| Next changeset 1:272c6e61dd0c (2015-05-22) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e8e971905f5fce11a99d51b1399af45288389d76 |
|
added:
macros.xml progressivemauve.xml test-data/1.mums test-data/1.nhx test-data/1.xmfa test-data/karma.fa test-data/merged.fa test-data/phagey.fa tool_dependencies.xml |
| b |
| diff -r 000000000000 -r aaa94e13ac60 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 21 22:49:06 2015 -0400 |
| b |
| @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.4.0">progressivemauve</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r aaa94e13ac60 progressivemauve.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/progressivemauve.xml Thu May 21 22:49:06 2015 -0400 |
| [ |
| b'@@ -0,0 +1,435 @@\n+<?xml version="1.0"?>\n+<tool id="progressivemauve" name="progressiveMauve" version="@WRAPPER_VERSION@.0">\n+ <description>constructs multiple genome alignments</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <version_command>progressiveMauve --version</version_command>\n+ <command><![CDATA[\n+## Symlink files in with correct extensions\n+#for $file in $sequences:\n+ ln -s $file `basename $file`;\n+#end for\n+\n+progressiveMauve\n+## Input Options\n+\n+#if $apply_backbone:\n+ --apply-backbone=$apply_backbone\n+#end if\n+--island-gap-size=$island_gap_size\n+$mums\n+\n+#if $seed_weight:\n+ --seed-weight=$seed_weight\n+#end if\n+\n+#if $max_gapped_aligner_length:\n+ --max-gapped-aligner-length=$max_gapped_aligner_length\n+#end if\n+\n+#if $match_input:\n+ --match-input=$match_input\n+#end if\n+\n+$collinear\n+--scoring-scheme=$scoring_scheme\n+$no_weight_scaling\n+\n+--max-breakpoint-distance-scale=$max_breakpoint_distance_scale\n+--conservation-distance-scale=$conservation_distance_scale\n+$skip_refinement\n+$skip_gapped_alignment\n+\n+#if $bp_dist_estimate_min_score:\n+ --bp-dist-estimate-min-score=$bp_dist_estimate_min_score\n+#end if\n+\n+#if $gap_open:\n+ --gap-open=$gap_open\n+#end if\n+\n+#if $gap_extend:\n+ --gap-extend=$gap_extend\n+#end if\n+\n+#if $weight:\n+ --weight=$weight\n+#end if\n+\n+#if $min_scaled_penalty:\n+ --min-scaled-penalty=$min_scaled_penalty\n+#end if\n+\n+--hmm-p-go-homologous=$hmm_p_go_homologous\n+--hmm-p-go-unrelated=$hmm_p_go_unrelated\n+--hmm-identity=$hmm_identity\n+\n+$seed_family\n+$solid_seeds\n+$coding_seeds\n+$no_recursion\n+$disable_backbone\n+\n+## Outputs\n+--output=$output\n+#if $output_guide_tree:\n+ --output-guide-tree=$output_guide_tree_file\n+#end if\n+\n+#if $output_backbone:\n+ --backbone-output=$output_backbone_file\n+#end if\n+\n+## Sequences\n+#for file in $sequences:\n+ `basename "${file}"`\n+#end for\n+\n+]]></command>\n+ <inputs>\n+ <param type="data" format="fasta" name="sequences" multiple="True"\n+ label="Select sequences to align" help="in fasta format" />\n+ <param type="data" format="xmfa" label="Apply Backbone" name="apply_backbone" optional="True"\n+ help="Read an existing sequence alignment in XMFA format and apply backbone statistics to it (--apply-backbone)" />\n+\n+ <param type="integer" label="Island gap size" value="20" name="island_gap_size"\n+ help="Alignment gaps above this size in nucleotides are considered to be islands (--island-gap-size)"/>\n+\n+ <param type="boolean" truevalue="--disable-backbone" falsevalue="" name="disable_backbone"\n+ label="Disable backbone" help="Disable backbone detection (--disable-backbone)" />\n+\n+ <param type="boolean" truevalue="True" falsevalue="" name="output_guide_tree"\n+ label="Output Guide Tree" help="Write out the guide tree used for alignment to a file (--output-guide-tree)" />\n+\n+ <param type="boolean" truevalue="True" falsevalue="" name="output_backbone"\n+ label="Output Backbone" help="Write out the backbone to a file (--backbone-output)" />\n+\n+ <param type="boolean" truevalue="--mums" falsevalue="" label="MUMs" name="mums"\n+ help="Find MUMs only, do not attempt to determine locally collinear blocks (LCBs) (--mums)" />\n+\n+ <param type="integer" label="Seed weight" name="seed_weight" value="0" optional="True"\n+ help="Use the specified seed weight for calculating initial anchors (--seed-weight)" />\n+\n+ <param type="data" format="tabular" label="Match Input" name="match_input"\n+ help="Use specified match file instead of searching for matches (--match-input)" />\n+\n+ <!--<param type="file" label="input-id-matrix" help="An identity matrix describing similarity among all pairs of input sequences/alignments (- -input-id-matrix)" />-->\n+ <param type="integer" label="Max gapped aligner length" value="0" optional="True" name="max_gapped_aligner_'..b'nference.\n+\n+Computing a pairwise breakpoint distance matrix\n+-----------------------------------------------\n+\n+Prior to alignment, progressiveMauve attempts to compute a conservative\n+estimate of the number of rearrangement breakpoints among any pair of genomes.\n+For each pair of genomes, pairwise alignments are created from the\n+local-multiple alignments and the pairwise alignments are subjected to greedy\n+breakpoint elimination. The breakpoint penalty used for greedy breakpoint\n+elimination is set high for closely related genomes and scaled downward\n+according to the estimate of genomic content distance. Because the breakpoint\n+penalty is high, the resulting set of locally collinear blocks represent\n+robustly supported segmental homology, and a conservative estimate of the\n+breakpoint distance can be made on this basis. The conservative estimate of\n+breakpoint distance is used later during progressive alignment to scale\n+breakpoint penalties.\n+\n+Progressive genome alignment\n+----------------------------\n+\n+A genome alignment is progressively built up according to the guide tree. At\n+each step of the progressive genome alignment, alignment anchors are selected\n+from the initial set of local multiple alignments. Anchors are selected so that\n+they maximize a Sum-of-pairs scoring scheme which applies a penalty for\n+predicting breakpoints among any pair of genomes. Because rates of genomic\n+rearrangement are highly variable, especially in some bacterial pathogens, some\n+genomes may be expected to exhibit greater rearrangement than others. As such,\n+a single choice of scoring penalty is unlikely to yield accurate alignments for\n+all genomes. To cope with this phenomenon, progressiveMauve scales the\n+breakpoint penalty according to the expected level of sequence divergence and\n+the number of well-supported genomic rearrangements among the pair of input\n+genomes. These scaling values are taken from the distance matrices computed\n+earlier in the algorithm.