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[hg] galaxy 2718: Unicode support for tags + sqlite
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cbf8667219a4 changeset: 2718:cbf8667219a4 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Sep 18 13:59:50 2009 -0400 description: Unicode support for tags + sqlite 1 file(s) affected in this change: templates/tagging_common.mako diffs (16 lines): diff -r 99b5db852719 -r cbf8667219a4 templates/tagging_common.mako --- a/templates/tagging_common.mako Fri Sep 18 13:58:43 2009 -0400 +++ b/templates/tagging_common.mako Fri Sep 18 13:59:50 2009 -0400 @@ -13,7 +13,11 @@ tag_value = "" if tag.value is not None: tag_value = tag.user_value - tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') + ## Tag names and values may be string or unicode object. + if isinstance( tag_name, str ): + tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') + else: ## isInstance( tag_name, unicode ): + tag_names_and_values[tag_name] = tag_value %> // // Returns the number of keys (elements) in an array/dictionary.

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[hg] galaxy 2716: lastz commented as per Anton's instructions, t...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/079541496366 changeset: 2716:079541496366 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Sep 18 13:45:14 2009 -0400 description: lastz commented as per Anton's instructions, the wrapper and params will be rewritten shortly. 1 file(s) affected in this change: tool_conf.xml.sample diffs (12 lines): diff -r 16993bf0803e -r 079541496366 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 12:11:43 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 13:45:14 2009 -0400 @@ -194,7 +194,7 @@ <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> <section name="NGS: Mapping" id="solexa_tools"> - <tool file="sr_mapping/lastz_wrapper.xml" /> +  <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="sr_mapping/bowtie_wrapper.xml" />

