= min_len: + negs += 1 + yield record + else: + short_neg += 1 + + in_handle = open(in_file, "rb") + try: + manifest = ReadRocheXmlManifest(in_handle) + except ValueError: + manifest = None + in_handle.seek(0) + out_handle = open(out_file, "wb") + writer = SffWriter(out_handle, xml=manifest) + writer.write_file(process(SffIterator(in_handle))) + #End of SFF code +elif seq_format.lower().startswith("fastq"): + in_handle = open(in_file, "rU") + out_handle = open(out_file, "w") + reader = fastqReader(in_handle) + writer = fastqWriter(out_handle) + if forward: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + cut = result.end() + record.sequence = seq[cut:] + if len(record.sequence) >= min_len: + record.quality = record.quality[cut:] + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 + else: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + cut = result.start() + record.sequence = seq[:cut] + if len(record.sequence) >= min_len: + record.quality = record.quality[:cut] + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 +elif seq_format.lower()=="fasta": + in_handle = open(in_file, "rU") + out_handle = open(out_file, "w") + reader = fastaReader(in_handle) + writer = fastaWriter(out_handle) + #Following code is identical to that for FASTQ but without editing qualities + if forward: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Forward primer, take everything after it + cut = result.end() + record.sequence = seq[cut:] + if len(record.sequence) >= min_len: + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 + else: + for record in reader: + seq = record.sequence.upper() + result = primer.search(seq) + if result: + #Reverse primer, take everything before it + cut = result.start() + record.sequence = seq[:cut] + if len(record.sequence) >= min_len: + clipped += 1 + writer.write(record) + else: + short_clipped += 1 + elif keep_negatives: + if len(record) >= min_len: + negs += 1 + writer.write(record) + else: + short_negs += 1 +else: + stop_err("Unsupported file type %r" % seq_format) +in_handle.close() +out_handle.close() + +print "Kept %i clipped reads," % clipped +print "discarded %i short." % short_clipped +if keep_negatives: + print "Kept %i non-matching reads," % negs + print "discarded %i short." % short_neg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.txt Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,103 @@ +Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads +=========================================================== + +This tool is copyright 2011 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using the Galaxy library functions and +Biopython). There are just two files to install: + +* seq_primer_clip.py (the Python script) +* seq_primer_clip.xml (the Galaxy tool definition) + +The suggested location is a new tools/primers folder. You will also need to +modify the tools_conf.xml file to tell Galaxy to offer the tool and also do +this to tools_conf.xml.sample in order to run the tests: + +<tool file="primers/seq_primer_clip.xml" /> + +There are optionally some example files required to run the functional tests, +put these in the test-data/primers folder. + +test-data/primers/dop_primers.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30.sff +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff + +You should then be able to run the tests with: + +sh run_functional_tests.sh -id seq_primer_clip + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +v0.0.1 - Initial version (not publicly released) +v0.0.2 - Sort primers by length (longest and therefore most specific first) +v0.0.3 - Consider missing bases at start/end of read as mismatches +v0.0.4 - Apply minimum length to sequences with no match too +v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes +v0.0.6 - Added some functional tests +v0.0.7 - Added error check for bad filename arguments +v0.0.8 - Record version of Python script when run from Galaxy. + - Check for errors using Python script's return code. + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +This incorporates the previously used hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/* + +Check this worked: + +$ tar -tzf seq_primer_clip.tar.gz +tools/primers/seq_primer_clip.py +tools/primers/seq_primer_clip.txt +tools/primers/seq_primer_clip.xml +test-data/primers/dop_primers.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fasta +test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger +test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff +test-data/primers/MID4_GLZRM4E04_rnd30.sff + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/primers/seq_primer_clip.xml Mon Apr 29 06:11:00 2013 -0400 @@ -0,0 +1,137 @@ +<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8"> + <description>Trim off 5' or 3' primers</description> + <version_command interpreter="python">seq_primer_clip.py --version</version_command> + <command interpreter="python"> +seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/> + <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> + <param name="primer_type" type="select" label="Type of primers"> + <option value="Forward">Forward (5') primers</option> + <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> + <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> + </param> + <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)"> + <validator type="in_range" min="0" max="2" /> + </param> + <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> + <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> + </inputs> + <outputs> + <data name="output_file" format="data" label="$primer_type primer clipped"> + <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> + <change_format> + <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> + <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" /> + <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> + <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> + <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> + <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> + <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Forward" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="false" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> + </test> + <test> + <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> + <param name="primer_fasta" value="primers/dop_primers.fasta" /> + <param name="primer_type" value="Reverse" /> + <param name="mm" value="2" /> + <param name="keep_negatives" value="true" /> + <param name="min_len" value="35" /> + <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> + </test> + </tests> + <requirements> + <requirement type="python-module">Bio</requirement> + </requirements> + <help> + +**What it does** + +Looks for the given primer sequences (within the existing clipped sequence) and +further clips the reads to remove the primers and any preceding/trailing sequence. + +Reads containing a forward primer are reduced to just the sequence after (and +excluding) the forward primer. + +Reads containing a reverse primer are reduced to just the sequence before (and +excluding) the reverse primer. + +Degenerate primers can be specified using the standard IUPAC ambiguity codes, +thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity +codes) and so on. + +Note that for SFF files only the clip/trim positions are edited - you will still +be able to extract the original full read (with any adapter sequence and poor +quality sequence) if you need to. + +.. class:: warningmark + +**Note**. This tool was initially written for Roche 454 data, and should also +work fine on Sanger or Ion Torrent as well. However, it is probably too slow +for use on large Illumina datasets. + + +**Citation** + +This tool uses Biopython. If you use this tool in scientific work leading to a +publication, please cite: + +Cock et al 2009. Biopython: freely available Python tools for computational +molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. +http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. + + </help> +</tool>