\n+\n+Anchored alignment\n+------------------\n+\n+Once anchors have been computed at a node in the guide tree, a global alignment\n+is computed on the basis of the anchors. Given a set of anchors among two\n+genomes, a genome and an alignment, or a pair of alignments, a modified MUSCLE\n+global alignment algorithm is applied to compute an anchored profile-profile\n+alignment. MUSCLE is then used to perform tree-independent iterative refinement\n+on the global genome alignment.\n+\n+Rejecting alignment of unrelated sequence\n+-----------------------------------------\n+\n+Although we compute a global alignment among sequences, genomes often contain\n+lineage-specific sequence and are thus not globally related. The global\n+alignment will often contain forced alignment of unrelated sequence. A simple\n+hidden Markov model structure is used to detect forced alignment of unrelated\n+sequence, which are then removed from the alignment.\n+\n+Strengths of the progressiveMauve algorithm\n+-------------------------------------------\n+\n+- It can be applied to a much larger number of genomes than the original Mauve\n+ algorithm\n+- It can align more divergent genomes than the original algorithm. Genomes\n+ with as little as 50% nucleotide identity can be alignable\n+- Manual adjustment of the alignment scoring parameters is usually not\n+ necessary\n+- It aligns the pan-genome, e.g. regions conserved among subsets of the input\n+ genomes\n+- It is more accurate than the previous Mauve algorithm\n+\n+Notes on Reproducibility\n+------------------------\n+\n+The command line programme progressiveMauve seems to behave differently when::\n+\n+ --max-breakpoint-distance-scale=0.5 --conservation-distance-scale=0.5\n+\n+are passed to the tool, compared to when those options are not passed. This\n+means that if you wish to precisely replicate the results you see in Galaxy at\n+the command line, you\'ll need to pass these flags with their "default" values.\n+\n+@ATTRIBUTION@\n+]]></help>\n+ <expand macro="citation" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/1.mums --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.mums Thu May 21 22:49:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,409 @@\n+FormatVersion\t3\n+SequenceCount\t2\n+Sequence0File\ttest-data/merged.fa\n+Sequence0Length\t159457\n+Sequence1File\ttest-data/merged.fa\n+Sequence1Length\t221828\n+MatchCount\t402\n+23\t9997\t10291\t0x9c7f540\t0\t0\n+23\t118799\t199132\t0x9c7f588\t0\t0\n+23\t26654\t-52948\t0x9c7f5c8\t0\t0\n+23\t126561\t47160\t0x9c7f610\t0\t0\n+23\t110233\t-209064\t0x9c7f650\t0\t0\n+23\t134387\t175263\t0x9c7f690\t0\t0\n+23\t93373\t-185643\t0x9c7f700\t0\t0\n+23\t6917\t167993\t0x9c7f740\t0\t0\n+23\t47238\t48379\t0x9c7f780\t0\t0\n+23\t8742\t-150092\t0x9c7f7c0\t0\t0\n+23\t144337\t65631\t0x9c7f800\t0\t0\n+23\t138300\t-100263\t0x9c7f890\t0\t0\n+23\t62837\t-15551\t0x9c7f8d0\t0\t0\n+23\t135219\t16958\t0x9c7f910\t0\t0\n+23\t19156\t-18956\t0x9c7f950\t0\t0\n+23\t109152\t-48925\t0x9c7f990\t0\t0\n+23\t76438\t-161554\t0x9c7f9d0\t0\t0\n+23\t71190\t-46655\t0x9c7fa10\t0\t0\n+23\t157575\t-160188\t0x9c7fa50\t0\t0\n+23\t143476\t-94179\t0x9c7fb20\t0\t0\n+23\t87012\t169379\t0x9c7fb60\t0\t0\n+23\t121064\t43686\t0x9c7fba0\t0\t0\n+23\t110470\t153107\t0x9c7fbe0\t0\t0\n+23\t20451\t103095\t0x9c7fc20\t0\t0\n+23\t49774\t172484\t0x9c7fc60\t0\t0\n+23\t143100\t-94112\t0x9c7fca0\t0\t0\n+23\t15931\t-101015\t0x9c7fce0\t0\t0\n+23\t7626\t90732\t0x9c7fd20\t0\t0\n+23\t108605\t151756\t0x9c7fd60\t0\t0\n+23\t21356\t-55347\t0x9c7fda0\t0\t0\n+23\t92245\t175565\t0x9c7fde0\t0\t0\n+23\t85283\t-31332\t0x9c7fe20\t0\t0\n+23\t132260\t-144338\t0x9c7fe68\t0\t0\n+23\t82694\t-33509\t0x9c7fea8\t0\t0\n+23\t118975\t-117043\t0x9c7fee8\t0\t0\n+23\t13544\t17526\t0x9c7ff28\t0\t0\n+23\t20115\t24166\t0x9c7ff68\t0\t0\n+23\t34236\t198417\t0x9c7ffa8\t0\t0\n+23\t20424\t184669\t0x9c7ffe8\t0\t0\n+23\t77531\t-118039\t0x9c80028\t0\t0\n+23\t143204\t27642\t0x9c80068\t0\t0\n+23\t17797\t-137711\t0x9c800a8\t0\t0\n+23\t120249\t84877\t0x9c800e8\t0\t0\n+23\t153224\t197896\t0x9c80128\t0\t0\n+23\t122607\t47346\t0x9c80168\t0\t0\n+23\t72091\t116861\t0x9c801a8\t0\t0\n+23\t69792\t-85354\t0x9c801e8\t0\t0\n+23\t91619\t-183522\t0x9c80228\t0\t0\n+23\t81809\t-153240\t0x9c80268\t0\t0\n+23\t131569\t96695\t0x9c802a8\t0\t0\n+23\t91755\t-22996\t0x9c802e8\t0\t0\n+23\t62255\t107528\t0x9c80328\t0\t0\n+23\t97762\t143048\t0x9c80368\t0\t0\n+23\t47846\t-26838\t0x9c804b8\t0\t0\n+23\t22429\t147746\t0x9c804f8\t0\t0\n+23\t89267\t-105382\t0x9c80538\t0\t0\n+23\t123104\t48452\t0x9c80578\t0\t0\n+23\t147441\t-167041\t0x9c805b8\t0\t0\n+23\t61655\t107258\t0x9c805f8\t0\t0\n+23\t49782\t55474\t0x9c80638\t0\t0\n+23\t126309\t-187960\t0x9c80678\t0\t0\n+23\t127565\t-186680\t0x9c806b8\t0\t0\n+23\t61393\t-172486\t0x9c806f8\t0\t0\n+23\t33894\t-119800\t0x9c80738\t0\t0\n+23\t126037\t-147581\t0x9c80778\t0\t0\n+23\t7047\t-26355\t0x9c807b8\t0\t0\n+23\t24627\t-208764\t0x9c807f8\t0\t0\n+23\t138565\t105206\t0x9c80838\t0\t0\n+23\t147900\t114644\t0x9c80878\t0\t0\n+23\t20788\t-92429\t0x9c808b8\t0\t0\n+23\t27788\t74637\t0x9c808f8\t0\t0\n+23\t26994\t-46081\t0x9c80938\t0\t0\n+23\t83342\t-109591\t0x9c80978\t0\t0\n+23\t125089\t172337\t0x9c809b8\t0\t0\n+23\t113543\t200874\t0x9c809f8\t0\t0\n+23\t29134\t36536\t0x9c80a38\t0\t0\n+23\t89477\t56997\t0x9c80a78\t0\t0\n+23\t54229\t101789\t0x9c80ab8\t0\t0\n+23\t119402\t87080\t0x9c80af8\t0\t0\n+23\t92871\t-59372\t0x9c80b38\t0\t0\n+23\t49176\t-183000\t0x9c80b78\t0\t0\n+23\t85491\t-186666\t0x9c80bb8\t0\t0\n+23\t77304\t125144\t0x9c80bf8\t0\t0\n+23\t94511\t-17550\t0x9c80c38\t0\t0\n+23\t98281\t-13676\t0x9c80c78\t0\t0\n+30\t115463\t43690\t0x9c80cb8\t0\t0\n+23\t159059\t207575\t0x9c80cf8\t0\t0\n+23\t41192\t-70232\t0x9cb5a30\t0\t0\n+23\t102968\t191563\t0x9cb5a70\t0\t0\n+23\t105399\t154037\t0x9cb5ab0\t0\t0\n+23\t30588\t-160589\t0x9cb5af0\t0\t0\n+23\t59421\t-91617\t0x9cb5b30\t0\t0\n+23\t45146\t-105380\t0x9cb5b70\t0\t0\n+23\t20221\t29677\t0x9cb5bb0\t0\t0\n+23\t10060\t59762\t0x9cb5bf0\t0\t0\n+23\t106991\t36748\t0x9cb5c30\t0\t0\n+23\t144321\t-205746\t0x9cb5c70\t0\t0\n+23\t10889\t-99127\t0x9cb5cb0\t0\t0\n+23\t10885\t140931\t0x9cb5cf0\t0\t0\n+23\t25842\t116035\t0x9cb5d30\t0\t0\n+23\t158122\t-71637\t0x9cb5d70\t0\t0\n+23\t11517\t-58234\t0x9cb5db0\t0\t0\n+23\t40493\t50789\t0x9cb5df0\t0\t0\n+23\t156492\t-73189\t0x9cb5e30\t0\t0\n+23\t122327\t-67250\t0x9cb5e70\t0\t0\n+23\t13805\t144236\t0x9cb5eb0\t0\t0\n+23\t55697\t146282\t0x9cb5ef0\t0\t0\n+23\t81819\t-27507\t0x9cb5f30\t0\t0\n+23\t38700\t49355\t0x9cb5f70\t0\t0\n+23\t152341\t-156898\t0x9cb5fb0\t0\t0\n+23