| Previous changeset 10:8da515fbc1bf (2021-09-21) Next changeset 12:329deb17a9f7 (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 0f75269223c0821c6c82acf98fde947d0f816f2b" |
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modified:
macros.xml samtools_mpileup.xml test-data/mpileup.out.1 test-data/samtools_mpileup_out_3.pileup |
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added:
test-data/mpileup.out.4 |
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| diff -r 8da515fbc1bf -r 111f83918fe6 macros.xml --- a/macros.xml Tue Sep 21 09:33:51 2021 +0000 +++ b/macros.xml Tue Sep 28 16:15:20 2021 +0000 |
| [ |
| @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <xml name="flag_options"> - <option value="1">Read is paired</option> - <option value="2">Read is mapped in a proper pair</option> - <option value="4">Read is unmapped</option> - <option value="8">Mate is unmapped</option> - <option value="16">Read is mapped to the reverse strand of the reference</option> - <option value="32">Mate is mapped to the reverse strand of the reference</option> - <option value="64">Read is the first in a pair</option> - <option value="128">Read is the second in a pair</option> - <option value="256">Alignment of the read is not primary</option> - <option value="512">Read fails platform/vendor quality checks</option> - <option value="1024">Read is a PCR or optical duplicate</option> - <option value="2048">Alignment is supplementary</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab': |
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| diff -r 8da515fbc1bf -r 111f83918fe6 samtools_mpileup.xml --- a/samtools_mpileup.xml Tue Sep 21 09:33:51 2021 +0000 +++ b/samtools_mpileup.xml Tue Sep 28 16:15:20 2021 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_mpileup" name="samtools mpileup" version="2.1.4">\n+<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.5" profile="@PROFILE@">\n <description>multi-way pileup of variants</description>\n <macros>\n <import>macros.xml</import>\n@@ -7,36 +7,25 @@\n <expand macro="stdio" />\n <expand macro="version_command" />\n <command><![CDATA[\n- \n- #set $input_bams = $reference_source.input_bam\n+\n+ #set $input_bams = $input\n @PREPARE_IDX_MULTIPLE@\n-\n- #if $reference_source.reference_source_selector == "history":\n- #set ref_fa = \'ref.fa\'\n- ln -s \'${reference_source.ref_file}\' \'ref.fa\' &&\n- samtools faidx ref.fa &&\n- #else:\n- #set ref_fa = str( $reference_source.ref_file.fields.path )\n- #end if\n+ @PREPARE_FASTA_IDX@\n \n samtools mpileup\n- -f \'$ref_fa\'\n+ -f \'$reffa\'\n #for $i in range(len( $input_bams )):\n \'${i}\'\n #end for\n \n #if str( $advanced_options.advanced_options_selector ) == "advanced":\n #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":\n- #if $advanced_options.filter_by_flags.require_flags:\n- #set $filter = $advanced_options.filter_by_flags.require_flags\n- @FLAGS@\n- --rf $flags\n- #end if\n- #if $advanced_options.filter_by_flags.exclude_flags:\n- #set $filter = $advanced_options.filter_by_flags.exclude_flags\n- @FLAGS@\n- --ff $flags\n- #end if\n+ #set $filter = $advanced_options.filter_by_flags.require_flags\n+ @FLAGS@\n+ --rf $flags\n+ #set $filter = $advanced_options.filter_by_flags.exclude_flags\n+ @FLAGS@\n+ --ff $flags\n #end if\n #if str($advanced_options.limit_by_region.limit_by_regions) == "limit":\n #if str( $advanced_options.limit_by_region.region_paste ) != "None":\n@@ -46,7 +35,7 @@\n -l \'$advanced_options.limit_by_region.bed_regions\'\n #end if\n #end if\n- \n+\n #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":\n -G \'$excluded_read_groups\'\n #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"\n@@ -67,31 +56,17 @@\n ${output_options_cond.output_mapping_quality}\n ${output_options_cond.output_read_names}\n ${output_options_cond.output_all_pos}\n+ #if $output_options_cond.output_tags:\n+ --output-extra \'$output_options_cond.output_tags\'\n+ #end if\n #end if\n --output \'$output_file_pu\'\n ]]></command>\n <inputs>\n- <conditional name="reference_source">\n- <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">\n- <option value="cached">Use a built-in genome</option>\n- <option value="history">Use a genome from the history</option>\n- </param>\n- <when value="cached">\n- <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">\n- <validator type="unspecified_build" />\n- <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />\n- </param>\n- <param name="ref_file" type="select" label="Using reference genome">\n- <options from_data_table="fasta_indexes" />\n- </param>\n- </when>\n- <when value="history">\n- <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">\n- <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect f'..b'e="true" />\n </conditional>\n@@ -262,6 +242,18 @@\n </conditional>\n <output name="output_file_pu" file="samtools_mpileup_out_3.pileup" ftype="pileup" />\n </test>\n+ <test>\n+ <param name="input" ftype="bam" value="mpileup.1.bam" />\n+ <conditional name="addref_cond">\n+ <param name="addref_select" value="history" />\n+ <param name="ref" ftype="fasta" value="mpileup.ref.fa" />\n+ </conditional>\n+ <conditional name="output_options_cond">\n+ <param name="output_options_selector" value="advanced" />\n+ <param name="output_tags" value="NM,AM" />\n+ </conditional>\n+ <output name="output_file_pu" file="mpileup.out.4" ftype="pileup" />\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n@@ -272,7 +264,7 @@\n \n In the pileup format (without -u or -g), each line represents a genomic position, consisting of chromosome name, 1-based coordinate, reference base, the number of reads covering the site, read bases, base qualities and alignment mapping qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a \'>\' or \'<\' for a reference skip, \'ACGTN\' for a mismatch on the forward strand and \'acgtn\' for a mismatch on the reverse strand. A pattern \'\\\\+[0-9]+[ACGTNacgtn]+\' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Similarly, a pattern \'-[0-9]+[ACGTNacgtn]+\' represents a deletion from the reference. The deleted bases will be presented as \'*\' in the following lines. Also at the read base column, a symbol \'^\' marks the start of a read. The ASCII of the character following \'^\' minus 33 gives the mapping quality. A symbol \'$\' marks the end of a read segment.\n \n-Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file. \n+Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file.\n \n **BAQ (Base Alignment Quality)**\n \n@@ -280,7 +272,7 @@\n \n BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.