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[hg] galaxy 2715: Added header removal option to BWA wrapper too...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/16993bf0803e changeset: 2715:16993bf0803e user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Sep 18 12:11:43 2009 -0400 description: Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool. 16 file(s) affected in this change: test-data/bwa_wrapper_in0.fastq test-data/bwa_wrapper_out0.sam test-data/bwa_wrapper_out0.tabular test-data/bwa_wrapper_out0b.sam test-data/bwa_wrapper_out0b.tabular test-data/bwa_wrapper_out1.sam test-data/bwa_wrapper_out1.tabular test-data/bwa_wrapper_out2.sam test-data/bwa_wrapper_out2.tabular test-data/bwa_wrapper_out3.sam test-data/bwa_wrapper_out3.tabular test-data/bwa_wrapper_out4.sam test-data/bwa_wrapper_out4.tabular tools/next_gen_conversion/bwa_solid2fastq_modified.pl tools/sr_mapping/bwa_wrapper.py tools/sr_mapping/bwa_wrapper.xml diffs (1125 lines): diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_in0.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in0.fastq Fri Sep 18 12:11:43 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0.sam --- a/test-data/bwa_wrapper_out0.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out0.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,2 +1,1 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0.tabular --- a/test-data/bwa_wrapper_out0.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0b.sam --- a/test-data/bwa_wrapper_out0b.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out0b.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:phiX LN:5386 1831_573_1004 0 phiX 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out0b.tabular --- a/test-data/bwa_wrapper_out0b.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 4 * 0 0 * * 0 0 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out1.sam --- a/test-data/bwa_wrapper_out1.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out1.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:PHIX174 LN:5386 1831_573_1004 0 PHIX174 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out1.tabular --- a/test-data/bwa_wrapper_out1.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,145 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -1831_573_1004 0 PHIX174 278 25 33M = 278 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -1831_573_1219 16 PHIX174 2202 37 33M = 2202 0 TGCAGTGGAATAGTCAGGTTAAATTTAATGTGA KJOOHX]KAP[]]MBQ\TUFO]QMFGG=CLZ]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1242 0 PHIX174 648 37 33M = 648 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) -1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -1831_573_1448 16 PHIX174 2563 25 33M = 2563 0 CTTCATTGCATTCAGATGGATACATCTGTCAAC :BMPX5.QUW6+R]RIOU]]]]]]]]WCTQS]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1490 0 PHIX174 1767 25 33M = 1767 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%&#0'%#*,2' -1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -1831_573_1647 16 PHIX174 1118 37 33M = 1118 0 GACTCCTTCGAGATGGACGCCGTTGGCGCTCTC XSU]YZSLKMZ]Y[]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1684 16 PHIX174 3696 37 33M = 3696 0 AGTGCTGAGGTTGACTTAGTTCATCAGCAAACG ]]]]V]]]]]]]]]]]]]]]]]]]]]U\]][TX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 -1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, -1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -1831_574_109 0 PHIX174 3729 37 33M = 3729 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGC VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_148 16 PHIX174 2369 37 33M = 2369 0 TAGGTTTTCTGCTTAGGAGTTTAATCATGTTTC XOQ[]]]TKWRCLJJZRR][]TWVGVZW]WZTQ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# -1831_574_243 0 PHIX174 2129 37 33M = 2129 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGC ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -1831_574_575 16 PHIX174 4006 37 33M = 4006 0 AATGTCACGCTGATTATTTTGACTTTGAGCGTA TMHGZ]UE<L]]]EM]K"&I]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_592 16 PHIX174 2950 37 33M = 2950 0 GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCA LLVSIV]]ZSPPSWNDIW\VOM[]]QANSCGKI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- -1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -1831_574_734 16 PHIX174 5263 25 33M = 5263 0 GAGAGATGAGATTGAGGCTGGGAAAAGTTACTG P]VXTGPLRN@KE=ALXC7ARL7;>;OKA/!!< XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_824 16 PHIX174 3997 37 33M = 3997 0 ACCCTTCTGAATGTCACGCTGATTATTTTGACT ]\MN]]U?I]]TAN]]ZGK][\RR]T@>M]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ -1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -1831_574_1194 0 PHIX174 1136 37 33M = 1136 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGT \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1204 16 PHIX174 1445 25 33M = 1445 0 CCTAATGAGCTTAATCAAGATGATGCTCGTTAT JGMO%.S]S>EW]V,=Y[]]PCU]]]X]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -1831_574_1591 16 PHIX174 5118 37 33M = 5118 0 AAGCTGTTCAGAATCAGAATGAGCCGCAACTTC MLII]]\K!7]ST][]]]OO]]]]]X]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1624 16 PHIX174 4058 37 33M = 4058 0 TATTGAGGCTTGTGGCATTTCTACTCTTTCTCA ?IM@DV]M?NRTK@JPXS?>ENI;=AML=7=M[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -1831_574_1903 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1961 0 PHIX174 3555 25 33M = 3555 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTT TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_54 16 PHIX174 3587 37 33M = 3587 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCG ]]4/WZUDARYXKAL]]MR]]]]\]]VW]W]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -1831_575_197 16 PHIX174 4861 37 33M = 4861 0 GCTTGCAAAATACGTGGCCTTATGGTTACAGTA G.<]KNV]]RH@AIT]\SP\]]]Y[]]\RS\]P XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. -1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -1831_575_444 16 PHIX174 5098 37 33M = 5098 0 AGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAA ]Y0/[]]MM]]]VT]]]]]]]]QP]]]TS]]][ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -1831_575_569 0 PHIX174 5043 25 33M = 5043 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAA IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_622 0 PHIX174 2485 37 33M = 2485 0 GTTTTACAGACACCTAAAGCTACATCGTCAACG ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -1831_575_663 16 PHIX174 1554 25 33M = 1554 0 CGACTTCTACCACATCTATTGACATTATGGGTC !&V]]NIPV]]YUXWZWTYPW]]]]]ST]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& -1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# -1831_575_938 16 PHIX174 1133 37 33M = 1133 0 GACGCCGTTGGCGCTCTCCGTCTTTCTCCATTG XJFX]]WUY[]RKYXU]]]]]]]]\]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_970 16 PHIX174 232 37 33M = 232 0 GAGGAGAAGTGGCTTAATATGCTTGGCACGTTC Z]]]XU]]]]]]]]]]]]]]]\]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -1831_575_1138 0 PHIX174 1913 37 33M = 1913 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCT VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1157 16 PHIX174 3736 25 33M = 3736 0 AGCGGTATGGCTCTTCTCATATTGGCGCTACTG TX//[\]PQ]]]Z]]]]GN]]O!']]]]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1180 0 PHIX174 4169 37 33M = 4169 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGT ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -1831_575_1302 16 PHIX174 5202 37 33M = 5202 0 CTTACCAAGCTGGGTTACGACGCGACGCCGTTC ?AGG9<JL@57BI,!6828KG54AH<6B>;VYL XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1310 16 PHIX174 1612 37 33M = 1612 0 TACTGACCAAGAACGTGATTACTTCATGCAGCG [M!!N]]]]]]]OX]]]ZKW]]QQ][][RU]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1321 0 PHIX174 2664 37 33M = 2664 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGAC ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1373 16 PHIX174 4221 37 33M = 4221 0 TCTGACGTTCGTGATGAGTTTGTATCTGTTACT WGIZ]OHLR]]QU]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -1831_575_1436 0 PHIX174 3460 37 33M = 3460 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATA []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1442 0 PHIX174 3317 37 33M = 3317 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTC \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -1831_575_1500 16 PHIX174 4269 37 33M = 4269 0 GAATTGGCACAATGCTACAATGTGCTCCCCCAA ]]]LQ]ZZX]]]][[[[][VZ\][[]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1535 16 PHIX174 1225 37 33M = 1225 0 TCACGTTTATGGTGAACAGTGGATTAAGTTCAT Z\]]][Y][]]]]]]]W]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -1831_576_32 16 PHIX174 988 25 33M = 988 0 TTGAGGATAAATTATGTCTAATATTCAAACTGG !6\NX[\]YMP]]YM]]]]]VMPGDW\]]]]]] XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? -1831_576_86 16 PHIX174 2981 37 33M = 2981 0 CATGTCTAAATTGTTTGGAGGCGGTCAAAAAGC JDKTAEKORA;<GOTUPHGVRTZI?BAMUDCKR XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -1831_576_266 16 PHIX174 280 37 33M = 280 0 AGATATGAGTCACATTTTGTTCATGGTAGAGAT E4FXQMCG]]R<FZG5#.Z]SN]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_327 16 PHIX174 4517 37 33M = 4517 0 TACTATTCAGCGTTTGATGAATGCAATGCGACA \[]]]XQ\]]\X]]]]\Y]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( -1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -1831_576_519 16 PHIX174 1625 37 33M = 1625 0 CGTGATTACTTCATGCAGCGTTACCGTGATGTT KMPKLIVPELLS]XRY]]YWV]]NJY]]Y][SZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_603 16 PHIX174 1576 37 33M = 1576 0 CATTATGGGTCTGCAAGCTGCTTATGCTAATTT ZWU]]ZS\]]]TY]]]RQ]]]Y]]]]VZ]]\S] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_655 16 PHIX174 3292 37 33M = 3292 0 TTGCTGCTGCATTTCCTGAGCTTAATGCTTGGG :@O]QV]]]TK]]]73]]]TM]]]QI[]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### -1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* -1831_576_815 0 PHIX174 5186 37 33M = 5186 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTA Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_882 0 PHIX174 5053 37 33M = 5053 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACT Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_898 0 PHIX174 518 37 33M = 518 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTG ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_923 0 PHIX174 1050 37 33M = 1050 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTC MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -1831_576_1131 16 PHIX174 4061 37 33M = 4061 0 TGAGGCTTGTGGCATTTCTACTCTTTCTCAATC WTLN]WUHL]]S<PZQUOYSFZ]][IUXX>>]M XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -1831_576_1289 16 PHIX174 1899 37 33M = 1899 0 TTCAGTACCTTAACGCTAAAGGTGCTTTGACTT NLU]YXTCQ]][JEJMSX]YRU]]][]]]\X]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -1831_576_1367 0 PHIX174 1839 37 33M = 1839 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTC ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1416 0 PHIX174 4522 37 33M = 4522 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -1831_576_1605 0 PHIX174 5209 37 33M = 5209 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGA ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -1831_576_1729 16 PHIX174 5194 37 33M = 5194 0 TAATCCAACTTACCAAGCTGGGTTACGACGCGA ]VDP]]][]]]]]]]]]]]]]]UW]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 -1831_576_1982 16 PHIX174 5024 37 33M = 5024 0 TAACAAAAAGTCAGATATGGACCTTGCTGCTAA TP\NU]]]W[]]]][]]]]]]]]]]]]]VU]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -1831_577_40 0 PHIX174 2772 25 33M = 2772 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGG JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 -1831_577_133 16 PHIX174 1714 37 33M = 1714 0 CATGCGCTCTAATCTCTGGGCATCTGGCTATGA &/BFXKGOZZEPOS]]]]]]PY]RN]YW]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -1831_577_281 16 PHIX174 4577 37 33M = 4577 0 TTTTGACACTCTCACGTTGGCTGACGACCGATT ]]OI]]]]]\ZY]]WTJS]]\[]]]]]]]\]]P XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_288 0 PHIX174 3201 25 33M = 3201 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGAT SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_322 16 PHIX174 458 37 33M = 458 0 TTCTGCCGTTTTGGATTTAACCGAAGATGATTT OIJWXWT]]WACVSEK5:RJSSRSPVZONR[]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_362 0 PHIX174 2153 37 33M = 2153 0 CTTATTCGCCACCATGATTATGACCAGTGTTTC ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_382 16 PHIX174 4686 37 33M = 4686 0 GGTCGCAAGGCTAATGATTCACACGCCGACTGC HMJXWWS<===S]NGHPXOE;GV]O;CTROUWT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_464 0 PHIX174 2126 25 33M = 2126 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATT ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_488 16 PHIX174 4948 37 33M = 4948 0 GGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG ]OTZ]]]]]][V]Z]YW]]]]]][UTT]Q?COU XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -1831_577_545 0 PHIX174 1711 37 33M = 1711 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTA ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_559 0 PHIX174 3840 25 33M = 3840 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAA ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -1831_577_637 0 PHIX174 4247 37 33M = 4247 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -1831_577_692 0 PHIX174 3905 37 33M = 3905 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTC WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out2.sam --- a/test-data/bwa_wrapper_out2.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out2.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,4 +1,3 @@ -@SQ SN:PHIX174 LN:5386 1378_11_329 77 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ 1378_11_329 141 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# 1378_17_1788 77 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out2.tabular --- a/test-data/bwa_wrapper_out2.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -1378_11_329 69 * 0 0 * * 0 0 GTTCGTGGCCGGTGGGTGTTTGGG ###$$#$#$&#####$'$#$###$ -1378_11_329 133 * 0 0 * * 0 0 AGACCGGGCGGGGTGGCGTTCGGT %##+'#######%###$#$##$(# -1378_17_1788 69 * 0 0 * * 0 0 TGGGTGGATGTGTTGTCGTTCATG #$#$###$#$#######$#$#### -1378_17_1788 133 * 0 0 * * 0 0 TGCCGTGTCTTGCTAACGCCGATT #'#$$#$###%%##$$$$###### -1378_25_2035 69 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% -1378_25_2035 133 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# -1378_28_770 69 * 0 0 * * 0 0 GGTTGGGAGTTGGCGCGCGTGGTT ###$##%%$####%#%$#%%#($$ -1378_28_770 133 * 0 0 * * 0 0 CTGCTATGCCGGCCGCCTGCCCCT %##(#$$#%$#$%###$%%$##$# -1378_33_1945 69 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG .6;?;55697>8779457986264 -1378_33_1945 133 * 0 0 * * 0 0 GGGGGGGGGGGGGGGGGGGGGGGG +9;64287788752796/576352 -1378_34_789 69 * 0 0 * * 0 0 GGGCTTGCGTTAGTGAGAGGTTGT ###%$%$%%###$####$###$#& -1378_34_789 133 * 0 0 * * 0 0 ATGGTGGCTGACGCGTTTGACTGT #$##%#$##$&$#%##$##$###$ -1378_35_263 69 * 0 0 * * 0 0 GGCGGGGGGGGGGGGGGGGGGGGG $%%&,)3/)%$-6'$&5&#$''5. -1378_35_263 133 * 0 0 * * 0 0 GGGCGGGGGGCGGCGGGGGGGGGG ),,#%'$)'-(%&%'%',%%&&(& -1378_43_186 69 * 0 0 * * 0 0 GCTAGGGTTTGGGTTTGCGGTGGG $%#$########%##%#$###'#' -1378_43_186 133 * 0 0 * * 0 0 ATACTAGTTGGGACGCGTTGTGCT #$(4%$########$#$###$$$# -1378_51_1671 69 * 0 0 * * 0 0 GGTGTTGTTCGGATGTAGCGTGGG ##%$$####$########$##0## -1378_51_1671 133 * 0 0 * * 0 0 TGGGTAGGTGCGGCTCTTGCGGTC ##$#$%###%%#%#$##$$##### -1378_56_324 69 * 0 0 * * 0 0 GCTGGGTGATCTAAGGAATGTAAT #$#####$$$#$$$$##%###*(# -1378_56_324 133 * 0 0 * * 0 0 AGGCTTGGATTGTTGCGCTGACCT /+#**###%%##%#####$$$#$# -1378_56_773 69 * 0 0 * * 0 0 TCTGGTCGGTTTCGGGGAGTGGAA ##%%#&$###$#$##%$####%%$ -1378_56_773 133 * 0 0 * * 0 0 TGTCGTGAGGTCACTTATCCCCAT &%#%##%%#####&#$%##$%##$ -1378_62_2027 69 * 0 0 * * 0 0 GTTGGCCTGGCCTGCCGTGCTGCG *##),/%##$)#%##1$#'%.#&# -1378_62_2027 133 * 0 0 * * 0 0 CTTCCACGATCTGCTCGCTGTGGT (#&&$##$$#$%#%$$$#$###'# -1378_62_2029 69 * 0 0 * * 0 0 GGCGGTGTGTGGTGCGGCTGTGCG /$$$=(####%####)$$%$-&%# -1378_62_2029 133 * 0 0 * * 0 0 TCTGGGCTGTCTTCGGGTCGGTGT $%$$####$##$$#)##%%#$### -1378_67_1795 69 * 0 0 * * 0 0 CGTGCCAACGACCGTCCTACGGAG @@.?7@@@.@:@A<<>>=>70<@7 -1378_67_1795 133 * 0 0 * * 0 0 TAGTGGGCTAGTCCGGGATCTACC B@C2@@?;-@@1>'A@@91@.@1' -1378_68_466 69 * 0 0 * * 0 0 GTGTCATCTGAGGTAAAGCATTGT /##$09#$#.=$#$76+$%1'### -1378_68_466 133 * 0 0 * * 0 0 GTGATCGTCGGTGCCAGTCCCTGT #(%)+##$#$#%#+$%##$##### -1378_68_1692 69 * 0 0 * * 0 0 TGTTCGATTTAGGTCTTGCCTCGC ###%%$%%##%$#$##$###$$#$ -1378_68_1692 133 * 0 0 * * 0 0 GGTCTTCTGGGCACGGGCCAAGTT ###)%'&%##$###%#######$# -1378_80_664 69 * 0 0 * * 0 0 TGTCTGCGTTGTATCTCTGGTGTA %##%,%$$#&$$###$#$%##'%# -1378_80_664 133 * 0 0 * * 0 0 CTGCTTTGATCCCCGGTGGAGCAC 7#%###$$6#######$##$$$## -1378_85_1786 69 * 0 0 * * 0 0 CCCTAGGAGCGTATACCGGACGAG ,'&/%/@,&1,&'/)&,6&&1)(( -1378_85_1786 133 * 0 0 * * 0 0 ATACTATGTCGATCTGTAAAAAAA )&.)#3%(a)$&%-,2#&+.-%0&./ -1378_86_1011 69 * 0 0 * * 0 0 AGGCGATGGGATATTATTTTACTT :$###)%##$9$###1$$#$2### -1378_86_1011 133 * 0 0 * * 0 0 CTACGTTATTGCTCTGTTTGTCCT ######$%##$$$%###%#$#### -1378_86_1789 69 * 0 0 * * 0 0 GGCCAGGTACTAATAAATTCAACA 1.51/&%#'$,*?%#6&0$$5,20 -1378_86_1789 133 * 0 0 * * 0 0 CGAATATCCCCTGGTTTAGAAGTA 61?1;@/>@<=/(.7'(<5@=%$= -1378_91_1596 69 * 0 0 * * 0 0 GCTTTTTCATTCGGTGCCTTTGGA '>%/3%=()8'#.%?50$&5>%)% -1378_91_1596 133 * 0 0 * * 0 0 TTAGCGGTTGACTATCTGCTGACA *&+'#9'(%*'#//,&<),/)'*# -1378_94_1595 69 * 0 0 * * 0 0 GCGGGTTAACCCAGTACCTCTGGC ,8@6'>8<76>@@(->9)7'*941 -1378_94_1595 133 * 0 0 * * 0 0 CGTGCGACAGCCCATGTTTTCAGA -=..5,3826&*+.+#+#%%6;%# -1378_95_1039 69 * 0 0 * * 0 0 GTTCTGTGCCAGGTGAGGTACGGA &##,./#$&)6##+,'#$$0(##$ -1378_95_1039 133 * 0 0 * * 0 0 CGGCGTCCATCTTCGCCTTGAGAT $##.#$##$$#%$#$%%$###$)$ -1378_95_1767 69 * 0 0 * * 0 0 CTAATTGACCGGGCAAGCTATTAA ',,2'(10/>:=/7).3&%6&)&6 -1378_95_1767 133 * 0 0 * * 0 0 ACACGCACCATCTGGCGGCTAACC 86<65<4<C27/$5+#;-$+#2%$ -1378_96_1037 69 * 0 0 * * 0 0 CTGCTGGGCCATTTGACTTACTCA '$#+#(##-%5##+*&###-.$$$ -1378_96_1037 133 * 0 0 * * 0 0 ATCCCCCAAGATGCCTGTTGATTG $#$'##$$$#%$$#%###+##$#$ -1378_96_1764 69 * 0 0 * * 0 0 TCTTTGTAACCCACTTAGTATTTC 4='28>.@4881B807:822>%)1 -1378_96_1764 133 * 0 0 * * 0 0 TACACCGGAACCTTGCACTAAAGC 6-9'<#+81?+*<8-=69&6;*3) -1378_98_1574 69 * 0 0 * * 0 0 AGGCGAGTGTGGGGGTTGTTTGAG +%%$#)##%##$####%###$%$# -1378_98_1574 133 * 0 0 * * 0 0 GTTCTGCCGGTGTCTGTGGCGGGC $$#+&$$####%$$$###$%#%%# -1378_107_1647 69 * 0 0 * * 0 0 GGTCTGGTTCTATGTTGGTCGACT ###'$$#$$$(#%###(#$##$%# -1378_107_1647 133 * 0 0 * * 0 0 AGGCCTACTACGCGTCATTGATAG &#$$#$(.#%#$$####&$%##($ -1378_111_829 69 * 0 0 * * 0 0 GGTCTTCTATGGTGCTAAATTAGT $##'&###$##)#%($#$%#$'%# -1378_111_829 133 * 0 0 * * 0 0 TGCGGCACTTGCTTCTTCGTATTT %#%##%#$%#$#%###$$##&#$$ -1378_111_1900 69 * 0 0 * * 0 0 GCACGCCTTTGGGCTAAGCCGTAA )$)'#%$########$'#&%$#(# -1378_111_1900 133 * 0 0 * * 0 0 TCCCCTCGCTCGGCTCTGTGCTGT $&%*$#(#)##$#'##%(##$#$% -1378_112_1483 69 * 0 0 * * 0 0 TGGAGTGGTGTGTTTGCTGAGCCA #$#)#############$#%#%'% -1378_112_1483 133 * 0 0 * * 0 0 TGTCCAGCTATGCGGCTTCCTCCT %#$+#%#&#$#####%####%$## -1378_125_1287 69 * 0 0 * * 0 0 TGACGTGGGTTGTCCCGTGAGATT ##$%%#$###$##$$#&%##$(%% -1378_125_1287 133 * 0 0 * * 0 0 TGTCTCTGGGGGGCCTGGTTAGGT $##13$'%#$###$$###$$$#&# -1378_126_468 69 * 0 0 * * 0 0 AAAAAACGGGCCGGGCGGACTAGG @@B@@@>@2>1+?:92)>@8&&<+ -1378_126_468 133 * 0 0 * * 0 0 TCTCCTGATTAGACATATCTCCGT 7>@318?=,=8@49579?..7,7) -1378_127_664 69 * 0 0 * * 0 0 TCGCTTTGCCTATGTTTGTTCGGA #%$%#&##$%#%%###$$###)-' -1378_127_664 133 * 0 0 * * 0 0 AGAGGTTGGTGTCTTGTCGCAGCT ##'#$######$$%######$$$# -1378_129_463 69 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAA ,)&20%8'(&35-***1-2&+510 -1378_129_463 133 * 0 0 * * 0 0 CCTGTGGGCCAAGCCCAATGAAAG 8),,<6(--)<()5&.