\t30693\t-158526\t0x9cb5ff0\t0\t0\n+23\t116061\t-113103\t0x9cb6030\t0\t0\n+23\t90637\t21513\t0x9cb6070\t0\t0\n+23\t147568\t78584\t0x9cb60b0\t0\t0\n+23\t152715\t123825\t0x9cb60f0\t0\t0\n+23\t113422\t-75417\t0x9cb6130\t0\t0\n+23\t35470\t166713\t0x9cb6170\t0\t0\n+23\t12748\t-135936\t0x9cb61b0\t0\t0\n+23\t86186\t-142470\t0x9cb61f0\t0\t0\n+23\t112214\t-76325\t0x9cb6230\t0\t0\n+23\t18205\t-90319\t0x9cb6270\t0\t0\n+23\t67644\t119184'..b'\t0\t0\n+23\t112101\t-142061\t0x9cb8d48\t0\t0\n+23\t157581\t-16531\t0x9cb8d88\t0\t0\n+23\t61775\t-112278\t0x9cb8dc8\t0\t0\n+23\t152960\t18947\t0x9cb8e08\t0\t0\n+23\t75128\t-138694\t0x9cb8e48\t0\t0\n+23\t61924\t88094\t0x9cb8e88\t0\t0\n+23\t148598\t-144890\t0x9cb8ec8\t0\t0\n+23\t55176\t-198167\t0x9cb8f08\t0\t0\n+23\t29460\t16109\t0x9cb8f48\t0\t0\n+23\t107172\t93852\t0x9cb8f88\t0\t0\n+23\t102861\t49641\t0x9cb8fc8\t0\t0\n+23\t124999\t111781\t0x9cb9008\t0\t0\n+23\t61278\t-191864\t0x9cb9048\t0\t0\n+23\t21405\t88383\t0x9cb9088\t0\t0\n+23\t120715\t-132242\t0x9cb90c8\t0\t0\n+23\t111135\t18433\t0x9cb9108\t0\t0\n+23\t126868\t-125790\t0x9cb9148\t0\t0\n+23\t17013\t-155583\t0x9cb9188\t0\t0\n+23\t145379\t132845\t0x9cb91c8\t0\t0\n+23\t94284\t-78112\t0x9cb9208\t0\t0\n+23\t71470\t-140870\t0x9cb9248\t0\t0\n+23\t157743\t145462\t0x9cb9288\t0\t0\n+23\t81867\t-170270\t0x9cb92c8\t0\t0\n+23\t101542\t209483\t0x9cb9308\t0\t0\n+23\t13036\t41112\t0x9cb9348\t0\t0\n+23\t41397\t-170432\t0x9cb9388\t0\t0\n+23\t60441\t168699\t0x9cb93c8\t0\t0\n+23\t83226\t-128363\t0x9cb9408\t0\t0\n+23\t146822\t-24765\t0x9cb9448\t0\t0\n+23\t50236\t158638\t0x9cb9488\t0\t0\n+23\t19418\t207934\t0x9cb94c8\t0\t0\n+23\t29487\t138044\t0x9cb9508\t0\t0\n+23\t29107\t17680\t0x9cb9548\t0\t0\n+23\t38177\t106900\t0x9cb9588\t0\t0\n+23\t54580\t-196582\t0x9cb95c8\t0\t0\n+23\t41828\t-129187\t0x9cb9608\t0\t0\n+23\t89417\t158389\t0x9cb9648\t0\t0\n+23\t7972\t-82982\t0x9cb9688\t0\t0\n+23\t107130\t136228\t0x9cb96c8\t0\t0\n+23\t119898\t-50726\t0x9cb9708\t0\t0\n+23\t131259\t200731\t0x9cb9748\t0\t0\n+23\t50121\t-120363\t0x9cb9788\t0\t0\n+23\t125127\t194847\t0x9cb97c8\t0\t0\n+23\t157870\t-12369\t0x9cb9808\t0\t0\n+23\t143651\t-146400\t0x9cb9848\t0\t0\n+23\t14774\t124768\t0x9cb9888\t0\t0\n+23\t137937\t127955\t0x9cb98c8\t0\t0\n+23\t81817\t72122\t0x9cb9908\t0\t0\n+23\t33156\t-136114\t0x9cb9948\t0\t0\n+23\t6195\t-202885\t0x9cb9988\t0\t0\n+23\t57455\t-111603\t0x9cb99c8\t0\t0\n+23\t111040\t181976\t0x9cb9a08\t0\t0\n+23\t80767\t-88175\t0x9cb9a48\t0\t0\n+23\t25242\t56363\t0x9cb9a88\t0\t0\n+23\t97613\t128759\t0x9cb9ac8\t0\t0\n+23\t147683\t178955\t0x9cb9b08\t0\t0\n+23\t117730\t189034\t0x9cb9b48\t0\t0\n+23\t13218\t-195398\t0x9cb9b88\t0\t0\n+23\t52604\t164004\t0x9cb9bc8\t0\t0\n+23\t66147\t17619\t0x9cb9c08\t0\t0\n+23\t111399\t-177083\t0x9cb9c48\t0\t0\n+23\t157336\t-51135\t0x9cb9c88\t0\t0\n+23\t23547\t-64888\t0x9cb9cc8\t0\t0\n+23\t100481\t132362\t0x9cb9d08\t0\t0\n+23\t132863\t-195111\t0x9cb9d48\t0\t0\n+23\t83786\t75872\t0x9cb9d88\t0\t0\n+23\t107625\t59869\t0x9cb9dc8\t0\t0\n+23\t29655\t182013\t0x9cb9e08\t0\t0\n+23\t116497\t149106\t0x9cb9e48\t0\t0\n+23\t117407\t-89849\t0x9cb9e88\t0\t0\n+23\t152873\t-54252\t0x9cb9ec8\t0\t0\n+23\t2751\t-164307\t0x9cb9f08\t0\t0\n+23\t121221\t-205785\t0x9cb9f48\t0\t0\n+23\t41150\t74307\t0x9cb9f88\t0\t0\n+23\t3986\t117300\t0x9cb9fc8\t0\t0\n+23\t82860\t-163618\t0x9cba008\t0\t0\n+23\t57602\t-148819\t0x9cba048\t0\t0\n+23\t5365\t-200679\t0x9cba088\t0\t0\n+23\t109119\t23062\t0x9cba0c8\t0\t0\n+23\t85651\t199620\t0x9cba108\t0\t0\n+23\t80100\t-205788\t0x9cba148\t0\t0\n+23\t42570\t-123167\t0x9cba188\t0\t0\n+23\t36020\t-209679\t0x9cba1c8\t0\t0\n+23\t88022\t-157623\t0x9cba208\t0\t0\n+23\t10181\t204771\t0x9cba248\t0\t0\n+23\t15512\t90151\t0x9cba288\t0\t0\n+23\t109992\t64672\t0x9cba2c8\t0\t0\n+23\t156218\t111072\t0x9cba308\t0\t0\n+23\t47242\t82126\t0x9cba348\t0\t0\n+23\t23935\t58853\t0x9cba388\t0\t0\n+23\t93453\t-71104\t0x9cbabd8\t0\t0\n+23\t99759\t95286\t0x9cbac18\t0\t0\n+23\t103075\t138610\t0x9cbac58\t0\t0\n+23\t149705\t-14676\t0x9cbac98\t0\t0\n+23\t123404\t39006\t0x9cbacd8\t0\t0\n+23\t122296\t157926\t0x9cbad18\t0\t0\n+23\t142815\t-21431\t0x9cbad58\t0\t0\n+23\t125617\t-78534\t0x9cbad98\t0\t0\n+23\t25902\t-17866\t0x9cbadd8\t0\t0\n+23\t152639\t-90975\t0x9cbae18\t0\t0\n+23\t21992\t178389\t0x9cbae58\t0\t0\n+23\t15947\t92384\t0x9cbae98\t0\t0\n+23\t101873\t98312\t0x9cbaed8\t0\t0\n+23\t3899\t-119389\t0x9cbaf18\t0\t0\n+23\t148397\t185112\t0x9cbaf58\t0\t0\n+23\t130431\t-112825\t0x9cbaf98\t0\t0\n+23\t143278\t180137\t0x9cbafd8\t0\t0\n+23\t66424\t103325\t0x9cbb018\t0\t0\n+23\t131360\t-111662\t0x9cbb058\t0\t0\n+23\t156677\t153981\t0x9cbb098\t0\t0\n+23\t143297\t20818\t0x9cbb0d8\t0\t0\n+23\t90241\t-111775\t0x9cbb118\t0\t0\n+23\t20107\t18248\t0x9cbb158\t0\t0\n+23\t83728\t82051\t0x9cbb198\t0\t0\n+23\t65721\t104098\t0x9cbb1d8\t0\t0\n+23\t70625\t189133\t0x9cbb218\t0\t0\n+23\t86074\t-115341\t0x9cbb258\t0\t0\n+23\t37121\t-204123\t0x9cbb298\t0\t0\n+23\t46528\t165402\t0x9cbb2d8\t0\t0\n+23\t106103\t104995\t0x9cbb318\t0\t0\n+23\t86707\t-74058\t0x9cbb358\t0\t0\n+23\t106556\t65846\t0x9cbb398\t0\t0\n+23\t131791\t-108777\t0x9cbb3d8\t0\t0\n+23\t66998\t66464\t0x9cbb418\t0\t0\n+23\t32437\t-167760\t0x9cbb458\t0\t0\n+23\t75950\t75816\t0x9cbb498\t0\t0\n+23\t69770\t109722\t0x9cbb4d8\t0\t0\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.nhx Thu May 21 22:49:06 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(seq2:0.476132,seq1:0.476132); |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/1.xmfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.xmfa Thu May 21 22:49:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,5967 @@\n+#FormatVersion Mauve1\n+#Sequence1File\ttest-data/phagey.fa\n+#Sequence1Format\tFastA\n+#Sequence2File\ttest-data/karma.fa\n+#Sequence2Format\tFastA\n+#BackboneFile\ttest-data/1.xmfa.bbcols\n+> 1:83031-140929 - test-data/phagey.fa\n+ttttctcctcttttttcttagt--gaccgagggctttttaccctcggatggtttactttcactgagtct--agatgttaa\n+atatttatgta---gtttaccagtgaatga-ccccattatacatcaccgccttagtgtaagacaagcctt--atttactt\n+ttagtca------cggaaaacgaagtagccaataccaagaccgatcattacgtggtaaaaatcattccaatatgcagctg\n+ctctagggaagtttaactcacctaaaatcgcccagatcatcgaaccaacaaatgaagatacaactaaccagattattagt\n+ttaccataactcatgcgtgttcccctcctcagtcaataataacgtatattttctttaactctttttctagttctacttcc\n+caggatcgtaactcacttctaagtgcgtataatgccacggttgggaggttatttcgttcttcgactaaacgtaccccctc\n+ctttaggcctgctatgccctgtcgtatggaacttatggagctacacacctgaatacctgttgttagcctcttttcgaaat\n+ttgcaagagacaagtcaccttcccagtgaattactcgggaagcacatacagcctggtaattttcctctgcttccttctct\n+gctttcgcatcatttccttggtagttgcctcgcatactacgccaaaactctatacgatcgtgtagctggtgccctgtaat\n+ttgctcaagattcactcacttacacctccttaaaggtaactttagcaaaattgtctaattcttctactgcagaaacgtga\n+gccccttttataagctcgtaggctaggctatcaaaacctagtttggattctgcctccaccgatgctttctccgttatatg\n+cactctgttctctaattcctcatatgttttaactatctgccctacagtcattgtacgttgcctcatattaactctcctcc\n+atttcttcttcttcttgtaaaataattcggtacttttcacgagtaagacgctcaatatatgcttcgacatcggatatata\n+agcctctagtagcggtggcgttttattttcgatgcaaccaccatacctgtacttatgctcaacctctcgtaacgtagcca\n+aatcgtcttgagccatttcgagtgccttctctatacccttcttgcctagcgcttgtatagcttctctgcttgccttagta\n+tcatatttacggataatagcctcaagcacaccaatatggtgctgtaatgttgctatctgcttcttcaactcgtatattgt\n+ttgtgaagcgcttttctctttttctgctttcgcatcatttccttggtagttgcctcgcatactacgccaaaactctatac\n+gatcgtgtagctggtgccctgtaatttgctcaaaattcattcgtctaccccccgaaacaataacatattttttccgcttc\n+tctttttctgctttgttatctctactattgaacataattaattctcctcctttgtcggtgtaaacctcactaacgcataa\n+tccgcagcacatagtccatttaactcttgttctagtcgagatagctccctgtttaacgtttgtgtagctgcattgatttg\n+aggtagtctagtattagctatagcatctttaccctctaatagttgttctttcttcttataggctgagtaaatgctaaagt\n+agatgtcataagcgtttcggtcaggtacacctagaactaagctacctcctggtttatcagctaaatgatacacatgtgcc\n+tctgctgcctccttaactttcattagcttatctcgttcctctaggagcacctgcgatccttttgataatcctcctcgttt\n+ctctactacatacattcttgccacttcaatttccttaatatcctccatcgtatgacgtagtgcctgataaatttcaatac\n+ctgttgtcagtttttcgaatttcatattatttgtcctcctctaatttagctattcttttttcaaggctcgctatacactt\n+agcttgctcgctcattaaagccataacatcgtcaaatgtatctgttaatttatcaagtatgatagtcatttttaacatgt\n+taaactctgttgtcggttccatattagttatcctcctaggggactacttagtttaagcatcccgtatagtgtaaatattc\n+ctgttaaaggtagtaaagggtcgagggccggagccttaaaagggttatgttcctcgactggttgggttgttacactcggc\n+tcctggactttcttttgtacaacgggttctttatatgtaggttgttgctctaaggtggcgatccgctgctctaactcgat\n+ggtgttggtatggtaagctttcctggtagcatccatttggagtgctagtctattgatctggtaatcttggtacttttgat\n+gttgcataagataagcgtacttccctgcaatcatatttgctgtaacaaagagtaacaatattagtaagagtatgagaaga\n+cgcttaaaccattttcgcttagttggtttgcgtttcttctgcataaggtttacttctcctttctgcggtgactggccatg\n+taacctagtgtataagcgcctagaaaagtaatcataagctgtgtaataactgacgtatgttggtcggccactaagccatc\n+tgtgacccctactgcagcagccgtcaataaaataataccagcgtcgattaaaaagtttttcatttaattttcctccttct\n+ctgaatctatctttattgtacaagcttatatactaaaagtcaatacttatttaaaaaaaaatctgagggagtttttagct\n+ccctacattgatccggaaattaactgcatcgatgtcgatatgtgatagtacagtctttaactcgtctaacttcgcaataa\n+cctcctccttagaaaccatttgaccagacacgttaaaattaaagttatactctactttagctttactctctttaactaat\n+tctggttcgtcccattgctctctatttaggctattggctagtgcagccatctcttcttttgaaaacttatttttctcgtc\n+cattttgttcacgtagttcatcatcccttctgcttgtactcttatcatatgtgtagctaactgtttaccttgctcctcca\n+ttcgttgcatagccggagacaactcagcgttacctaacacgtatatatcttttggtggagtcggtgttgcaataggctgt\n+aacggtaccttcttagctaccggaacactaataggtggcgtagcctgtacaggagtagcttgagtaggtgctggtttctt\n+tttcatcgtctccttatttttaggcttcttattacctttacgaggtgcattattcgctctatttttattcttaactgctt\n+tagaacgatacttactagctaagtaacctatagtactcaatggaacctctgtacgagttgcaatctccttgtacgttagc\n+tctgtagactccaataaacgaatcgcttcctcacggtttccttttggatttttattataacccacagtatccatctcctc\n+ttctttttgttttttaactttacccacagcaacaaccatctttttaactttaggttctggtttaactactacctgttcct\n+cttcgttaaacccttctttcatactagctaagattttcttctctaacctagagatttgaacttgggat'..b'cggtatcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggcccgctccccatgggg\n+cgcggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagctacagcgacgacaaggccgacgccctggccac\n+cgcccgcgacatgtccgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcacaaccccgcctaagacc\n+ccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatgaccgcccgtaagccc\n+ctgaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcg\n+cgaattcgagcgtcaagcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagccgccc\n+gcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggattaacgccctggccgcg\n+catccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcaccctcacgccctggcgctgatcgccctcgccg\n+aaaaggtgttaccgcttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctctaccgc\n+ctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagccatgaacccgaaccg\n+ctaccgcctcgcgccccgcgaccgcttcagccgtgagcttgccgaaacgctctatcaggcggccgaagccgtcgcccgcg\n+tgattccgctcatgccggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgaccttctaacccatagc\n+gccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttgggttgtcgagatggcgcaagatcgcgc\n+gactaacgccgatttcaacaccgcccaagaaggactcgacgagcacgagtccctagcctttgtcgccgactggctggaag\n+ccgaaggccaggacgtgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactcgccgcccgccgcgac\n+gccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgggcgacgtgatcaccgacgccttgcg\n+cccctatctgggcgccgccctggccgaaaaccacgccgacgacgtgctagacgccctcacgcgcgccggcttccaaatca\n+cccgcaaggaggcctaaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcgccatcgcggccgata\n+atctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctgtaactacgccctgacgcgcgcgacc\n+atgctcaaggccgccgaccaaatcggcgaggcgctggaggcgctgggcgccctgcaagcgggcggctatgtgatcgcccg\n+ccgccgcgacgttttcaccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacgccgtcccgaactacg\n+ccgtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtctatcagccccggttccgggtcaagctg\n+gacgccgcgcccggcgcgcttttgaccgactgcgacacgggcgcaacggtctatttccagccgggcgacgacgccgacgc\n+cttccgggccgaattcgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctggcctcgatgatgaacc\n+cgaccgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctgaccttcgccccgcaatcgacgcgct\n+acgccgtggaagtccccgaacgcgactttctggccctgacccgcgccgaggaaattctagcccctggcccctatctggag\n+ccgtcgcttagcgagcgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccatttcggcgcggccgttta\n+cttgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcgatcatcgccgaccaactggccaagg\n+ccaaggcgtggaagcgccagcccgcctaagtcatcattcctatcgtctatgacttgtcaccggccgaactcttgcccggt\n+gacagtctgggcaagtaaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcctcgaa\n+gctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaacggtttgttaacccctggccctctag\n+ggtcgaattcccggcgcggcaatcccgccgcccggccttccttcggagcttctgatcatgttcgcttccgtgacccttcc\n+cgcccatgacgcccaaggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgcaacatttcgaccacg\n+tgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgaccacgcgcaagccgccgtttgcttcacc\n+gtctcggcgacccccgccgcgtgggaagccaagggcgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgc\n+cgccgactgcgacgccccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagccctgg\n+cgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctcccccgccagcgtgaggacaaggccgcc\n+cgcttcgatcgcctgaccgcctagcccctggcctccccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtc\n+tgtttacttgttgttaaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccgcccctttctggatcg\n+ctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctggcttgccttgagcctatcgccgccgc\n+cgctaagaccgccccggccgccgaccgcgccgccctttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgcc\n+gcaacctcacggaaaccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacgcctat\n+cagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccgccgccctaaaggtcctgctagacgg\n+ggagccggtcaaggcggtgcgcgccgccgaaggcgcggcgctttcggtccgcgctcgctacgccaacacccgcctttaac\n+ctcttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcctcgctc\n+ctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgccgattcgccagccgcg\n+cggcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtc\n+tggtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgccacctag\n+tatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc\n+=\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/karma.