\n \n-It is possible to store pre-calculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment. \n+It is possible to store pre-calculated BAQ values in a SAM BQ:Z tag. Samtools mpileup will use the precalculated values if it finds them. The -E option can be used to make it ignore the contents of the BQ:Z tag and force it to recalculate the BAQ scores by making a new alignment.\n ]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 8da515fbc1bf -r 111f83918fe6 test-data/mpileup.out.1 --- a/test-data/mpileup.out.1 Tue Sep 21 09:33:51 2021 +0000 +++ b/test-data/mpileup.out.1 Tue Sep 28 16:15:20 2021 +0000 |
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| @@ -1,36 +1,36 @@ -17 100 C 9 ......... JLJMLLGG4 3 ... DmH 5 ..... HIJ?G -17 101 C 9 ......... HFLJKMH97 3 ... Aq5 5 ..... FEIEG -17 102 C 9 ......... FKKLLLKF5 3 ... GpA 5 ..... HHIJG -17 103 T 8 ........ KLLLMLKG 3 ... Fu; 5 ..... MIMHI -17 104 G 8 ........ ;HLGKLIH 2 .. Dp 5 ..... ICHCI -17 105 G 9 ........^]. HB6KKKG8; 3 ... Cj0 5 ..... GBCAH -17 106 G 10 .......... GMKKIKJE2> 2 .. @i 5 ..... GCF5J -17 107 C 9 ......... IKMKLJKI? 3 ... Gm; 5 ..... JGH?K -17 108 C 9 ......... HGKLLKLG? 3 ... Fq< 5 ..... IFGBK -17 109 T 9 ......... ILLOLJJFB 3 ... FvI 5 ..... JJMLL -17 110 G 9 ......... JJMMKLIHD 3 ... ?t? 5 ..... IDFII -17 111 G 10 .......... G77HJJBA/C 2 .. Cr 4 .... GCHK -17 112 C 9 ......... IKILKKLI? 3 ... 6t; 5 ..... J?IEJ -17 113 A 9 ......... CGIFIGJE? 2 .. Bs 5 ..... JBJJI -17 114 C 9 ......... IDGIJJIHB 3 ... Ar; 5 ..... GEDHI -17 115 C 10 .......... EJJILNGF/A 2 .. Ds 6 .....^]. HFHIH? -17 116 A 9 ......... DHGJJJIHF 2 .. Ev 7 ......, F8JGIGG -17 117 G 9 .$........ >BJIMIFJF 2 .. @t 7 ......, H>IFJDD -17 118 G 9 ......... BFKLJGF/A 1 . s 7 ......, A>CEECE -17 119 G 8 ........ F?HLKJGG 2 .. s1 7 ......, A1ABLCB -17 120 A 8 ........ FCIIKHGJ 2 .. w= 7 ......, E;I@GIE -17 121 G 8 ........ GFMMMG@H 2 .. u9 7 ......, A<DBJGB -17 122 C 8 .$....... DEIKLLJI 3 ..^]. u2C 7 .$....., E=JGKFH -17 123 T 7 ....... EMKIEFH 3 ... y>I 6 ....., EJ;LKK -17 124 T 9 .$.......^]. ?HEIE?/7> 3 ... q6F 6 ....., ?FBCGI -17 125 A 7 ....... DHICDGA 3 ... s6F 6 ....., CIBHFD -17 126 A 8 ........ JEKAG0GB 3 ... p6I 6 ....., GHEMKC -17 127 C 8 ........ JGGJG/DD 3 ... p@E 6 ....., ?GDHGI -17 128 A 8 ........ HJIIE8IE 3 ... rFG 6 .$...., >GGJHF -17 129 A 8 ........ HFKJD8IC 3 ... oCJ 5 ...., IIMKD -17 130 A 8 ......$.. IJKCE8JD 3 ... kHJ 5 ...., BEMKI -17 131 C 7 ....... JKKFGGG 3 ... jCF 5 ...., BDKHF -17 132 A 7 ....... JGKJGKF 3 .$.. nIF 5 ...., HGJGG +17 100 C 9 ......... JLJMLLGG4 3 .., DHm 5 ..... HIJ?G +17 101 C 9 ......... HFLJKMH97 3 .., A5q 5 ..... FEIEG +17 102 C 9 ......... FKKLLLKF5 3 .., GAp 5 ..... HHIJG +17 103 T 8 ........ KLLLMLKG 3 .., F;u 5 ..... MIMHI +17 104 G 8 ........ ;HLGKLIH 2 ., Dp 5 ..... ICHCI +17 105 G 9 ........^]. HB6KKKG8; 3 .., C0j 5 ..... GBCAH +17 106 G 10 .......... GMKKIKJE2> 2 ., @i 5 ..... GCF5J +17 107 C 9 ......... IKMKLJKI? 3 .., G;m 5 ..... JGH?K +17 108 C 9 ......... HGKLLKLG? 3 .., F<q 5 ..... IFGBK +17 109 T 9 ......... ILLOLJJFB 3 .., FIv 5 ..... JJMLL +17 110 G 9 ......... JJMMKLIHD 3 .., ??t 5 ..... IDFII +17 111 G 10 .......... G77HJJBA/C 2 ., Cr 4 .... GCHK +17 112 C 9 ......... IKILKKLI? 3 .., 6;t 5 ..... J?IEJ +17 113 A 9 ......... CGIFIGJE? 2 ., Bs 5 ..... JBJJI +17 114 C 9 ......... IDGIJJIHB 3 .., A;r 5 ..... GEDHI +17 115 C 10 .......... EJJILNGF/A 2 ., Ds 6 .....^]. HFHIH? +17 116 A 9 ......... DHGJJJIHF 2 ., Ev 7 ......, F8JGIGG +17 117 G 9 .$........ >BJIMIFJF 2 ., @t 7 ......, H>IFJDD +17 118 G 9 ......... BFKLJGF/A 1 , s 7 ......, A>CEECE +17 119 G 8 ........ F?HLKJGG 2 ., 1s 7 ......, A1ABLCB +17 120 A 8 ........ FCIIKHGJ 2 ., =w 7 ......, E;I@GIE +17 121 G 8 ........ GFMMMG@H 2 ., 9u 7 ......, A<DBJGB +17 122 C 8 .$....... DEIKLLJI 3 .,^]. 2uC 7 .$....., E=JGKFH +17 123 T 7 ....... EMKIEFH 3 .,. >yI 6 ....., EJ;LKK +17 124 T 9 .$.......^]. ?HEIE?/7> 3 .,. 6qF 6 ....., ?FBCGI +17 125 A 7 ....... DHICDGA 3 .,. 6sF 6 ....., CIBHFD +17 126 A 8 ........ JEKAG0GB 3 .,. 6pI 6 ....., GHEMKC +17 127 C 8 ........ JGGJG/DD 3 .,. @pE 6 ....., ?GDHGI +17 128 A 8 ........ HJIIE8IE 3 .,. FrG 6 .$...., >GGJHF +17 129 A 8 ........ HFKJD8IC 3 .,. CoJ 5 ...., IIMKD +17 130 A 8 ......$.. IJKCE8JD 3 .,. HkJ 5 ...., BEMKI +17 131 C 7 ....... JKKFGGG 3 .,. CjF 5 ...., BDKHF +17 132 A 7 ....... JGKJGKF 3 .,. InF 5 ...., HGJGG 17 133 T 7 ....... GKHIEGE 3 .,. ELH 5 ...., EGJIK 17 134 C 7 ....... KLMKKJH 3 .,. IKI 5 ...., EGJKD 17 135 T 7 ....... JLKLHIG 3 .,. HJK 5 .$..., DLLJ? |
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| diff -r 8da515fbc1bf -r 111f83918fe6 test-data/mpileup.out.4 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpileup.out.4 Tue Sep 28 16:15:20 2021 +0000 |
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| b'@@ -0,0 +1,4101 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| diff -r 8da515fbc1bf -r 111f83918fe6 test-data/samtools_mpileup_out_3.pileup --- a/test-data/samtools_mpileup_out_3.pileup Tue Sep 21 09:33:51 2021 +0000 +++ b/test-data/samtools_mpileup_out_3.pileup Tue Sep 28 16:15:20 2021 +0000 |
| b |
| @@ -1,43 +1,43 @@ -phiX174 1411 A 1 ^P. $ -phiX174 1412 G 3 .^D.^F. "$$ -phiX174 1413 C 5 ...^D.^F. """$$ -phiX174 1414 G 6 .....^F. #####$ -phiX174 1415 C 7 ......^F. %%%%%%& -phiX174 1416 C 8 .......^F. $$$$$$$$ -phiX174 1417 G 9 ........^F. "#######$ -phiX174 1418 T 10 .........^F. """""""""$ -phiX174 1419 G 10 .......... """""'&'%$ -phiX174 1420 G 10 .......... """""""""" -phiX174 1421 A 10 .......... """""""""" -phiX174 1422 T 10 .......... """""""""" -phiX174 1423 G 10 .......... """""""""# -phiX174 1424 C 10 ..A.AAAAAA %""""""""" -phiX174 1425 C 10 .......... $$$""""""" -phiX174 1426 T 10 .......... #####""""" -phiX174 1427 G 10 .......... ######"""" -phiX174 1428 A 10 .......... """""""""" -phiX174 1429 C 10 .......... ((((((&("" -phiX174 1430 C 10 .......... $$$$$$$$$" -phiX174 1431 G 10 .......... ########## -phiX174 1432 T 10 .......... """""""""" -phiX174 1433 A 10 .......... ########## -phiX174 1434 C 10 .......... ((((((&(%$ -phiX174 1435 C 10 .......... $$$$$$$$$$ -phiX174 1436 G 10 .......... ########## -phiX174 1437 A 10 .......... """""""""! -phiX174 1438 G 10 .......... """""####! -phiX174 1439 G 10 .......... """""""""! -phiX174 1440 C 10 .......... """""""""! -phiX174 1441 T 10 .......... """"""""#! -phiX174 1442 A 10 .......... $$$%%%&&%! -phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! -phiX174 1444 C 10 **.*...... !!"!"""""! -phiX174 1445 C 10 .......... !!&!%%%&%! -phiX174 1446 C 10 .......... !!"!"""""! -phiX174 1447 T 10 .$..$....... !!#!"""""! -phiX174 1448 A 8 .$..$..... !!#%%$$! -phiX174 1449 A 6 .$.$.... !""""! -phiX174 1450 T 4 .$... """! -phiX174 1451 G 3 .$.. #"! -phiX174 1452 A 2 .$. "! -phiX174 1453 G 1 .$ ! +phiX174 1411 A 1 ^P. $ P 1 +phiX174 1412 G 3 .^D.^F. "$$ PDF 2,1,1 +phiX174 1413 C 5 ...^D.^F. """$$ PDFDF 3,2,2,1,1 +phiX174 1414 G 6 .....^F. #####$ PDFDFF 4,3,3,2,2,1 +phiX174 1415 C 7 ......^F. %%%%%%& PDFDFFF 5,4,4,3,3,2,1 +phiX174 1416 C 8 .......^F. $$$$$$$$ PDFDFFFF 6,5,5,4,4,3,2,1 +phiX174 1417 G 9 ........^F. "#######$ PDFDFFFFF 7,6,6,5,5,4,3,2,1 +phiX174 1418 T 10 .........^F. """""""""$ PDFDFFFFFF 8,7,7,6,6,5,4,3,2,1 +phiX174 1419 G 10 .......... """""'&'%$ PDFDFFFFFF 9,8,8,7,7,6,5,4,3,2 +phiX174 1420 G 10 .......... """""""""" PDFDFFFFFF 10,9,9,8,8,7,6,5,4,3 +phiX174 1421 A 10 .......... """""""""" PDFDFFFFFF 11,10,10,9,9,8,7,6,5,4 +phiX174 1422 T 10 .......... """""""""" PDFDFFFFFF 12,11,11,10,10,9,8,7,6,5 +phiX174 1423 G 10 .......... """""""""# PDFDFFFFFF 13,12,12,11,11,10,9,8,7,6 +phiX174 1424 C 10 ..A.AAAAAA %""""""""" PDFDFFFFFF 14,13,13,12,12,11,10,9,8,7 +phiX174 1425 C 10 .......... $$$""""""" PDFDFFFFFF 15,14,14,13,13,12,11,10,9,8 +phiX174 1426 T 10 .......... #####""""" PDFDFFFFFF 16,15,15,14,14,13,12,11,10,9 +phiX174 1427 G 10 .......... ######"""" PDFDFFFFFF 17,16,16,15,15,14,13,12,11,10 +phiX174 1428 A 10 .......... """""""""" PDFDFFFFFF 18,17,17,16,16,15,14,13,12,11 +phiX174 1429 C 10 .......... ((((((&("" PDFDFFFFFF 19,18,18,17,17,16,15,14,13,12 +phiX174 1430 C 10 .......... $$$$$$$$$" PDFDFFFFFF 20,19,19,18,18,17,16,15,14,13 +phiX174 1431 G 10 .......... ########## PDFDFFFFFF 21,20,20,19,19,18,17,16,15,14 +phiX174 1432 T 10 .......... """""""""" PDFDFFFFFF 22,21,21,20,20,19,18,17,16,15 +phiX174 1433 A 10 .......... ########## PDFDFFFFFF 23,22,22,21,21,20,19,18,17,16 +phiX174 1434 C 10 .......... ((((((&(%$ PDFDFFFFFF 24,23,23,22,22,21,20,19,18,17 +phiX174 1435 C 10 .......... $$$$$$$$$$ PDFDFFFFFF 25,24,24,23,23,22,21,20,19,18 +phiX174 1436 G 10 .......... ########## PDFDFFFFFF 26,25,25,24,24,23,22,21,20,19 +phiX174 1437 A 10 .......... """""""""! PDFDFFFFFF 27,26,26,25,25,24,23,22,21,20 +phiX174 1438 G 10 .......... """""####! PDFDFFFFFF 28,27,27,26,26,25,24,23,22,21 +phiX174 1439 G 10 .......... """""""""! PDFDFFFFFF 29,28,28,27,27,26,25,24,23,22 +phiX174 1440 C 10 .......... """""""""! PDFDFFFFFF 30,29,29,28,28,27,26,25,24,23 +phiX174 1441 T 10 .......... """"""""#! PDFDFFFFFF 31,30,30,29,29,28,27,26,25,24 +phiX174 1442 A 10 .......... $$$%%%&&%! PDFDFFFFFF 32,31,31,30,30,29,28,27,26,25 +phiX174 1443 A 10 .-1C.-1C..-1C...... """""""""! PDFDFFFFFF 33,32,32,31,31,30,29,28,27,26 +phiX174 1444 C 10 **.*...... !!"!"""""! PDFDFFFFFF 34,33,33,32,32,31,30,29,28,27 +phiX174 1445 C 10 .......... !!&!%%%&%! PDFDFFFFFF 34,33,34,32,33,32,31,30,29,28 +phiX174 1446 C 10 .......... !!"!"""""! PDFDFFFFFF 35,34,35,33,34,33,32,31,30,29 +phiX174 1447 T 10 .$..$....... !!#!"""""! PDFDFFFFFF 36,35,36,34,35,34,33,32,31,30 +phiX174 1448 A 8 .$..$..... !!#%%$$! DDFFFFFF 36,35,36,35,34,33,32,31 +phiX174 1449 A 6 .$.$.... !""""! DFFFFF 36,36,35,34,33,32 +phiX174 1450 T 4 .$... """! FFFF 36,35,34,33 +phiX174 1451 G 3 .$.. #"! FFF 36,35,34 +phiX174 1452 A 2 .$. "! FF 36,35 +phiX174 1453 G 1 .$ ! F 36 |