&/8+;.2+ -1378_129_875 69 * 0 0 * * 0 0 GACCTTTACGTATTGGGGGTTGGC ###)###+###$##$#&%##$,#$ -1378_129_875 133 * 0 0 * * 0 0 TTTCTATGGCTTACGCTGTCTGCC #$($##%####%$#$#####$### -1378_140_1251 69 * 0 0 * * 0 0 TTTCCTTCGTGTGCGTGCGGAGTG #%#%$##$$$######.$$$%#%( -1378_140_1251 133 * 0 0 * * 0 0 ATCCTAGCGCGGTGTCTTGGGGAC #$%1#$$$##$##$#$#$##$%$$ -1378_141_809 69 * 0 0 * * 0 0 TCTCGTGGTTTCTTTTTTATGTGT ##%)##$$#####%$#$#%%#'## -1378_141_809 133 * 0 0 * * 0 0 TGTCCTCCAGTGTCTGTTGGGTGT %&,-##$$#(%###$#$$'###'# -1378_144_983 69 * 0 0 * * 0 0 GTTCGTTCGTGGTGTACGAGGGTG #(#%#####($#%##$$#%##%#) -1378_144_983 133 * 0 0 * * 0 0 AGCGCCCGGTTGGTGCGGCTCGTC -$(&%*$#*#))#$$$#%%$#$## -1378_153_270 69 * 0 0 * * 0 0 GGCCGTGTGCGGGTGTAGATTGGA %$##($######&##$&$$$$%## -1378_153_270 133 * 0 0 * * 0 0 AGTCCTTGTCCCCTGGGTTTTCCC +''$#&%$%#$##&$$($#&#$$# -1378_155_1689 69 * 0 0 * * 0 0 CGCGTTCGGACAAAGCTAGCACCT @4@@=6=@@<4:@@681@@@.24. -1378_155_1689 133 * 0 0 * * 0 0 TTGGGAGGGAGAGAGACTAGACCG ?4@@4<<??<?-@4@=4<5<?:/> -1378_157_1580 69 * 0 0 * * 0 0 GGGATTGAAGGGATGTATGCTAGG #%$&%#$$'%$%#$##*#%$$$$# -1378_157_1580 133 * 0 0 * * 0 0 TGGGCCTCGGTGCCCTTGGTCTGT #%)$##'#$$$&#####%#$#$## -1378_161_317 69 * 0 0 * * 0 0 AATCCATACCCACAAAAGCAGGCC .&%','(@''?7//+&)+2.+)0) -1378_161_317 133 * 0 0 * * 0 0 TTGGCCGGCAACCCCGGTACCTAA 7<,<'@)@>.)2@/')'&(?/-<( -1378_177_735 69 * 0 0 * * 0 0 CGAGCCCTAAACCATGAGATCGGA @@B>@AC9@A<B8@=9>7@5)>,0 -1378_177_735 133 * 0 0 * * 0 0 AGTACGCCATGTATTTGCGACCAG =?@?C<88@=>:7>@55/.,416, -1378_181_1684 69 * 0 0 * * 0 0 TTTCTGTTGTGGTTTTGTTGGGGT $##'$%'##%##$%$#$$####$* -1378_181_1684 133 * 0 0 * * 0 0 CGACTCCCGCATTCACGGTCAAGT &*#,##$#&$*$$#$#$$$#%$## -1378_187_1407 69 * 0 0 * * 0 0 TTGGGTGAAATCTTGTCGAGTGGA ####&##$$###$#####%##%%) -1378_187_1407 133 * 0 0 * * 0 0 TGGCGTCCACTCGTGGGTCTATCG $#$'%#$%$%&$%#####$#$#%# -1378_203_721 69 * 0 0 * * 0 0 CCTTTACGATCATAAACCATGACC 9<&./1&@;12')?<1',?/)&/. -1378_203_721 133 * 0 0 * * 0 0 CCTAAATAACCCAGGGTAAAAGAT 9<1+2+1@=259@+;2.71&@+2& -1378_206_2039 69 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC ?=>>?=:;<>>4::<=56199(05 -1378_206_2039 133 * 0 0 * * 0 0 CCCCCCCCCCCCCCCCCCCCCCCC 9@?8>;>>><<994;=895895-8 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out3.sam --- a/test-data/bwa_wrapper_out3.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out3.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,2 +1,1 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out3.tabular --- a/test-data/bwa_wrapper_out3.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M = 322 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out4.sam --- a/test-data/bwa_wrapper_out4.sam Fri Sep 18 11:11:41 2009 -0400 +++ b/test-data/bwa_wrapper_out4.sam Fri Sep 18 12:11:43 2009 -0400 @@ -1,3 +1,2 @@ -@SQ SN:PHIX174 LN:5386 081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 76759e07013b -r 16993bf0803e test-data/bwa_wrapper_out4.tabular --- a/test-data/bwa_wrapper_out4.tabular Fri Sep 18 11:11:41 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT -081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 diff -r 76759e07013b -r 16993bf0803e tools/next_gen_conversion/bwa_solid2fastq_modified.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/next_gen_conversion/bwa_solid2fastq_modified.pl Fri Sep 18 12:11:43 2009 -0400 @@ -0,0 +1,112 @@ +#!/usr/bin/perl -w + +# Author: lh3 +# Note: Ideally, this script should be written in C. It is a bit slow at present. + +use strict; +use warnings; +use Getopt::Std; + +my %opts; +my $version = '0.1.2'; +my $usage = qq{ +Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <outfile3> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual> + +Note: <in.title> is the string showed in the `# Title:' line of a + ".csfasta" read file. Then <in.title>F3.csfasta is read sequence + file and <in.title>F3_QV.qual is the quality file. If + <in.title>R3.csfasta is present, this script assumes reads are + paired; otherwise reads will be regarded as single-end. + + The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3 + tag and `2' for F3. Usually you may want to use short <out.prefix> + to save diskspace. Long <out.prefix> also causes troubles to maq. + +}; + +getopts('', \%opts); +die($usage) if (@ARGV != 8); +my ($is_paired,$outfile1,$outfile2,$outfile3,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV; +my (@fhr, @fhw); +my $fn = ''; +my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual); +#my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual'); +#my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0; +if ($is_paired eq "yes") { # paired end + for (0 .. 3) { + $fn = $fn_suff[$_]; + $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz"); + open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n"); + } + open($fhw[0], "|gzip >$outfile2") || die; + open($fhw[1], "|gzip >$outfile1") || die; + open($fhw[2], "|gzip >$outfile3") || die; + my (@df, @dr); + @df = &read1(1); @dr = &read1(2); + while (@df && @dr) { + if ($df[0] eq $dr[0]) { # mate pair + print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1]; + @df = &read1(1); @dr = &read1(2); + } else { + if ($df[0] le $dr[0]) { + print {$fhw[2]} $df[1]; + @df = &read1(1); + } else { + print {$fhw[2]} $dr[1]; + @dr = &read1(2); + } + } + } + if (@df) { + print {$fhw[2]} $df[1]; + while (@df = &read1(1, $fhr[0], $fhr[1])) { + print {$fhw[2]} $df[1]; + } + } + if (@dr) { + print {$fhw[2]} $dr[1]; + while (@dr = &read1(2, $fhr[2], $fhr[3])) { + print {$fhw[2]} $dr[1]; + } + } + close($fhr[$_]) for (0 .. $#fhr); + close($fhw[$_]) for (0 .. $#fhw); +} else { # single end + for (0 .. 1) { + my $fn = "$fn_suff[$_]"; + $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz"); + open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n"); + } + open($fhw[2], "|gzip >$outfile1") || die; + my @df; + while (@df = &read1(1, $fhr[0], $fhr[1])) { + print {$fhw[2]} $df[1]; + } + close($fhr[$_]) for (0 .. $#fhr); + close($fhw[2]); +} + +sub read1 { + my $i = shift(@_); + my $j = ($i-1)<<1; + my ($key, $seq); + my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]); + while (<$fhs>) { + my $t = <$fhq>; + if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) { + $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines + #print $key; + die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t); + my $name = "$1_$2_$3/$i"; + $_ = substr(<$fhs>, 2); + tr/0123./ACGTN/; + my $s = $_; + $_ = <$fhq>; + s/^(\d+)\s*//; + s/(\d+)\s*/chr($1+33)/eg; + $seq = qq/\@$name\n$s+\n$_\n/; + last; + } + } + return defined($seq)? ($key, $seq) : (); +} diff -r 76759e07013b -r 16993bf0803e tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Fri Sep 18 11:11:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Fri Sep 18 12:11:43 2009 -0400 @@ -41,6 +41,7 @@ parser.add_option('', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good') parser.add_option('', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings') parser.add_option('', '--dbkey', dest='dbkey', help='') + parser.add_option('', '--suppressHeader', dest='suppressHeader', help='Suppress header') (options, args) = parser.parse_args() # index if necessary @@ -119,5 +120,29 @@ # clean up temp files tmp_align_out.close() tmp_align_out2.close() + # remove header if necessary + if options.suppressHeader == 'true': + tmp_out = tempfile.NamedTemporaryFile() + cmd4 = 'cp %s %s' % (options.output, tmp_out.name) + try: + os.system(cmd4) + except Exception, erf: + stop_err("Error copying output file before removing headers\n" + str(erf)) + output = file(tmp_out.name, 'r') + fout = file(options.output, 'w') + header = True + line = output.readline() + while line.strip() != '': + if header: + if line.startswith('@HD') or line.startswith('@SQ') or line.startswith('@RG') or line.startswith('@PG') or line.startswith('@CO'): + pass + else: + header = False + fout.write(line) + else: + fout.write(line) + line = output.readline() + fout.close() + tmp_out.close() if __name__=="__main__": __main__() diff -r 76759e07013b -r 16993bf0803e tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Sep 18 11:11:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Sep 18 12:11:43 2009 -0400 @@ -61,6 +61,7 @@ #else: --dbkey="None" #end if + --suppressHeader=$suppressHeader </command> <inputs> <conditional name="solidOrSolexa"> @@ -151,6 +152,7 @@ <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> </when> </conditional> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> </inputs> <outputs> <data format="sam" name="output" /> @@ -163,6 +165,7 @@ <param name="sPaired" value="single" /> <param name="input1" value="bwa_wrapper_in1.fastq" /> <param name="source_select" value="pre_set" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0.sam" ftype="sam" /> </test> <test> @@ -172,6 +175,7 @@ <param name="sPaired" value="single" /> <param name="input1" value="bwa_wrapper_in0.fastq" /> <param name="source_select" value="pre_set" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0b.sam" ftype="sam" /> </test> <test> @@ -198,6 +202,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" /> </test> <test> @@ -225,6 +230,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" /> </test> <test> @@ -251,6 +257,7 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" /> </test> <test> @@ -278,8 +285,9 @@ <param name="outputTopN" value="-1" /> <param name="maxInsertSize" value="500" /> <param name="maxOccurPairing" value="100000" /> + <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" /> - </test> + </test> </tests> <help>

1 0

[hg] galaxy 2714: small tweaks
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/76759e07013b changeset: 2714:76759e07013b user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 18 11:11:41 2009 -0400 description: small tweaks 2 file(s) affected in this change: tools/metag_tools/split_paired_reads.xml tools/sr_mapping/bowtie_wrapper.xml diffs (26 lines): diff -r 5ffb934ab613 -r 76759e07013b tools/metag_tools/split_paired_reads.xml --- a/tools/metag_tools/split_paired_reads.xml Fri Sep 18 10:40:53 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.xml Fri Sep 18 11:11:41 2009 -0400 @@ -7,8 +7,8 @@ <param name="input" type="data" format="fastqsolexa,fastqsanger" label="Your paired-end file" /> </inputs> <outputs> - <data name="output1" format="fastqsolexa"/> - <data name="output2" format="fastqsolexa"/> + <data name="output1" format="input"/> + <data name="output2" format="input"/> </outputs> <tests> <test> diff -r 5ffb934ab613 -r 76759e07013b tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 18 10:40:53 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Fri Sep 18 11:11:41 2009 -0400 @@ -275,7 +275,7 @@ <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> <conditional name="params"> - <param name="settings_type" type="select" label="BWA settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <param name="settings_type" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="pre_set">Commonly used</option> <option value="full">Full parameter list</option> </param>

1 0

[hg] galaxy 2713: getting rid of maq
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5ffb934ab613 changeset: 2713:5ffb934ab613 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 18 10:40:53 2009 -0400 description: getting rid of maq 1 file(s) affected in this change: tool_conf.xml.sample diffs (11 lines): diff -r c1e0a15b5cd5 -r 5ffb934ab613 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 10:29:34 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:40:53 2009 -0400 @@ -192,7 +192,6 @@ <section name="SOLiD: QC" id="solid_tools"> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> - <tool file="solid_tools/maq_cs_wrapper.xml" /> </section> <section name="NGS: Mapping" id="solexa_tools"> <tool file="sr_mapping/lastz_wrapper.xml" />

1 0

[hg] galaxy 2707: Two fixes - functional tests should pass.
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bac909f808c2 changeset: 2707:bac909f808c2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Sep 17 09:08:37 2009 -0400 description: Two fixes - functional tests should pass. 3 file(s) affected in this change: lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/user.py templates/admin/user/grid.mako diffs (39 lines): diff -r a9c4d314ac89 -r bac909f808c2 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Wed Sep 16 16:00:09 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Thu Sep 17 09:08:37 2009 -0400 @@ -539,8 +539,8 @@ message = 'Enter a real email address' elif len( email) > 255: message = 'Email address exceeds maximum allowable length' - elif trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first(): - message = 'A user with that email already exists' + elif trans.app.model.User.filter_by( email=email ).all(): + message = 'User with that email already exists' elif len( password ) < 6: message = 'Use a password of at least 6 characters' elif password != confirm: diff -r a9c4d314ac89 -r bac909f808c2 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Wed Sep 16 16:00:09 2009 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu Sep 17 09:08:37 2009 -0400 @@ -177,8 +177,7 @@ email_error = "Please enter a real email address" elif len( email ) > 255: email_error = "Email address exceeds maximum allowable length" - elif trans.app.model.User.filter( and_( trans.app.model.User.table.c.email==email, - trans.app.model.User.table.c.deleted==False ) ).first(): + elif trans.app.model.User.filter_by( email=email ).all(): email_error = "User with that email already exists" elif len( password ) < 6: password_error = "Please use a password of at least 6 characters" diff -r a9c4d314ac89 -r bac909f808c2 templates/admin/user/grid.mako --- a/templates/admin/user/grid.mako Wed Sep 16 16:00:09 2009 -0400 +++ b/templates/admin/user/grid.mako Thu Sep 17 09:08:37 2009 -0400 @@ -95,7 +95,7 @@ No users were returned for the current query. Click the Show all users button or a letter below. %endif: <% - letters = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z', '0'] + letters = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] %> <div class="toolFormBody"> <div class="form-row">

1 0

[hg] galaxy 2709: html escaping for tags
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8fc33cdc1857 changeset: 2709:8fc33cdc1857 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 17 12:45:36 2009 -0400 description: html escaping for tags 4 file(s) affected in this change: lib/galaxy/web/framework/helpers/__init__.py static/scripts/autocomplete_tagging.js static/scripts/packed/autocomplete_tagging.js templates/tagging_common.mako diffs (116 lines): diff -r 2afb7110c649 -r 8fc33cdc1857 lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py Thu Sep 17 11:47:37 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/__init__.py Thu Sep 17 12:45:36 2009 -0400 @@ -3,6 +3,7 @@ pkg_resources.require( "WebHelpers" ) from webhelpers import * +from galaxy.util.json import to_json_string from datetime import datetime, timedelta # If the date is more than one week ago, then display the actual date instead of in words diff -r 2afb7110c649 -r 8fc33cdc1857 static/scripts/autocomplete_tagging.js --- a/static/scripts/autocomplete_tagging.js Thu Sep 17 11:47:37 2009 -0400 +++ b/static/scripts/autocomplete_tagging.js Thu Sep 17 12:45:36 2009 -0400 @@ -49,7 +49,7 @@ // Tag area. var area_id = "tag-area-" + (ac_tag_area_id_gen)++; - var tag_area = $("<div></div>").attr("id", area_id).addClass("tag-area"); + var tag_area = $("<div>").attr("id", area_id).addClass("tag-area"); this.append(tag_area); // @@ -72,7 +72,7 @@ var build_toggle_link = function() { var link_text = settings.get_toggle_link_text_fn(settings.tags); - var toggle_link = $("<a href='/history/tags'>" + link_text + "</a>").addClass("toggle-link"); + var toggle_link = $("<a href='/history/tags'>").text(link_text).addClass("toggle-link"); // Link toggles the display state of the tag area. toggle_link.click( function() { @@ -238,7 +238,7 @@ }); // Build tag button. - var tag_name_elt = $("<span>" + tag_str + "</span>").addClass("tag-name"); + var tag_name_elt = $("<span>").text(tag_str).addClass("tag-name"); tag_name_elt.click( function() { settings.tag_click_fn(tag_str); @@ -261,10 +261,10 @@ var t; if (settings.in_form) t = $( "<textarea id='history-tag-input' rows='1' cols='" + - settings.input_size + "' value='" + tag_text + "'></textarea>" ); + settings.input_size + "' value='" + escape(tag_text) + "'></textarea>" ); else // element not in form. t = $( "<input id='history-tag-input' type='text' size='" + - settings.input_size + "' value='" + tag_text + "'></input>" ); + settings.input_size + "' value='" + escape(tag_text) + "'></input>" ); t.keyup( function( e ) { if ( e.keyCode == 27 ) diff -r 2afb7110c649 -r 8fc33cdc1857 static/scripts/packed/autocomplete_tagging.js --- a/static/scripts/packed/autocomplete_tagging.js Thu Sep 17 11:47:37 2009 -0400 +++ b/static/scripts/packed/autocomplete_tagging.js Thu Sep 17 12:45:36 2009 -0400 @@ -1,1 +1,1 @@ -var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u){},input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div></div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>"+u+"</a>").addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};var s=b(); if(p.use_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E.after(D) }else{m.prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>"+u+"</span>").addClass("tag-name");w.click(function(){p.tag_click_fn(u);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);x.append(v);return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+v+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+v+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1){thi s.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,formatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag-input ");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false});if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file +var ac_tag_area_id_gen=1;jQuery.fn.autocomplete_tagging=function(c){var e={get_toggle_link_text_fn:function(u){var w="";var v=o(u);if(v!=0){w=v+(v!=0?" Tags":" Tag")}else{w="Add tags"}return w},tag_click_fn:function(u){},input_size:20,in_form:false,tags:{},use_toggle_link:true,item_id:"",add_tag_img:"",add_tag_img_rollover:"",delete_tag_img:"",ajax_autocomplete_tag_url:"",ajax_retag_url:"",ajax_delete_tag_url:"",ajax_add_tag_url:""};var p=jQuery.extend(e,c);var k="tag-area-"+(ac_tag_area_id_gen)++;var m=$("<div>").attr("id",k).addClass("tag-area");this.append(m);var o=function(u){if(u.length){return u.length}var v=0;for(element in u){v++}return v};var b=function(){var u=p.get_toggle_link_text_fn(p.tags);var v=$("<a href='/history/tags'>").text(u).addClass("toggle-link");v.click(function(){var w=(m.css("display")=="none");var x;if(w){x=function(){var y=o(p.tags);if(y==0){m.click()}}}else{x=function(){m.blur()}}m.slideToggle("fast",x);return false});return v};var s=b();if(p.us e_toggle_link){this.prepend(s)}var t=function(u){var v=new Array();for(key in u){v[v.length]=key+"-->"+u[key]}return"{"+v.join(",")+"}"};var a=function(v,u){return v+((u!=""&&u)?":"+u:"")};var h=function(u){return u.split(":")};var i=function(u){var v=$("<img src='"+p.add_tag_img+"' rollover='"+p.add_tag_img_rollover+"'/>").addClass("add-tag-button");v.click(function(){$(this).hide();m.click();return false});return v};var j=function(u){var v=$("<img src='"+p.delete_tag_img+"'/>").addClass("delete-tag-img");v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)});v.click(function(){var D=$(this).parent();var C=D.find(".tag-name").eq(0);var B=C.text();var z=h(B);var F=z[0];var y=z[1];var E=D.prev();D.remove();delete p.tags[F];var A=p.get_toggle_link_text_fn(p.tags);s.text(A);$.ajax({url:p.ajax_delete_tag_url,data:{tag_name:F},error:function(){p.tags[F]=y;if(E.hasClass("tag-button")){E.after(D)}else{m .prepend(D)}var G=p.get_toggle_link_text_fn(p.tags);alert("Remove tag failed");s.text(G);v.mouseenter(function(){$(this).attr("src",p.delete_tag_img_rollover)});v.mouseleave(function(){$(this).attr("src",p.delete_tag_img)})},success:function(){}});return true});var w=$("<span>").text(u).addClass("tag-name");w.click(function(){p.tag_click_fn(u);return true});var x=$("<span></span>").addClass("tag-button");x.append(w);x.append(v);return x};var d=function(v){var u;if(p.in_form){u=$("<textarea id='history-tag-input' rows='1' cols='"+p.input_size+"' value='"+escape(v)+"'></textarea>")}else{u=$("<input id='history-tag-input' type='text' size='"+p.input_size+"' value='"+escape(v)+"'></input>")}u.keyup(function(D){if(D.keyCode==27){$(this).trigger("blur")}else{if((D.keyCode==13)||(D.keyCode==188)||(D.keyCode==32)){new_value=this.value;if(return_key_pressed_for_autocomplete==true){return_key_pressed_for_autocomplete=false;return false}if(new_value.indexOf(": ",new_value.length-2)!=-1 ){this.value=new_value.substring(0,new_value.length-1);return false}if((D.keyCode==188)||(D.keyCode==32)){new_value=new_value.substring(0,new_value.length-1)}new_value=new_value.replace(/^\s+|\s+$/g,"");if(new_value.length<3){return false}this.value="";var A=j(new_value);var z=m.children(".tag-button");if(z.length!=0){var E=z.slice(z.length-1);E.after(A)}else{m.prepend(A)}var y=new_value.split(":");p.tags[y[0]]=y[1];var B=p.get_toggle_link_text_fn(p.tags);s.text(B);var C=$(this);$.ajax({url:p.ajax_add_tag_url,data:{new_tag:new_value},error:function(){A.remove();delete p.tags[y[0]];var F=p.get_toggle_link_text_fn(p.tags);s.text(F);alert("Add tag failed")},success:function(){C.flushCache()}});return false}}});var w=function(A,z,y,C,B){tag_name_and_value=C.split(":");return(tag_name_and_value.length==1?tag_name_and_value[0]:tag_name_and_value[1])};var x={selectFirst:false,formatItem:w,autoFill:false,highlight:false};u.autocomplete(p.ajax_autocomplete_tag_url,x);u.addClass("tag- input");return u};for(tag_name in p.tags){var q=p.tags[tag_name];var l=a(tag_name,q);var g=j(l,s,p.tags);m.append(g)}var n=d("");var f=i(n);m.blur(function(u){r=o(p.tags);if(r!=0){f.show();n.hide();m.removeClass("active-tag-area")}else{}});m.append(f);m.append(n);n.hide();m.click(function(w){var v=$(this).hasClass("active-tag-area");if($(w.target).hasClass("delete-tag-img")&&!v){return false}if($(w.target).hasClass("tag-name")&&!v){return false}$(this).addClass("active-tag-area");f.hide();n.show();n.focus();var u=function(y){var x=m.attr("id");if(($(y.target).attr("id")!=x)&&($(y.target).parents().filter(x).length==0)){m.blur();$(document).unbind("click",u)}};$(window).click(u);return false});if(p.use_toggle_link){m.hide()}else{var r=o(p.tags);if(r==0){f.hide();n.show()}}return this.addClass("tag-element")}; \ No newline at end of file diff -r 2afb7110c649 -r 8fc33cdc1857 templates/tagging_common.mako --- a/templates/tagging_common.mako Thu Sep 17 11:47:37 2009 -0400 +++ b/templates/tagging_common.mako Thu Sep 17 12:45:36 2009 -0400 @@ -7,13 +7,13 @@ // <% ## Build string of tag name, values. - tag_names_and_values = list() + tag_names_and_values = dict() for tag in tagged_item.tags: tag_name = tag.user_tname tag_value = "" if tag.value is not None: tag_value = tag.user_value - tag_names_and_values.append( ("\"" + tag_name + "\" : \"" + tag_value + "\"") ) + tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') %> // // Returns the number of keys (elements) in an array/dictionary. @@ -71,20 +71,20 @@ var options = { - tags : {${unicode(", ".join(tag_names_and_values), 'utf-8')}}, - get_toggle_link_text_fn: get_toggle_link_text, - tag_click_fn: function(tag) { /* Do nothing. */ }, - <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> - ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", - delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", - add_tag_img: "${h.url_for('/static/images/add_icon.png')}", - add_tag_img_rollover: "${h.url_for('/static/images/add_icon_dark.png')}", - input_size: ${input_size}, - in_form: ${in_form}, - use_toggle_link: ${use_toggle_link} + tags : ${h.to_json_string(tag_names_and_values)}, + get_toggle_link_text_fn: get_toggle_link_text, + tag_click_fn: function(tag) { /* Do nothing. */ }, + <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> + ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", + delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", + add_tag_img: "${h.url_for('/static/images/add_icon.png')}", + add_tag_img_rollover: "${h.url_for('/static/images/add_icon_dark.png')}", + input_size: ${input_size}, + in_form: ${in_form}, + use_toggle_link: ${use_toggle_link} }; $("#${elt_id}").autocomplete_tagging(options)

1 0

[hg] galaxy 2708: Add a MAF to Interval converter that produces ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2afb7110c649 changeset: 2708:2afb7110c649 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 17 11:47:37 2009 -0400 description: Add a MAF to Interval converter that produces a set of intervals with sequence data. 7 file(s) affected in this change: test-data/maf_to_interval_out_hg17.interval test-data/maf_to_interval_out_panTro1.interval tool_conf.xml.main tool_conf.xml.sample tools/maf/maf_reverse_complement.xml tools/maf/maf_to_interval.py tools/maf/maf_to_interval.xml diffs (246 lines): diff -r bac909f808c2 -r 2afb7110c649 test-data/maf_to_interval_out_hg17.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_to_interval_out_hg17.interval Thu Sep 17 11:47:37 2009 -0400 @@ -0,0 +1,2 @@ +#chrom start end strand score name bosTau2 canFam2 dasNov1 hg17 mm7 panTro1 rheMac2 rn3 +chr7 127471910 127472074 + 94204.0 hg17_5_0 atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA CAGTGAGCAA-----------------------------------------------------------------------------------------------CAGCCTGGCTCCGT-CC--GGGGGCCGCTCAGCAGCTC-GGGAGCGTGGAGACG---GGAAGTCTGTCACGCGATGCG-----------CTGGGCCCG------------CTGTTCCCGCCCCCCTCC---CCCC----------------TTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGA AACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG caaaaaccaa------------------------------------------------------------------------------------------------aaaaACCTATAGC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G --ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTTGTG CTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG diff -r bac909f808c2 -r 2afb7110c649 test-data/maf_to_interval_out_panTro1.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/maf_to_interval_out_panTro1.interval Thu Sep 17 11:47:37 2009 -0400 @@ -0,0 +1,2 @@ +#chrom start end strand score name bosTau2 canFam2 dasNov1 hg17 mm7 panTro1 rheMac2 rn3 +chr6 129885791 129885955 + 94204.0 panTro1_5_0 atgtgaacaa---------------------------------------------------------------------------------------------aacggacccgtgtgggactcggcggagcacacagattttgcgggagCACGTTCCCGTTAGGAAGTCTCTGATGCAATACGACCGGTGCCTTCAGGACCTG-TG--AGGCTGACTTTCCTTA-CCCCTCCACACCATCATCAAGGCAGGTGTGATTTTCCAGG cagtgaacaa---------------------------------------------------------------------------------------------aacagagccctgcagt-cttgatggagcacacaacctttg-gggaaCATGTTTCCATAAGAAAGTCTCCAATGTGATCTGA-TGGTGCCGCCAGGACCTA-TGTCAGCCTACCGTTCCATGTCCCCTCCACACCATCATCACTGCAGGTGTGTTTTCCCACA CAGTGAGCAA-----------------------------------------------------------------------------------------------CAGCCTGGCTCCGT-CC--GGGGGCCGCTCAGCAGCTC-GGGAGCGTGGAGACG---GGAAGTCTGTCACGCGATGCG-----------CTGGGCCCG------------CTGTTCCCGCCCCCCTCC---CCCC----------------TTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG- GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACCTG-TGTGATCCTGGCTTTTCCTGTTCCCTCCG---CATCATCACTGCAGGTGTGTTTTCCCAAG caaaaaccaa------------------------------------------------------------------------------------------------aaaaACCTATAGC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAACATGCATCCGCTAGAAAGTCCCAAGTACACTATGACAGTTG--CCCAGGCCCCGCCTTAAACCTGGTTTTCCTGGTTTCTTTCA---CATCATTACCACGAATATATTTCCTCAAG caatgaccaa----------------------------------------------------------------------------------------------atagactcctaccaa-ctc-aaagaatgcacattctCTG-GGAAACATGTTTCCATTAGGAAGCCTCGAATGCAATGTGACTGTGGTCTCCAGGACATG-TGTGATCCTGGCTTTTCCTGTTCCCTCTG---CATCATCACTGCAGGTGTATTTTCCCAAG caatgaccaa----------------------------------------------------------------------------------------------atagacccctaccga-ctc-aaagaatgtacattctTTG-GGAAACATGTTTCCATCAGAAAATCTCAAATGCAATGTGACTGGGGTCTCCAGGACCTG-TGTGAGCCTGGCTTTTCCTGTTCCCTCCA---CATCATCACTGCAGGTGTATTTTCCC--G --ATGACCAATATACACTGTTTACATGTATAGCATTGTGAATGGAGACATAAAAAGATAATCTAGCTTT GTGCTAGGTAGGTGCTGAGCTCTTAACAGTGCTGGGCAGAAACCTATAAC-CTC-ACAGGGTGGGTTGTCTTTG-AGGAGCGTGCTAACCCTAGGAAGTCTCAAATACAATGTGATGGTTGCCCCCAGGCACCACCTTGAACCTGGTCTTCCTGGTTTCTTTCA---CACCATTACCACAAATACATTTTCTCAGG diff -r bac909f808c2 -r 2afb7110c649 tool_conf.xml.main --- a/tool_conf.xml.main Thu Sep 17 09:08:37 2009 -0400 +++ b/tool_conf.xml.main Thu Sep 17 11:47:37 2009 -0400 @@ -40,6 +40,7 @@ <tool file="fasta_tools/fasta_to_tabular.xml" /> <tool file="filters/gff2bed.xml" /> <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> </section> diff -r bac909f808c2 -r 2afb7110c649 tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Sep 17 09:08:37 2009 -0400 +++ b/tool_conf.xml.sample Thu Sep 17 11:47:37 2009 -0400 @@ -75,6 +75,7 @@ <tool file="filters/gff2bed.xml" /> <tool file="filters/lav_to_bed.xml" /> <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> <tool file="next_gen_conversion/solid_to_fastq.xml" /> diff -r bac909f808c2 -r 2afb7110c649 tools/maf/maf_reverse_complement.xml --- a/tools/maf/maf_reverse_complement.xml Thu Sep 17 09:08:37 2009 -0400 +++ b/tools/maf/maf_reverse_complement.xml Thu Sep 17 11:47:37 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="MAF_Reverse_Complement_1" name="Reverse Compliment" version="1.0.1"> +<tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1"> <description>a MAF file</description> <command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command> <inputs> diff -r bac909f808c2 -r 2afb7110c649 tools/maf/maf_to_interval.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/maf_to_interval.py Thu Sep 17 11:47:37 2009 -0400 @@ -0,0 +1,68 @@ +#!/usr/bin/env python + +""" +Read a maf and output intervals for specified list of species. +""" +import sys, os +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.align import maf +from galaxy.tools.util import maf_utilities + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + input_filename = sys.argv[1] + output_filename = sys.argv[2] + output_id = sys.argv[3] + #where to store files that become additional output + database_tmp_dir = sys.argv[4] + primary_spec = sys.argv[5] + species = sys.argv[6].split( ',' ) + all_species = sys.argv[7].split( ',' ) + partial = sys.argv[8] + keep_gaps = sys.argv[9] + out_files = {} + + if "None" in species: + species = [] + + if primary_spec not in species: + species.append( primary_spec ) + if primary_spec not in all_species: + all_species.append( primary_spec ) + + all_species.sort() + for spec in species: + if spec == primary_spec: + out_files[ spec ] = open( output_filename, 'wb+' ) + else: + out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' ) + out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) ) + num_species = len( all_species ) + + file_in = open( input_filename, 'r' ) + maf_reader = maf.Reader( file_in ) + + for i, m in enumerate( maf_reader ): + for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ): + if len( block.components ) < num_species and partial == "partial_disallowed": continue + sequences = {} + for c in block.components: + spec, chrom = maf_utilities.src_split( c.src ) + if keep_gaps == 'remove_gaps': + sequences[ spec ] = c.text.replace( '-', '' ) + else: + sequences[ spec ] = c.text + sequences = '\t'.join( [ sequences.get( spec, '' ) for spec in all_species ] ) + for spec in species: + c = block.get_component_by_src_start( spec ) + if c is not None: + spec2, chrom = maf_utilities.src_split( c.src ) + assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) ) + out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) ) + file_in.close() + for file_out in out_files.values(): + file_out.close() + +if __name__ == "__main__": __main__() diff -r bac909f808c2 -r 2afb7110c649 tools/maf/maf_to_interval.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/maf_to_interval.xml Thu Sep 17 11:47:37 2009 -0400 @@ -0,0 +1,127 @@ +<tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"> + <description>Converts a MAF formated file to the Interval format</description> + <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command> + <inputs> + <param format="maf" name="input1" type="data" label="MAF file to convert"/> + <param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species."> + <options> + <filter type="data_meta" ref="input1" key="species" /> + <filter type="remove_value" meta_ref="input1" key="dbkey" /> + </options> + </param> + <param name="complete_blocks" type="select" label="Exclude blocks which have a species missing"> + <option value="partial_allowed">include blocks with missing species</option> + <option value="partial_disallowed">exclude blocks with missing species</option> + </param> + <param name="remove_gaps" type="select" label="Remove Gap characters from sequences"> + <option value="keep_gaps">keep gaps</option> + <option value="remove_gaps">remove gaps</option> + </param> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="4.maf" dbkey="hg17"/> + <param name="complete_blocks" value="partial_disallowed"/> + <param name="remove_gaps" value="keep_gaps"/> + <param name="species" value="panTro1" /> +  + <output name="out_file1" file="maf_to_interval_out_panTro1.interval"/> + </test> + </tests> + <help> + +**What it does** + +This tool converts every MAF block to a set of genomic intervals describing the position of that alignment block within a corresponding genome. Sequences from aligning species are also included in the output. + +The interface for this tool contains several options: + + * **MAF file to convert**. Choose multiple alignments from history to be converted to BED format. + * **Choose species**. Choose additional species from the alignment to be included in the output + * **Exclude blocks which have a species missing**. if an alignment block does not contain any one of the species found in the alignment set and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below). + * **Remove Gap characters from sequences**. Gaps can be removed from sequences before they are output. + + +----- + +**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**: + +For the following alignment:: + + ##maf version=1 + a score=68686.000000 + s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- + s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- + s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- + s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- + s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C + + a score=10289.000000 + s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG + s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG + s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG + +the tool will create **a single** history item containing the following (**note** the name field is numbered iteratively: hg18_0_0, hg18_1_0 etc. where the first number is the block number and the second number is the iteration through the block (if a species appears twice in a block, that interval will be repeated) and sequences for each species are included in the order specified in the header: the field is left empty when no sequence is available for that species):: + + #chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2 + chr20 56827368 56827443 + 68686.0 hg18_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- + chr20 56827443 56827480 + 10289.0 hg18_1_0 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG + + +----- + +**Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**: + +For the following alignment:: + + ##maf version=1 + a score=68686.000000 + s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- + s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- + s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- + s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- + s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C + + a score=10289.000000 + s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG + s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG + s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG + +the tool will create **two** history items (one for hg18 and one for mm8) containing the following (**note** that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8): + +History item **1** (for hg18):: + + #chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2 + chr20 56827368 56827443 + 68686.0 hg18_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- + + +History item **2** (for mm8):: + + #chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2 + chr2 173910832 173910893 + 68686.0 mm8_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- + + +------- + +.. class:: infomark + +**About formats** + +**MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes. + + - The .maf format is line-oriented. Each multiple alignment ends with a blank line. + - Each sequence in an alignment is on a single line. + - Lines starting with # are considered to be comments. + - Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment. + - Some MAF files may contain two optional line types: + + - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; + - An "e" line containing information about the size of the gap between the alignments that span the current block. + + + </help> +</tool> +

1 0

[hg] galaxy 2711: First pass of consolidating NGS tools
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8d3037d55621 changeset: 2711:8d3037d55621 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 18 10:27:03 2009 -0400 description: First pass of consolidating NGS tools 2 file(s) affected in this change: tool_conf.xml.sample tools/samtools/sam2interval.xml diffs (117 lines): diff -r cf02fb92ee6a -r 8d3037d55621 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 10:15:09 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:27:03 2009 -0400 @@ -19,14 +19,6 @@ <tool file="data_source/epigraph_import_test.xml" /> <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> - </section> - <section name="Get ENCODE Data" id="encode"> - <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/> - <tool file="data_source/encode_import_genes_and_transcripts.xml"/> - <tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/> - <tool file="data_source/encode_import_transcription_regulation.xml"/> - <tool file="data_source/encode_import_all_latest_datasets.xml" /> - <tool file="data_source/encode_import_gencode.xml" /> </section> <section name="Send Data" id="send"> <tool file="data_destination/epigraph.xml" /> @@ -167,17 +159,63 @@ <tool file="taxonomy/lca.xml" /> <tool file="taxonomy/poisson2test.xml" /> </section> - <section name="Solexa tools" id="solexa_tools"> - <tool file="sr_mapping/fastq_statistics.xml" /> - <tool file="sr_mapping/lastz_wrapper.xml" /> - </section> -  + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> +  + <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> + <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> + <tool file="fastx_toolkit/fastq_quality_filter.xml" /> +  + <tool file="metag_tools/split_paired_reads.xml" /> + </section> + <section name="454: QC" id="short_read_analysis"> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + </section> + <section name="SOLiD: QC" id="solid_tools"> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <tool file="solid_tools/maq_cs_wrapper.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + </section> + <section name="NGS: SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + </section> + -  + +======= --> <section name="SOLiD Data Analysis" id="solid_tools"> <tool file="solid_tools/solid_qual_stats.xml" /> @@ -351,4 +392,5 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> +>>>>>>> other </toolbox> diff -r cf02fb92ee6a -r 8d3037d55621 tools/samtools/sam2interval.xml --- a/tools/samtools/sam2interval.xml Fri Sep 18 10:15:09 2009 -0400 +++ b/tools/samtools/sam2interval.xml Fri Sep 18 10:27:03 2009 -0400 @@ -31,7 +31,7 @@ **What it does** -Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. To calculate the end position the tool uses the CIGAR string. +Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is usd to compute the end coordinate. -----

1 0

[hg] galaxy 2710: Added the Pileup-to-Interval tool to condense ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cf02fb92ee6a changeset: 2710:cf02fb92ee6a user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Sep 18 10:15:09 2009 -0400 description: Added the Pileup-to-Interval tool to condense pileup format 7 file(s) affected in this change: test-data/pileup_interval_in1.tabular test-data/pileup_interval_in2.tabular test-data/pileup_interval_out1.tabular test-data/pileup_interval_out2.tabular tool_conf.xml.sample tools/samtools/pileup_interval.py tools/samtools/pileup_interval.xml diffs (559 lines): diff -r 8fc33cdc1857 -r cf02fb92ee6a test-data/pileup_interval_in1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_interval_in1.tabular Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,118 @@ +chr1 1 G 3 , 3 +chr1 5 A 5 , I +chr1 10 T 2 , I +chr1 11 C 3 , I +chr1 12 G 4 , I +chr1 13 C 2 , I +chr1 14 A 3 , I +chr1 15 T 3 , 6 +chr1 16 A 2 , 3 +chr1 17 T 4 , I +chr1 2735 C 3 , I +chrM 2736 t 3 , 9 +chrM 2737 t 3 , I +chrM 2738 a 3 , I +chrM 2739 c 3 , I +chrM 2740 a 3 , I +chrM 2741 c 3 , I +chrM 2742 t 4 , 5 +chrM 2743 c 5 , I +chrM 2744 a 2 , I +chrM 2745 g 1 , I +chrM 2746 a 1 , I +chrM 2747 g 1 , I +chrM 2748 g 1 , I +chrM 2749 t 1 , I +chrM 2750 t 1 , I +chrM 2751 c 1 , I +chrM 2752 a 1 , I +chrM 2753 a 1 , I +chrM 2754 c 1 , I +chrM 2755 t 1 , I +chrM 2756 c 1 , I +chrM 2757 c 1 , I +chrM 2758 t 5 , I +chrM 2759 c 3 , I +chrM 2760 t 1 , I +chrM 2761 c 1 , I +chrM 2762 c 1 n " +chrM 2763 c 1 n " +chrM 2764 t 1 , I +chrM 2765 a 1 , I +chrM 2766 a 1 , I +chrM 2767 c 1 , I +chrM 2768 a 1 , I +chrM 2769 a 1 , I +chrM 2770 c 1 ,$ I +chrM 9563 C 1 ^:, I +chrM 9564 T 1 , + +chrM 9565 G 1 , - +chrM 9566 A 1 , I +chrM 9567 C 1 , I +chrM 9568 T 1 , ? +chrM 9569 A 1 , I +chrM 9570 C 1 , D +chrM 9571 C 1 , I +chrM 9572 A 1 , I +chrM 9573 C 1 , I +chrM 9574 A 1 , I +chrM 9575 A 1 , I +chrM 9576 C 1 , I +chrM 9577 T 1 , I +chrM 9578 A 1 , I +chrM 9579 A 1 , I +chrM 9580 A 1 , I +chrM 9581 C 1 , I +chrM 9582 A 1 , I +chrM 9583 T 1 , I +chrM 9584 C 1 , I +chrM 9585 T 1 , I +chrM 9586 A 1 , I +chrM 9587 T 1 , I +chrM 9588 G 1 , I +chrM 9589 C 1 , I +chrM 9590 A 1 n " +chrM 9591 G 1 n " +chrM 9592 A 1 , I +chrM 9593 A 1 , I +chrM 9594 A 1 , I +chrM 9595 A 1 , I +chrM 9596 A 1 , I +chrM 9597 A 1 , I +chrM 9598 C 1 ,$ I +chrM 10864 T 1 ^!, ~ +chrM 10865 G 1 , ~ +chrM 10866 T 1 , ~ +chrM 10867 A 1 , ~ +chrM 10868 G 1 , ~ +chrM 10869 A 1 , ~ +chrM 10870 A 1 , ~ +chrM 10871 G 1 , ~ +chrM 10872 C 1 , ~ +chrM 10873 C 3 , ~ +chrM 10874 C 3 , ~ +chrM 10875 C 3 , ~ +chrM 10876 A 3 , ~ +chrM 10877 A 3 , ~ +chrM 10878 T 3 , ~ +chrM 10879 T 3 , ~ +chrM 10880 G 3 , ~ +chrM 10881 C 3 , ~ +chrM 10882 C 3 , ~ +chrM 10883 G 3 , ~ +chrM 10884 G 3 , ~ +chrM 10885 A 1 , ~ +chrM 10886 T 1 , ~ +chrM 10887 C 1 , ~ +chrM 10888 C 1 , ~ +chrM 10889 A 1 , ~ +chrM 10890 T 1 , ~ +chrM 10891 A 1 n ~ +chrM 10892 G 1 n ~ +chrM 10893 T 1 , ~ +chrM 10894 G 1 , ~ +chrM 10895 C 1 , ~ +chrM 10896 T 3 , ~ +chrM 10897 A 3 , ~ +chrM 10898 G 3 , ~ +chrM 10899 C 3 ,$ ~ diff -r 8fc33cdc1857 -r cf02fb92ee6a test-data/pileup_interval_in2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_interval_in2.tabular Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,99 @@ +chr1 5016020 t T 33 0 25 2 .. II +chr1 5016021 g G 32 0 25 2 .. )I +chr1 5016022 t T 28 0 25 2 .. I$ +chr1 5016023 t T 33 0 25 2 .. II +chr1 5016024 t T 33 0 25 2 .. II +chr1 5016025 c C 39 0 25 4 ..^:,^:, II:/ +chr1 5016026 t T 28 0 25 4 ..,c III$ +chr1 5016027 c C 39 0 25 4 ..,, H0+7 +chr1 5016028 t T 28 0 25 4 ..,g III$ +chr1 5016029 g G 10 0 25 4 T.,t BII# +chr1 5016030 c C 39 0 25 4 .$.$,, @)6I +chr1 5016031 t T 33 0 25 2 ,, IF +chr1 5016032 t G 0 0 25 2 ,g IC +chr1 5016033 c C 33 0 25 2 ,, 1I +chr1 5016034 t T 33 0 25 2 ,, II +chr1 12459316 G G 7 0 0 2 .. II +chr1 12459317 G G 7 0 0 2 .. II +chr1 12459318 A A 10 0 0 3 ..^!. III +chr1 12459319 T T 10 0 0 3 ... III +chr1 12459320 C C 10 0 0 3 ... III +chr1 12459321 T T 10 0 0 3 ... III +chr1 12459322 A A 10 0 0 3 ... .II +chr1 12459323 C C 10 0 0 3 ... ?II +chr1 12459324 A A 10 0 0 3 ... G?I +chr1 12459325 C C 10 0 0 3 ... II; +chr1 12459326 A A 10 0 0 3 ... I@B +chr1 12459327 C C 10 0 0 3 ... 8II +chr1 12459328 A A 10 0 0 3 ... IH5 +chr1 12459329 T T 10 0 0 3 ... I;I +chr1 12459330 C C 10 0 0 3 ... IAI +chr1 12459331 T T 10 0 0 3 ... 3HI +chr1 49116109 C C 28 0 18 2 .. G? +chr1 49116110 A A 28 0 18 2 .. '@ +chr1 49116111 G G 26 0 18 2 .. 68 +chr1 49116112 A A 9 0 18 2 .. 1' +chr1 49116113 G G 20 0 18 2 .. I2 +chr1 49116114 G G 2 0 20 3 A.^:, &&$ +chr1 49116115 G G 21 0 20 3 .A, 8$I +chr1 49116116 T T 31 0 20 3 .., .9% +chr1 49116117 T T 36 0 20 3 .., I55 +chr1 49116118 T T 36 0 20 3 .., II+ +chr1 49116119 T T 36 0 20 3 .., II8 +chr1 49116120 G G 32 0 20 3 .., &%B +chr1 49116121 T T 36 0 20 3 .$., <63 +chr1 49116122 C C 33 0 25 2 ., +I +chr1 49116123 T T 33 0 25 2 ., -7 +chr1 49116124 G G 29 0 25 2 ., %I +chr1 49116125 C C 24 0 25 2 .$, +/ +chr1 126866554 G G 7 0 0 2 .. (I +chr1 126866555 C C 10 0 0 3 .$.^!. III +chr1 126866556 C C 7 0 0 2 .. II +chr11 1021425 C C 4 0 0 1 . I +chr11 1021426 A A 4 0 0 1 . I +chr11 1021427 G G 4 0 0 1 . I +chr11 1021428 G G 28 0 18 2 .^:. 0I +chr11 1021429 G G 19 0 18 2 C. $I +chr11 1021430 G G 36 0 20 3 ..^:. III +chr11 1021431 T T 36 0 20 3 ... III +chr11 1021432 G G 36 0 20 3 ... III +chr11 1021433 A A 36 0 20 3 ... @II +chr11 1021434 C C 36 0 20 3 ... %II +chr11 1021435 G G 36 0 20 3 ... #II +chr11 1021436 T T 36 0 20 3 ... 8II +chr11 1021437 G G 36 0 20 3 ... /II +chr11 1021438 G G 36 0 20 3 ... III +chr11 1021439 G G 36 0 20 3 ... ;II +chr11 1021440 C C 28 0 20 3 N.. "II +chr11 1021441 T T 36 0 20 3 ... IFI +chr11 1021442 G G 36 0 20 3 ... III +chr11 1021443 T T 36 0 20 3 ... III +chr11 1021444 G G 28 0 20 3 T.. #II +chr11 1021445 T T 28 0 20 3 C.. #II +chr11 1021446 C C 36 0 20 3 .$.. :II +chr11 1021447 T T 33 0 25 2 .. II +chr11 1021448 G G 33 0 25 2 .. II +chr11 1021449 T T 33 0 25 2 .. 7I +chr11 1021450 G G 33 0 25 2 .. II +chr14 1021451 T A 33 0 25 3 .. 4I +chr14 80839355 A A 33 0 25 2 .. I* +chr14 80839356 G G 28 0 25 2 .. I# +chr14 80839357 A A 31 0 25 2 .. I( +chr14 80839358 A A 32 0 25 2 .. I) +chr14 80839359 T T 39 0 25 4 ..^:,^:, I+I( +chr14 80839360 T T 39 0 25 4 ..,, I+I+ +chr14 80839361 C C 39 0 25 4 ..,, I&5( +chr14 80839362 T T 39 0 25 4 ..,, I3II +chr14 80839363 G G 39 0 25 4 ..,, G#I4 +chr14 80839364 G G 39 0 25 4 ..,, I'II +chr14 80839365 A A 39 0 25 4 ..,, @)IH +chr14 80839366 T T 39 0 25 4 ..,, I/I2 +chr14 80839367 A A 39 0 25 4 ..,, I,I= +chr14 80839368 T T 39 0 25 4 ..,, I.I7 +chr14 80839369 T T 39 0 25 4 ..,, I4II +chr14 80839370 T T 39 0 25 4 ..,, I2I0 +chr14 80839371 A A 39 0 25 4 .$.$,, ;+I? +chr14 80839372 C C 14 0 25 2 ,a 5$ +chr14 80839373 A A 33 0 25 2 ,, II +chr14 80839374 T T 33 0 25 2 ,, II +chr14 80839375 T T 33 0 25 2 ,, I? diff -r 8fc33cdc1857 -r cf02fb92ee6a test-data/pileup_interval_out1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_interval_out1.tabular Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,10 @@ +chr1 0 1 G +chr1 4 5 A +chr1 10 12 CG +chr1 13 15 AT +chr1 16 17 T +chr1 2734 2735 C +chrM 2735 2743 ttacactc +chrM 2757 2759 tc +chrM 10872 10884 CCCAATTGCCGG +chrM 10895 10899 TAGC diff -r 8fc33cdc1857 -r cf02fb92ee6a test-data/pileup_interval_out2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_interval_out2.tabular Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,7 @@ +chr1 5016024 5016030 ctctgc +chr1 12459317 12459331 ATCTACACACATCT +chr1 49116113 49116121 GGTTTTGT +chr1 126866554 126866555 C +chr11 1021429 1021446 GTGACGTGGGCTGTGTC +chr14 1021450 1021451 T +chr14 80839358 80839371 TTCTGGATATTTA diff -r 8fc33cdc1857 -r cf02fb92ee6a tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Sep 17 12:45:36 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:15:09 2009 -0400 @@ -349,5 +349,6 @@ <tool file="samtools/sam_merge.xml" /> <tool file="samtools/sam_pileup.xml" /> <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> </section> </toolbox> diff -r 8fc33cdc1857 -r cf02fb92ee6a tools/samtools/pileup_interval.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools/pileup_interval.py Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,105 @@ +#! /usr/bin/python + +""" +Creates a pileup file from a bam file and a reference. + +usage: %prog [options] + -i, --input=i: Input pileup file + -o, --output=o: Output pileup + -c, --coverage=c: Coverage + -f, --format=f: Pileup format + -b, --base=b: Base to select + -s, --seq_column=s: Sequence column + -l, --loc_column=l: Base location column + -r, --base_column=r: Reference base column + -C, --cvrg_column=C: Coverage column +""" + +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + strout = '' + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) + coverage = int(options.coverage) + fin = file(options.input, 'r') + fout = file(options.output, 'w') + inLine = fin.readline() + if options.format == 'six': + seqIndex = 0 + locIndex = 1 + baseIndex = 2 + covIndex = 3 + elif options.format == 'ten': + seqIndex = 0 + locIndex = 1 + if options.base == 'first': + baseIndex = 2 + else: + baseIndex = 3 + covIndex = 7 + else: + seqIndex = int(options.seq_column) - 1 + locIndex = int(options.loc_column) - 1 + baseIndex = int(options.base_column) - 1 + covIndex = int(options.cvrg_column) - 1 + lastSeq = '' + lastLoc = -1 + locs = [] + startLoc = -1 + bases = [] + while inLine.strip() != '': + lineParts = inLine.split('\t') + seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) +# strout += str(startLoc) + '\n' +# strout += str(bases) + '\n' +# strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov) + if loc == lastLoc+1 or lastLoc == -1: + if cov >= coverage: + if seq == lastSeq or lastSeq == '': + if startLoc == -1: + startLoc = loc + locs.append(loc) + bases.append(base) + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + startLoc = loc + locs = [loc] + bases = [base] + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + startLoc = -1 + locs = [] + bases = [] + else: + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + if cov >= coverage: + startLoc = loc + locs = [loc] + bases = [base] + else: + startLoc = -1 + locs = [] + bases = [] + lastSeq = seq + lastLoc = loc + inLine = fin.readline() + if len(bases) > 0: + fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases))) + fout.close() + fin.close() + +# import sys +# strout += file(fout.name,'r').read() +# sys.stderr.write(strout) + +if __name__ == "__main__" : __main__() diff -r 8fc33cdc1857 -r cf02fb92ee6a tools/samtools/pileup_interval.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/samtools/pileup_interval.xml Fri Sep 18 10:15:09 2009 -0400 @@ -0,0 +1,186 @@ +<tool id="pileup_interval" name="Pileup-to-Interval" version="1.0.0"> + <description>condenses pileup format into ranges of bases</description> + <command interpreter="python"> + pileup_interval.py + --input=$input + --output=$output + --coverage=$coverage + --format=$format_type.format + #if $format_type.format == "ten": + --base=$format_type.which_base + --seq_column="None" + --loc_column="None" + --base_column="None" + --cvrg_column="None" + #elif $format_type.format == "manual": + --base="None" + --seq_column=$format_type.seq_column + --loc_column=$format_type.loc_column + --base_column=$format_type.base_column + --cvrg_column=$format_type.cvrg_column + #else: + --base="None" + --seq_column="None" + --loc_column="None" + --base_column="None" + --cvrg_column="None" + #end if + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Choose a pileup file to condense:" /> + <conditional name="format_type"> + <param name="format" type="select" label="which contains:" help="See "Types of pileup datasets" below for examples"> + <option value="six" selected="true">Pileup with six columns (simple)</option> + <option value="ten">Pileup with ten columns (with consensus)</option> + <option value="manual">Set columns manually</option> + </param> + <when value="six" /> + <when value="ten"> + <param name="which_base" type="select" label="Which base do you want to concatenate"> + <option value="first" selected="true">Reference base (first)</option> + <option value="second">Consensus base (second)</option> + </param> + </when> + <when value="manual"> + <param name="seq_column" label="Select column with sequence name" type="data_column" numerical="false" data_ref="input" /> + <param name="loc_column" label="Select column with base location" type="data_column" numerical="false" data_ref="input" /> + <param name="base_column" label="Select column with base to concatenate" type="data_column" numerical="false" data_ref="input" /> + <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" /> + </when> + </conditional> + <param name="coverage" type="integer" value="3" label="Do not report bases with coverage less than:" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <test> + <param name="input" value="pileup_interval_in1.tabular" /> + <param name="format" value="six" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out1.tabular" /> + </test> + <test> + <param name="input" value="pileup_interval_in2.tabular" /> + <param name="format" value="ten" /> + <param name="which_base" value="first" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out2.tabular" /> + </test> + <test> + <param name="input" value="pileup_interval_in2.tabular" /> + <param name="format" value="manual" /> + <param name="seq_column" value="1" /> + <param name="loc_column" value="2" /> + <param name="base_column" value="3" /> + <param name="cvrg_column" value="8" /> + <param name="coverage" value="3" /> + <output name="output" file="pileup_interval_out2.tabular" /> + </test> + </tests> + <help> + +**What is does** + +Reduces the size of a results set by taking a pileup file and producing a condensed version showing consecutive sequences of bases meeting coverage criteria. The tool works on six and ten column pileup formats produced with *samtools pileup* command. You also can specify columns for the input file manually. The tool assumes that the pileup dataset was produced by *samtools pileup* command (although you can override this by setting column assignments manually). + +-------- + +**Types of pileup datasets** + +The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below. + +.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml + +**Six column pileup**:: + + 1 2 3 4 5 6 + --------------------------------- + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + +where:: + + Column Definition + ------ ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Coverage (# reads aligning over that position) + 5 Bases within reads where (see Galaxy wiki for more info) + 6 Quality values (phred33 scale, see Galaxy wiki for more) + +**Ten column pileup** + +The `ten-column`__ pileup incorporates additional consensus information generated with *-c* option of *samtools pileup* command:: + + + 1 2 3 4 5 6 7 8 9 10 + ------------------------------------------------ + chrM 412 A A 75 0 25 2 ., II + chrM 413 G G 72 0 25 4 ..t, IIIH + chrM 414 C C 75 0 25 4 ...a III2 + chrM 415 C T 75 75 25 4 TTTt III7 + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Position (1-based) + 3 Reference base at that position + 4 Consensus bases + 5 Consensus quality + 6 SNP quality + 7 Maximum mapping quality + 8 Coverage (# reads aligning over that position) + 9 Bases within reads where (see Galaxy wiki for more info) + 10 Quality values (phred33 scale, see Galaxy wiki for more) + + +.. __: http://samtools.sourceforge.net/cns0.shtml + +------ + +**The output format** + +The output file condenses the information in the pileup file so that consecutive bases are listed together as sequences. The starting and ending points of the sequence range are listed, with the starting value converted to a 0-based value. + +Given the following input with minimum coverage set to 3:: + + 1 2 3 4 5 6 + --------------------------------- + chr1 112 G 3 ..Ta III6 + chr1 113 T 2 aT.. III5 + chr1 114 A 5 ,,.. IIH2 + chr1 115 C 4 ,., III + chrM 412 A 2 ., II + chrM 413 G 4 ..t, IIIH + chrM 414 C 4 ...a III2 + chrM 415 C 4 TTTt III7 + chrM 490 T 3 a I + +the following would be the output:: + + 1 2 3 4 + ------------------- + chr1 111 112 G + chr1 113 115 AC + chrM 412 415 GCC + chrM 489 490 T + +where:: + + Column Definition + ------- ---------------------------- + 1 Chromosome + 2 Starting position (0-based) + 3 Ending position (1-based) + 4 Sequence of bases + + </help> +</tool> + +

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