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/karma.fa Thu May 21 22:49:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,3699 @@\n+>karma\n+gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggt\n+ccgagtggaagtaccaaagatttgctttggtttatcaacaacttgccgacgcggcctcgg\n+acacctccatcgcgtccaagtttcagacctacgatcacctgccccacctggagccgaagg\n+tgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc\n+gcaaggagcacttccggcgggtggtggtcagcgtcgactcggccaacaagcccggcgccc\n+gcaacgactacagcgtcgcccaggtctggggggagacccacgcccgcaagcactacctga\n+tctaccaggagcgcaagaaggtcgacatcaccggcctgaccgagatgatcgagcgggtgg\n+ccaagcgctacgaggtcgacgccatcctggtcgaagacaagggcaacggcaccgcctaca\n+tccaggcgcggggccagaccgacagccagcggcggctcgccccggccccgatcgaggcga\n+tccaggtcccgagcacctattccaaggagttccgcttcaacgagatcgtcccgatgatcg\n+aggccggcgaggtcttcctgccgggcaaggccccgtggctcgacctgctgatccgcgaaa\n+tcggtcagttccccgaaggcgcccatgacgaccaagtcgacgccatgacgcagtacctcc\n+gctgggccaagtccaagcgcacgcggttcggcgcgcgcaaggtcggctcgatgggctgac\n+gaggcccgttaaccacgtttgttaacctccgccggggccttaaccctaacacggcgaggg\n+ttaacaggtccagggacccttcgaaattaacctttcggggaccctgggaaatcgtaaggc\n+agggaccctggccattttccggctggggaccctggcaaattcaccgccggggaccctccg\n+aaattcatcctcggggaccctggcaaatcaaggagccggcgatggccgaatttctcgccc\n+tgatccccaacctcgcgccgttcctggtctggggaatcctcctctggatcgccgccgagg\n+tggtctggagcgtctgcctctgggtctatggcctgcggaccctgttcaagttgcaccgcg\n+atgatctggccgaggcgatcagcttcgagcgggccttgagccccttcgactaggcgcggc\n+ctgccgacctaagtcacggactgtaggtttcgtgacaaggtgagatattccacaacgatt\n+tcaaaggcttactgcgatgtcgatccgcacgttcttccacgatctggccgtccgtttcgt\n+cgttttggggtggatttttgcccgaaaaccgctgaaatgggctccaaaagggcataattt\n+tcagcctaaaccgccggtccaggtcggcgccctggcggccggctcgctcctcgccctcag\n+tctggcgctcggcgggctctggttccgcttcacgtttccggacaaaagtcaagtggtctc\n+gcgccggccgcaggctatgtcatagaccgtgggcttcgtgaccagatcacgcttccgtta\n+ccgctccagcccttgtgaggcctcggatgttcgcctttctccgccggctcagcctcgccg\n+ccgtccatggcgtgctctgggcgatcctcctggcgatgctcgccctgggcgggccgcgcc\n+gcccgctctaaagcgtcatatctgacgcctaaggccccctaaggcctcatctgtgagaca\n+ttcaacgccctcgtgttcctctgaacgcgggggcgttttgacgtcggcgcatttttgact\n+tgacgcgcgagcgttttgacgcgggcgcatttttgattcgacgggcgagcgttttgacgt\n+ccgagcatttttcaacttgacgtcgttccatttaccgggagcgccttagggttaacgccg\n+gccgccgagccctggggcgatttaccaccgccacgttaacctaacgcctgttaacctatc\n+ggttgttaaggttaacgccccgttagggttaacgccccttaaccctgcccgcgttaaggt\n+taacgcgccccggcccaggccctacccgttaaccttaaccgcccgacccccgcgcccagg\n+ccatacccggtagggcctgacggccctaccgggtatgaccccgcgccccggcggaggcca\n+gggaccgccccggcgctttttcgcgccccgtttaccttttgttaacgtctggcctctagg\n+gtcgcccttgtccccgccgcactcccgcgccgggcaaggagcttcccgccatggtccccg\n+actcgatcatgaacccccgcgaccacttccaccgcctgcgcgaggaaaccgcccgcgctc\n+tggtcgaggccttcgccgaatccgaccccggcgaggattaccgcgccgaggaaaaggccg\n+gcgcgtgggttgtcgcctattacgacgcggcgggcgaattcgtcgcctatctctagccgc\n+cttcgccccctggcgccgcgttaacggtttgttaacatgtcggcgccagggtcgccctag\n+cccggcgcgtcgccgcgccttcggagaaaaccgccatgctctacacccccgccgcccgcc\n+gccttcgcggctatcgcgaaaccgccgcgaagaacgccgaaattcacgcccgcccgcaca\n+tggccggcaacgtcgccggctacaacgagtcggtgtggccgacgacggcgctaggcgtcg\n+ccgccaaggccggcgccttcaagcgccccgaaaccgccggcaactggtcggaggatcgca\n+aagcctattacgcccccgcgtggccggccggctggcgcgtgctgggcacggccgaagagg\n+tctgccgcaaggaaggctcgcgccgggtggaacattccggatggtacacgacgcccgacg\n+actacagcgccacgctttcgggctatgtgctgcaaatccccgcccgcgacggccgcccgc\n+aatacgtcgccgggaccgcccatagtgaatgggacggggtgaccctctaccccgccgacc\n+gctacgacaacccgcttgacgcggcgagcgccgccgaccgtcacgccgaacgcgacgccg\n+aagaggaacgcgaatatcaaaccgcgtggcaagcgggccagcgctacgccgaactcggcg\n+ccgaagccaaggaggcccgcaaggaagcgctggcgatcctcgccgaacgccgcaaggtca\n+aggggctggaaacccccgccttgtgcggcgcgatccgggcgcaagtcgcggccctgctag\n+gccggatcgaagaggcgcgcgcctcgcgcgccaagctcaaggaaggcgaggactcgcgcc\n+tcatgttctacccctccgccgccatggtcgcggccttcaatgacggcgcggcgtcgtgaa\n+ggtcgcccgcgatagcttcgccgtgttctggaccctcccgcaaggcggggtccaatttca\n+cgccgacataaaacgggcgctctatccgaccgcccgcgacgccgcccgcgcttttagcgc\n+catgttcccccgtgaccgggtccggagcgtccgcgacgcctccggccgcttcctggcctt\n+caaggagtccgccccgtgcgcctgacaagctacaacgtcaacggaaccggctttaagggc\n+ggctccgccccgcccgtccccgcccaaggcctgaccggtcacgccgacggcttgaacctt\n+tgggttccctcgcgcgagcatatcgccgccatgctcccgcaacgctggcgccacgccttc\n+gcccgcgcgtcgttttggtatgacgcgcacgacaataaaaagccgtgtcgcgccgacctc\n+tacgactcgcgcggccggtacctgactcaggtctgggcgcacccggttttcagctaggcc\n+agg'..b'ggcgaatatcgcgtgaccct\n+gcgctttggcccgctccccatggggcgcggcgcccaagagtggatgcgcgcgcgccgcga\n+agccgtcgccagctacagcgacgacaaggccgacgccctggccaccgcccgcgacatgtc\n+cgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcacaaccccgccta\n+agaccccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatc\n+gcaccccatgaccgcccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgac\n+ccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcgcgaattcgagcgtca\n+agcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagc\n+cgcccgcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctg\n+cgcccggattaacgccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggccc\n+gcccgatgacgcaccctcacgccctggcgctgatcgccctcgccgaaaaggtgttaccgc\n+ttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctct\n+accgcctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaagg\n+ccgcctaagccatgaacccgaaccgctaccgcctcgcgccccgcgaccgcttcagccgtg\n+agcttgccgaaacgctctatcaggcggccgaagccgtcgcccgcgtgattccgctcatgc\n+cggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgaccttctaaccc\n+atagcgccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttggg\n+ttgtcgagatggcgcaagatcgcgcgactaacgccgatttcaacaccgcccaagaaggac\n+tcgacgagcacgagtccctagcctttgtcgccgactggctggaagccgaaggccaggacg\n+tgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactcgccgcccgcc\n+gcgacgccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgg\n+gcgacgtgatcaccgacgccttgcgcccctatctgggcgccgccctggccgaaaaccacg\n+ccgacgacgtgctagacgccctcacgcgcgccggcttccaaatcacccgcaaggaggcct\n+aaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcgccatcgcggc\n+cgataatctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctg\n+taactacgccctgacgcgcgcgaccatgctcaaggccgccgaccaaatcggcgaggcgct\n+ggaggcgctgggcgccctgcaagcgggcggctatgtgatcgcccgccgccgcgacgtttt\n+caccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacgccgtcccgaa\n+ctacgccgtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtcta\n+tcagccccggttccgggtcaagctggacgccgcgcccggcgcgcttttgaccgactgcga\n+cacgggcgcaacggtctatttccagccgggcgacgacgccgacgccttccgggccgaatt\n+cgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctggcctcgatgat\n+gaacccgaccgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctg\n+accttcgccccgcaatcgacgcgctacgccgtggaagtccccgaacgcgactttctggcc\n+ctgacccgcgccgaggaaattctagcccctggcccctatctggagccgtcgcttagcgag\n+cgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccatttcggcgcggcc\n+gtttacttgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcg\n+atcatcgccgaccaactggccaaggccaaggcgtggaagcgccagcccgcctaagtcatc\n+attcctatcgtctatgacttgtcaccggccgaactcttgcccggtgacagtctgggcaag\n+taaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcc\n+tcgaagctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaac\n+ggtttgttaacccctggccctctagggtcgaattcccggcgcggcaatcccgccgcccgg\n+ccttccttcggagcttctgatcatgttcgcttccgtgacccttcccgcccatgacgccca\n+aggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgcaacatttcga\n+ccacgtgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgacca\n+cgcgcaagccgccgtttgcttcaccgtctcggcgacccccgccgcgtgggaagccaaggg\n+cgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgccgccgactgcgacgc\n+cccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagc\n+cctggcgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctccc\n+ccgccagcgtgaggacaaggccgcccgcttcgatcgcctgaccgcctagcccctggcctc\n+cccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtctgtttacttgttgtt\n+aaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccgcccctttctg\n+gatcgctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctgg\n+cttgccttgagcctatcgccgccgccgctaagaccgccccggccgccgaccgcgccgccc\n+tttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgccgcaacctcacggaaa\n+ccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacg\n+cctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccg\n+ccgccctaaaggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcg\n+cggcgctttcggtccgcgctcgctacgccaacacccgcctttaacctcttgttaacacct\n+cccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcct\n+cgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcgg\n+ctcccatgccgattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcg\n+tgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtctggtctgaccagacc\n+cccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgcca\n+cctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcg\n+gcgccccc\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/merged.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.fa Thu May 21 22:49:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,6360 @@\n+>phagey\n+tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac\n+aaccagaaggtttacatctttacatggcaattggatcgtatgagtcggccattaacaaat\n+atgcgcacccatataatcctggttactggaataagtataagaaactaaaacagaaaatcc\n+ttcagtggcagcagcaaatcagttaatacatagaagaagggttagaggagggaaaggaaa\n+tgggaacaggattaaatgaacaattcgtagatgacatcgtgaaactaacgaaagaagcgg\n+gttcaaaagtggaggcagtattaaaggtgatgagttatctttcagctgagtattatgtaa\n+tagacgcagacattgtaccagacccggataactacttgtacgaaagagatatattccata\n+tggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg\n+aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttac\n+tatacaacagaggatacagaaaaggttcggatgacgcggccactattatactagatcgca\n+tggaggaagtctttgagttatcagaagaagacaaggagtatagaagaaaaatgcagggag\n+gtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg\n+gagaaactattcgattattttgcttcagaagggtataccgtgtcattagctggtgcggag\n+attaacacaggtacagaaggtagtattaactctaagcaactaacaatctttaaaccaggg\n+gaagagaggaagtataacagtgtagacgaaatggtgaaagacttgaatggtgtactttat\n+ctattcgaagaccaaccctgtacatttagtgtaggttgtgacgtagtgatgattatagga\n+gaccagacacacttcgatgttgaagactggggagtgtacgaggatgaaaagacgggtaac\n+gtaacgatctataacgcggattctgatagggttattacactgtttaaaggtatagagtgt\n+ggaacgatcgccacaacagccctgcaggtaactaccttagcaagaatggcaaagttgccc\n+gaccgatggaacgtgtctctacgtgacgatgagagccttaaatcggtaagtaagtctaga\n+gctatcggactaagtgaactaacggaggagggaatgaaagatgtataacgaagaacgaga\n+cattgccattaacgatgcatttgtaaatgtatatgatcgctgtccgacacaggaagagat\n+aaacgagattacagataatctacccgcacatgtcgtagaagaagcaatgcgatgggggtg\n+gaacgacacgcctgtaggggacgctatcttccgctatatccaggctaataagattaaaca\n+tgtaccaaaggaagtaaagttttacttgaatggtgaatatattgcaagtgcgactacgct\n+tgatcctgctaaggtatttaagagtggggaggggaacaaatgaagacaccaactgaatgg\n+gttgacgatatagtaggtgcctgggtcggggatgacccgattaattacgcttatcatatc\n+gcttgtttgtataatacactggacatgactatgattagccaagttataccagaggtaaac\n+gagcagcaagccagttacttagaagacgtaaaagaaaatccgtataaaccattataagga\n+gggaaactagtatggaaaaaacggagttagctttagacattgcaaacattctgtattctg\n+cacagagcgataaagatgccttatggaaggttatcgctctgttgcaaaagaagtacctag\n+taatagataatcatcaccttcatcaagataacccatacaaccgcatgggcgaggaaggct\n+atttagttgaatctgtccaagtgcttctagccgagtttaaggagggggagtagtatgacc\n+gaggaaaataagtacacaatagagctgaaaagtaaaacagtagaggaacatattatgaaa\n+gaaaaacaccttcgtaagatgctccataaggattgtaactatttggttctttctaaaata\n+atgtataaacgaatgatagtagaggcccaacgagcaatattaggtgaaatagacgtaact\n+gcacctgcttttgactatacgaaatacattgaggagccaaacgagtatatgggcatgaag\n+gttattgttctcgatgacgaggacgagacaattaggatagggtaagtataccggccttta\n+gtagcacaccacgctaggggccggaaaataaaatcttttttttaaatagttgttgacttt\n+aaggaaaccgtattatacaatagagttacagataaggaggagataacaaatgataattca\n+aacagtacttaaaatgtacgactcggaggggacgctagtgtctcaacgcaaagtacactc\n+acctacagaagctacaatagagaagatgatggacttaacacccgatgtagtctacagtga\n+gctagaaactaggtatgttaaaacgaggtcagaaaatgcaaaaaattaaagacggtctat\n+atatcataggagctatagtcgggtttattctctttcttatgatagccgctttcttactaa\n+caaatgtatatgatgcagaaggaattccagttataacgctcatcggattatgttcggcca\n+tcggaacattactactagacttaacaattgagaggtggaaagaggagtatgaggaggaag\n+acaaatgagtcagctactggttactataatcggttctgcaataggttctattctagcaat\n+aaccatcatatcaatattaaagagaaaataaggaggaagaaggaaaatgagtctaatgtt\n+attcattcaaattgctttaactgttatagcccttagcggggttgcactaattataagtat\n+ggtgttcttaacaagatcaattaaccgtttaaaccgtgcaacacttagaaacttggatac\n+agtagaaaggatgagacgtaatggagccgtataaaattattgaaatgttacagaaagcag\n+atgttgatccaaacatacatagtgtactcactctagactatctaacaggtatcgactcat\n+tagacaaaggaaaccaaccaactgaagaagaatggtacgctatgggtctagtagaaggac\n+taatcgagggagggaataacaaatgagtagtactaaaacagcaaaagcggaggaaaaacg\n+tgttaagcacattatggactctctaaccaggtactataccgggaaagagaatagcttaga\n+caatgctagtgagttgtttaaaggtctaataacagtaccagggcttattgttccagccga\n+tgatgtaatattcttcaaatcactagtagtacctgctatttttattcaaactaagggaag\n+aataaacctaattgagttgcacgagtgtgaacgtgggttaatcaacagtgtggtctataa\n+cgcagaattagttaacaaatttcttaaacgttataaaactaaggaggagactaaaatgaa\n+agaacttgaagggtttgagatactaccaacaatcgaggaagacagcagtgaagagtataa\n+acctctattagaggtgctacctgaactaaaagaaggggatgtacttgaggtaccttctaa\n+tacaatgaatattactgttgttaatacacagctggtgtggcaagatatagccggtgagtt\n+aggtagtcccgtagactttaatctacctagactaaaaacacctgtacgtatacaacctaa\n+atatgtaggctggcgagaagcacttgaagcatacgaggacggctaccgaattgaatgcaa\n+at'..b'ggcgaatatcgcgtgaccct\n+gcgctttggcccgctccccatggggcgcggcgcccaagagtggatgcgcgcgcgccgcga\n+agccgtcgccagctacagcgacgacaaggccgacgccctggccaccgcccgcgacatgtc\n+cgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcacaaccccgccta\n+agaccccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatc\n+gcaccccatgaccgcccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgac\n+ccgccgcgccgcccgcctcaactggtcggatgagcgccgcgctcgcgaattcgagcgtca\n+agcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaaggccaggaagc\n+cgcccgcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctg\n+cgcccggattaacgccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggccc\n+gcccgatgacgcaccctcacgccctggcgctgatcgccctcgccgaaaaggtgttaccgc\n+ttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatcggcgacctct\n+accgcctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaagg\n+ccgcctaagccatgaacccgaaccgctaccgcctcgcgccccgcgaccgcttcagccgtg\n+agcttgccgaaacgctctatcaggcggccgaagccgtcgcccgcgtgattccgctcatgc\n+cggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgaccttctaaccc\n+atagcgccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttggg\n+ttgtcgagatggcgcaagatcgcgcgactaacgccgatttcaacaccgcccaagaaggac\n+tcgacgagcacgagtccctagcctttgtcgccgactggctggaagccgaaggccaggacg\n+tgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactcgccgcccgcc\n+gcgacgccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgg\n+gcgacgtgatcaccgacgccttgcgcccctatctgggcgccgccctggccgaaaaccacg\n+ccgacgacgtgctagacgccctcacgcgcgccggcttccaaatcacccgcaaggaggcct\n+aaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcgccatcgcggc\n+cgataatctccgccaaggcccggccatgtccaaggccgccgacaacgtcaccaacgtctg\n+taactacgccctgacgcgcgcgaccatgctcaaggccgccgaccaaatcggcgaggcgct\n+ggaggcgctgggcgccctgcaagcgggcggctatgtgatcgcccgccgccgcgacgtttt\n+caccgatgcgggcgagaagctgggcgacctgttggcggcgctttatgacgccgtcccgaa\n+ctacgccgtaagatcgcagcgcctcgccgacgccctgagtcccgcgcgaaattacgtcta\n+tcagccccggttccgggtcaagctggacgccgcgcccggcgcgcttttgaccgactgcga\n+cacgggcgcaacggtctatttccagccgggcgacgacgccgacgccttccgggccgaatt\n+cgccccgtgggttcacgccgccaacgtgacggccgaaggcgcggccctggcctcgatgat\n+gaacccgaccgccgaagagtatttcagccccgccacgggggtctaacgcccgtggccctg\n+accttcgccccgcaatcgacgcgctacgccgtggaagtccccgaacgcgactttctggcc\n+ctgacccgcgccgaggaaattctagcccctggcccctatctggagccgtcgcttagcgag\n+cgtttggaggcgcaagccggcgtttgggatgtcgagtataacggccatttcggcgcggcc\n+gtttacttgacgctcgacgttgacgccgactccccggccgcccgcgacgccctggcctcg\n+atcatcgccgaccaactggccaaggccaaggcgtggaagcgccagcccgcctaagtcatc\n+attcctatcgtctatgacttgtcaccggccgaactcttgcccggtgacagtctgggcaag\n+taaagctcactctggattttatgacttagcgcaaaggattgaaattgctcgaaaaattcc\n+tcgaagctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaac\n+ggtttgttaacccctggccctctagggtcgaattcccggcgcggcaatcccgccgcccgg\n+ccttccttcggagcttctgatcatgttcgcttccgtgacccttcccgcccatgacgccca\n+aggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgcaacatttcga\n+ccacgtgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgacca\n+cgcgcaagccgccgtttgcttcaccgtctcggcgacccccgccgcgtgggaagccaaggg\n+cgggcgcctcgcgcgccggctggaaaacctcgccgcgcgctatgccgccgactgcgacgc\n+cccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcgctctggaagc\n+cctggcgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctccc\n+ccgccagcgtgaggacaaggccgcccgcttcgatcgcctgaccgcctagcccctggcctc\n+cccctagcgcaccgcccctagaaaggcggtgcgcttttctgtgtctgtttacttgttgtt\n+aaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccgcccctttctg\n+gatcgctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctgg\n+cttgccttgagcctatcgccgccgccgctaagaccgccccggccgccgaccgcgccgccc\n+tttcctacctgctcgacgctggcgagtatgtcgccgcgtggcgccgcaacctcacggaaa\n+ccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcgctcgctaacg\n+cctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccg\n+ccgccctaaaggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcg\n+cggcgctttcggtccgcgctcgctacgccaacacccgcctttaacctcttgttaacacct\n+cccggctatggtcgggaggtcgcaaggagacacccgacatgacccgccccggccccgcct\n+cgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcgg\n+ctcccatgccgattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcg\n+tgacgctgggcgcggcgctctacctcgccgcccgcgtgttcggtctggtctgaccagacc\n+cccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacacacccccgcca\n+cctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcg\n+gcgccccc\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 test-data/phagey.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phagey.fa Thu May 21 22:49:06 2015 -0400 |
| b |
| b'@@ -0,0 +1,2661 @@\n+>phagey\n+tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacac\n+aaccagaaggtttacatctttacatggcaattggatcgtatgagtcggccattaacaaat\n+atgcgcacccatataatcctggttactggaataagtataagaaactaaaacagaaaatcc\n+ttcagtggcagcagcaaatcagttaatacatagaagaagggttagaggagggaaaggaaa\n+tgggaacaggattaaatgaacaattcgtagatgacatcgtgaaactaacgaaagaagcgg\n+gttcaaaagtggaggcagtattaaaggtgatgagttatctttcagctgagtattatgtaa\n+tagacgcagacattgtaccagacccggataactacttgtacgaaagagatatattccata\n+tggataatgagacagaatttcttttagaagaaacatttaataaggaggacaattaaatgg\n+aagtaaatggggatgttatcctaggcggggttgcggcttttgtactttactcgtggttac\n+tatacaacagaggatacagaaaaggttcggatgacgcggccactattatactagatcgca\n+tggaggaagtctttgagttatcagaagaagacaaggagtatagaagaaaaatgcagggag\n+gtaaataatatgtatgaaaatgtgttagacgttatcaattgtagaacaaaagaggtagcg\n+gagaaactattcgattattttgcttcagaagggtataccgtgtcattagctggtgcggag\n+attaacacaggtacagaaggtagtattaactctaagcaactaacaatctttaaaccaggg\n+gaagagaggaagtataacagtgtagacgaaatggtgaaagacttgaatggtgtactttat\n+ctattcgaagaccaaccctgtacatttagtgtaggttgtgacgtagtgatgattatagga\n+gaccagacacacttcgatgttgaagactggggagtgtacgaggatgaaaagacgggtaac\n+gtaacgatctataacgcggattctgatagggttattacactgtttaaaggtatagagtgt\n+ggaacgatcgccacaacagccctgcaggtaactaccttagcaagaatggcaaagttgccc\n+gaccgatggaacgtgtctctacgtgacgatgagagccttaaatcggtaagtaagtctaga\n+gctatcggactaagtgaactaacggaggagggaatgaaagatgtataacgaagaacgaga\n+cattgccattaacgatgcatttgtaaatgtatatgatcgctgtccgacacaggaagagat\n+aaacgagattacagataatctacccgcacatgtcgtagaagaagcaatgcgatgggggtg\n+gaacgacacgcctgtaggggacgctatcttccgctatatccaggctaataagattaaaca\n+tgtaccaaaggaagtaaagttttacttgaatggtgaatatattgcaagtgcgactacgct\n+tgatcctgctaaggtatttaagagtggggaggggaacaaatgaagacaccaactgaatgg\n+gttgacgatatagtaggtgcctgggtcggggatgacccgattaattacgcttatcatatc\n+gcttgtttgtataatacactggacatgactatgattagccaagttataccagaggtaaac\n+gagcagcaagccagttacttagaagacgtaaaagaaaatccgtataaaccattataagga\n+gggaaactagtatggaaaaaacggagttagctttagacattgcaaacattctgtattctg\n+cacagagcgataaagatgccttatggaaggttatcgctctgttgcaaaagaagtacctag\n+taatagataatcatcaccttcatcaagataacccatacaaccgcatgggcgaggaaggct\n+atttagttgaatctgtccaagtgcttctagccgagtttaaggagggggagtagtatgacc\n+gaggaaaataagtacacaatagagctgaaaagtaaaacagtagaggaacatattatgaaa\n+gaaaaacaccttcgtaagatgctccataaggattgtaactatttggttctttctaaaata\n+atgtataaacgaatgatagtagaggcccaacgagcaatattaggtgaaatagacgtaact\n+gcacctgcttttgactatacgaaatacattgaggagccaaacgagtatatgggcatgaag\n+gttattgttctcgatgacgaggacgagacaattaggatagggtaagtataccggccttta\n+gtagcacaccacgctaggggccggaaaataaaatcttttttttaaatagttgttgacttt\n+aaggaaaccgtattatacaatagagttacagataaggaggagataacaaatgataattca\n+aacagtacttaaaatgtacgactcggaggggacgctagtgtctcaacgcaaagtacactc\n+acctacagaagctacaatagagaagatgatggacttaacacccgatgtagtctacagtga\n+gctagaaactaggtatgttaaaacgaggtcagaaaatgcaaaaaattaaagacggtctat\n+atatcataggagctatagtcgggtttattctctttcttatgatagccgctttcttactaa\n+caaatgtatatgatgcagaaggaattccagttataacgctcatcggattatgttcggcca\n+tcggaacattactactagacttaacaattgagaggtggaaagaggagtatgaggaggaag\n+acaaatgagtcagctactggttactataatcggttctgcaataggttctattctagcaat\n+aaccatcatatcaatattaaagagaaaataaggaggaagaaggaaaatgagtctaatgtt\n+attcattcaaattgctttaactgttatagcccttagcggggttgcactaattataagtat\n+ggtgttcttaacaagatcaattaaccgtttaaaccgtgcaacacttagaaacttggatac\n+agtagaaaggatgagacgtaatggagccgtataaaattattgaaatgttacagaaagcag\n+atgttgatccaaacatacatagtgtactcactctagactatctaacaggtatcgactcat\n+tagacaaaggaaaccaaccaactgaagaagaatggtacgctatgggtctagtagaaggac\n+taatcgagggagggaataacaaatgagtagtactaaaacagcaaaagcggaggaaaaacg\n+tgttaagcacattatggactctctaaccaggtactataccgggaaagagaatagcttaga\n+caatgctagtgagttgtttaaaggtctaataacagtaccagggcttattgttccagccga\n+tgatgtaatattcttcaaatcactagtagtacctgctatttttattcaaactaagggaag\n+aataaacctaattgagttgcacgagtgtgaacgtgggttaatcaacagtgtggtctataa\n+cgcagaattagttaacaaatttcttaaacgttataaaactaaggaggagactaaaatgaa\n+agaacttgaagggtttgagatactaccaacaatcgaggaagacagcagtgaagagtataa\n+acctctattagaggtgctacctgaactaaaagaaggggatgtacttgaggtaccttctaa\n+tacaatgaatattactgttgttaatacacagctggtgtggcaagatatagccggtgagtt\n+aggtagtcccgtagactttaatctacctagactaaaaacacctgtacgtatacaacctaa\n+atatgtaggctggcgagaagcacttgaagcatacgaggacggctaccgaattgaatgcaa\n+at'..b'acaggtaatgaacactttatttatatggaggagttcgaaacaggagaac\n+tactaactctaatagtattggagggaaattagatgactctaaagtatgattaccgtgtac\n+aagcaaaagccaaccacgtttgtcatatgatttgggaagaaacaggaaaagtagatcacc\n+cgtcacctaagcttagatcagatgtagaagacaccatgatggctgcagttaattattata\n+aggtagcgttagataatgaattacagaagaagaacgagtataagctaaacgaacttagaa\n+gaggtatacataggttaaagcctaactcgcatgaagatattatagatttattcgctaagg\n+ttatggccggtgaaagtgtacaaacaatgaaaccatataaaagggagagagaattagtat\n+gacaaaattgctaaaagaagaatggccgaagaatattgatgaacttatcgcttacttcca\n+ggagttaaaagagtactctagagattacaacacatctgcggaagcagtagcctatggtac\n+agtagcggcatttaactatttagcagcagacgaacacggattgactggattccaggctag\n+ttggtctgctatgaaagctttgtctattattagaaatattgatggtgcgtttactattgt\n+tagtacggatgccttaaagtttaataccatcgaagatgaattagctcgtgtaaagaagtt\n+tttacacgacagcattaaaaagcaggaggagaataacaatgagtaacatatttgttgtcc\n+agtattctaatgggttagaacatgagcagttagagaccgatgtagtagcggtattcgatt\n+ctgaaaaggaaatacgagcgtacgcagaacgagaagggtttgttccttataatggtattc\n+ttatttgtgggttctatagagagtacaagagcggacaccgggacttactatttgtctcac\n+cagtgaaaataaacgagcctattgtggcttgtttggaggagttagagtgagcaagtcaga\n+tataactcgtaggctagaaaaggcaatttacacggcgacgattaaacaaggtgtgtttgg\n+ttgttttgaggttacaatcggttggttcgggaaagagcgtgtggatttcataacctacga\n+cacaaaaaatatctggcgatgctatgagattaagtcctctgttgcggactttagaagtga\n+ggcttacaagactttctgcggtaattacaactactatgtgatgactaaggaactttatga\n+gaaggttaaactagaaattcccacccatattggggtttatattgagggccgttgtgtcaa\n+gcgacctaaaaggcaagaagtaactgtggaagaggaaatactaaagaattcactaatacg\n+ttcactagctagagaagccgacaaacttgctaagagcaatgatcctgatttgttaaatcg\n+gctacgaagaagcttagctagagaacaagaagacaaaagaaggtacagtcgggagtacac\n+agacttgaaaaataaattatataggaagtacggccgaaactgggaggaggtactagagtt\n+agaatgaattatacagatgctaagatagcaattcaagtattacatgcagcgggatatagg\n+aaatggataaaaggggagccgtactaccacaaacgatgggaacggggctcgaatgactat\n+aaccagcttatatcattcaatgaaattaaatattcgctaatggatatcccttggattata\n+cagaagtacgaagaaaaagccgaaggagagttagaaaaattaaatgaaggagagtgctgt\n+taaatgggcggttacattgcgttacaacccaacgggctatactgcaggtattccacagtg\n+gtagaggctttaacacatataaacatgacgagggaagattatgtatctaattttacaggt\n+acagtaagaagccgagaggaagcggaagacatcttgggtaactatctacatagcttcagt\n+accgtagagaaaatggtcactcgactgaatgtagaggaagcggaatggaagagaattaag\n+acgcatgttacactacctaaaaacagtatatttgtctacccgaaagttttataaaaagta\n+ttgacaggtattggttggtgtagtaaactctaactatatcaaccaatacaaggaaaggat\n+gagtacaagttggcaaagaagaactttagttgggattcagaggagttactaggtatttac\n+cctgtatcagataaaaagcagtttgaatataagttatgtatgctaaaggacaaggagtac\n+gtatcagtagctgagcagcgcatgacagacgaaggctggaagtactacggaaacaaaacg\n+ttagagatgagtgtatacagacagttagtagcatttatggacaaccgttaatattttagt\n+aggtggttgacttatagcatatgttagccacctatcatactaaaggaggagttagtaatg\n+cggagaaaaattaagtgtgaattgtgtgatggtagcggtgcctcgccttggtctgctcta\n+ggagggccttgtatacaatgcgagggtgcggggtttctatttgaacctgaagggaagcct\n+aagtttaaggtagacttcggtgagttagacgggcttactaaaatggaagatactacagac\n+ttaagtgatccacatattaaaatagatatgaacggcatcagctttaaagacaaggatggt\n+aactggactgatccgacaaaaccattcgctaactttgaaaatatcacaattaaccactca\n+aatggtaaaactataaaaggcgggaaaggggttctgaaaccgatgggattattcgatgat\n+tttatggaggctattgaagcagaagagacaggaagaccaatcgtaaagcatttgctagtt\n+tggagtgttgatgagctactagaccttcacaacgattacaagcagctgtacgatctattt\n+aaggacgaggagtacttgctatatatgaaggacgtactaaaagttataaaagcaaaaaca\n+aattagtagtcattctttatagactgcacgcatagtataaactataacaagaagggagga\n+attacagtgaatgcggaagataaacgaattctaatgaaaatagtaggaagtatagccggg\n+atgtttataatgggatacctattcggtttcctaggggttattattagtttagtagctatt\n+tactttgtgtttaagaatgataatggtaagcaggtaggagaagacccggagagtgaagct\n+aaggccgcctttatctggttctgtgtgatgctagtgttagggatcgtgcttgcgtatcta\n+ttcggtatcattggagtaattatcggtttagggttaatcgcaggagccatctataatata\n+atgttcgggtaaataaagaattttttttaaatagttgttgactttaaagaaacatggtgc\n+tagaattagcttatcaaccaaaggaggtaacaaagtgagaataacacatgaacagaagat\n+ggaaattctcgaagagtggaaccttataggagagaacgattgtagaacggctctacctca\n+cttaacagagctacttactaaaatacttgatagtgtttctgatcctgaaaagataaactg\n+tgggtgttatgtgtggagtgaaaaactacaagagcatgttgaacctaatccactctgtaa\n+gaaatgcggcgggatgggttggtattacaagagagaaaggaagtaatcgatatgcaacag\n+acagcagctaagaacacacaaccagaaggtttacatctttacatggcaattggatcgtat\n+gagtcggccattaacaaatatgcgcacccatataatcctggttactggaataagtataag\n+aaactaaaacagaaaatccttcagtggcagcagcaaa\n+\n+\n' |
| b |
| diff -r 000000000000 -r aaa94e13ac60 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 21 22:49:06 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="progressivemauve" version="2.4.0"> + <repository changeset_revision="2a5b50fd549f" name="package_progressivemauve_2_4_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |