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Commit message:
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added:
busco.xml test-data/arthropoda/ancestral test-data/arthropoda/clade_parameters test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm test-data/arthropoda/lengths_cutoff test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl test-data/arthropoda/scores_cutoff test-data/genome.fa test-data/genome_results/full_table test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/proteome.fa test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/transcriptome.fa test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/short_summary tool_dependencies.xml |
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removed:
busco/.shed.yml busco/busco.xml busco/test-data/arthropoda/ancestral busco/test-data/arthropoda/clade_parameters busco/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm busco/test-data/arthropoda/lengths_cutoff busco/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl busco/test-data/arthropoda/scores_cutoff busco/test-data/genome.fa busco/test-data/genome_results/full_table busco/test-data/genome_results/missing_buscos_list busco/test-data/genome_results/short_summary busco/test-data/proteome.fa busco/test-data/proteome_results/full_table busco/test-data/proteome_results/missing_buscos_list busco/test-data/proteome_results/short_summary busco/test-data/transcriptome.fa busco/test-data/transcriptome_results/full_table busco/test-data/transcriptome_results/missing_buscos_list busco/test-data/transcriptome_results/short_summary busco/tool_dependencies.xml |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/busco.xml Mon Jan 18 11:00:29 2016 -0500 |
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| @@ -0,0 +1,97 @@ +<tool id="busco" name="Busco" version="1.1b1"> + <description>assess genome assembly and annotation completeness</description> + + <requirements> + <requirement type="package" version="1.1b1">busco</requirement> + <requirement type="package" version="3.1">augustus</requirement> + <requirement type="package" version="2.2.31">blast+</requirement> + <requirement type="package" version="3.1b2">hmmer</requirement> + <requirement type="package" version="3.4">python</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <command><![CDATA[ + python3 \${BUSCO_ROOT_PATH}/BUSCO.py + -in "${input}" + -l "\${BUSCO_DATA_PATH}/${lineage}" + -m "${mode}" + -o "busco_galaxy" + -c \${GALAXY_SLOTS:-4} + -ev ${adv.ev} + ${adv.long} + #if ($adv.flank): + -flank ${adv.flank} + #end if + -sp ${adv.species} + ]]></command> + + <inputs> + + <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> + + <param name="lineage" type="select" label="Lineage"> + <option value="arthropoda">Arthropoda</option> + <option value="bacteria">Bacteria</option> + <option value="eukaryota">Eukaryota</option> + <option value="fungi">Fungi</option> + <option value="metazoa">Metazoa</option> + <option value="vertebrata">Vertebrata</option> + </param> + + <param name="mode" type="select" label="Mode"> + <option value="all">Genome</option> + <option value="trans">Transcriptome</option> + <option value="OGS">Proteome</option> + </param> + + <section name="adv" title="Advanced Options" expanded="False"> + <param name="ev" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> + <param name="flank" type="integer" value="" optional="True" label="Flanking sequence size for candidate regions" help="If not provided, flank size is calculated based on genome size with a range from 5 to 20 Kbp."/> + <param name="species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> + <param name="long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds ~20h extra run time, but can improve results for some non-model organisms"/> + </section> + </inputs> + <outputs> + <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy"/> + <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy"/> + <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_buscos_list_busco_galaxy"/> + </outputs> + <tests> + <test> + <param name="input" value="genome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="all"/> + <output name="busco_sum" file="genome_results/short_summary" compare="contains"/> + <output name="busco_table" file="genome_results/full_table" compare="contains"/> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="contains"/> + </test> + <test> + <param name="input" value="proteome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="OGS"/> + <output name="busco_sum" file="proteome_results/short_summary" compare="contains"/> + <output name="busco_table" file="proteome_results/full_table" compare="contains"/> + <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="contains"/> + </test> + <test> + <param name="input" value="transcriptome.fa"/> + <param name="lineage" value="arthropoda"/> + <param name="mode" value="trans"/> + <output name="busco_sum" file="transcriptome_results/short_summary" compare="contains"/> + <output name="busco_table" file="transcriptome_results/full_table" compare="contains"/> + <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="contains"/> + </test> + </tests> + <help> + BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs + + .. _BUSCO: http://busco.ezlab.org/ + </help> + + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> + </citations> +</tool> |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/.shed.yml --- a/busco/.shed.yml Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -categories: [Sequence Analysis] -description: BUSCO assess genome and annotation completeness -homepage_url: http://busco.ezlab.org/ -long_description: Assessing genome assembly and annotation completeness with Benchmarking - Universal Single-Copy Orthologs -name: busco -owner: abretaudeau |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/busco.xml --- a/busco/busco.xml Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,97 +0,0 @@ -<tool id="busco" name="Busco" version="1.1b1"> - <description>assess genome assembly and annotation completeness</description> - - <requirements> - <requirement type="package" version="1.1b1">busco</requirement> - <requirement type="package" version="3.1">augustus</requirement> - <requirement type="package" version="2.2.31">blast+</requirement> - <requirement type="package" version="3.1b2">hmmer</requirement> - <requirement type="package" version="3.4">python</requirement> - </requirements> - - <stdio> - <exit_code range="1:" /> - </stdio> - - <command><![CDATA[ - python3 \${BUSCO_ROOT_PATH}/BUSCO.py - -in "${input}" - -l "\${BUSCO_DATA_PATH}/${lineage}" - -m "${mode}" - -o "busco_galaxy" - -c \${GALAXY_SLOTS:-4} - -ev ${adv.ev} - ${adv.long} - #if ($adv.flank): - -flank ${adv.flank} - #end if - -sp ${adv.species} - ]]></command> - - <inputs> - - <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" /> - - <param name="lineage" type="select" label="Lineage"> - <option value="arthropoda">Arthropoda</option> - <option value="bacteria">Bacteria</option> - <option value="eukaryota">Eukaryota</option> - <option value="fungi">Fungi</option> - <option value="metazoa">Metazoa</option> - <option value="vertebrata">Vertebrata</option> - </param> - - <param name="mode" type="select" label="Mode"> - <option value="all">Genome</option> - <option value="trans">Transcriptome</option> - <option value="OGS">Proteome</option> - </param> - - <section name="adv" title="Advanced Options" expanded="False"> - <param name="ev" type="float" value="0.01" label="E-value cutoff for BLAST searches."/> - <param name="flank" type="integer" value="" optional="True" label="Flanking sequence size for candidate regions" help="If not provided, flank size is calculated based on genome size with a range from 5 to 20 Kbp."/> - <param name="species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/> - <param name="long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds ~20h extra run time, but can improve results for some non-model organisms"/> - </section> - </inputs> - <outputs> - <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy"/> - <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy"/> - <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_buscos_list_busco_galaxy"/> - </outputs> - <tests> - <test> - <param name="input" value="genome.fa"/> - <param name="lineage" value="arthropoda"/> - <param name="mode" value="all"/> - <output name="busco_sum" file="genome_results/short_summary" compare="contains"/> - <output name="busco_table" file="genome_results/full_table" compare="contains"/> - <output name="busco_missing" file="genome_results/missing_buscos_list" compare="contains"/> - </test> - <test> - <param name="input" value="proteome.fa"/> - <param name="lineage" value="arthropoda"/> - <param name="mode" value="OGS"/> - <output name="busco_sum" file="proteome_results/short_summary" compare="contains"/> - <output name="busco_table" file="proteome_results/full_table" compare="contains"/> - <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="contains"/> - </test> - <test> - <param name="input" value="transcriptome.fa"/> - <param name="lineage" value="arthropoda"/> - <param name="mode" value="trans"/> - <output name="busco_sum" file="transcriptome_results/short_summary" compare="contains"/> - <output name="busco_table" file="transcriptome_results/full_table" compare="contains"/> - <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="contains"/> - </test> - </tests> - <help> - BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs - - .. _BUSCO: http://busco.ezlab.org/ - </help> - - <citations> - <citation type="doi">doi:10.1093/bioinformatics/btv351</citation> - </citations> -</tool> |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/ancestral --- a/busco/test-data/arthropoda/ancestral Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ ->BUSCOaEOG7B0HST -MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA -VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE -DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED -TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID -LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI -VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE -AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN -AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY -LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI -IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT -SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS -LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT -AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG -AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK -VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK -YQEIFLRALLQYVSDKSAEVRQAAAYGCGVLGQFGGEQFAEACAEALPKLVEVINDPESR -ELENINATENAISAVTKILKYNKSAITNVDELLAVWLSWLPVVEDEEEAAHVYGYLCDLI -EANHPVVLGANNANLPRIVSILAEAFLREVVEAESAVAKRLLSIVKQIESNEELLQACIS -ELSAEQQQALKEALRELAA |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/clade_parameters --- a/busco/test-data/arthropoda/clade_parameters Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#ARTHROPODA Clade parameters for BUSCOS -Z 102785 -sp1 fly -sp2 nasonia -sp3 generic -flank 5000 |
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| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm --- a/busco/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3319 +0,0 @@\n-HMMER3/f [3.1b1 | May 2013]\n-NAME BUSCOaEOG7B0HST\n-LENG 1099\n-ALPH amino\n-RF no\n-MM no\n-CONS yes\n-CS no\n-MAP yes\n-DATE Tue Apr 15 12:38:52 2014\n-NSEQ 23\n-EFFN 0.603638\n-CKSUM 3500044453\n-STATS LOCAL MSV -12.8285 0.69537\n-STATS LOCAL VITERBI -13.9416 0.69537\n-STATS LOCAL FORWARD -6.9634 0.69537\n-HMM A C D E F G H I K L M N P Q R S T V W Y \n- m->m m->i m->d i->m i->i d->m d->d\n- COMPO 2.48078 4.06146 2.86181 2.63028 3.29447 3.05836 3.78580 2.74928 2.73520 2.31160 3.52187 3.11102 3.40692 3.07770 2.99944 2.73817 2.93658 2.56860 4.67180 3.56430\n- 2.68613 4.42194 2.77509 2.73133 3.46348 2.40518 3.72504 3.29351 2.67743 2.69350 4.24642 2.90347 2.73745 3.18156 2.89802 2.37884 2.77522 2.98518 4.58487 3.61513\n- 0.08969 2.57172 4.66890 1.68962 0.20406 0.00000 *\n- 1 2.57261 4.35167 3.86119 3.40692 3.39776 3.63900 4.23782 2.41302 3.22676 2.05613 1.62924 3.68308 4.13489 3.59563 3.47552 3.02060 2.87665 2.31461 5.12383 3.92328 24 m - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 2 1.67850 4.50203 3.03694 2.37498 3.89784 3.30262 3.77719 3.19331 2.62660 2.92462 3.55380 3.06800 3.81401 2.99279 3.01679 2.53568 2.82599 2.89438 5.25006 3.96735 25 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 3 1.72593 4.51596 3.03450 2.62358 3.94870 3.02850 3.77178 3.31742 2.58759 2.83773 3.85577 3.06024 3.80166 2.49425 2.96418 2.62424 2.82773 2.99569 5.27761 3.99238 26 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 4 3.06989 5.20867 0.81737 2.38286 4.59580 3.26742 3.99737 4.20098 3.09568 3.79622 4.77615 2.94287 3.92548 3.23679 3.62179 3.02404 3.41012 3.83236 5.74996 4.45674 27 d - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 5 2.80194 4.77013 3.14922 2.71763 3.71311 3.52519 3.75923 3.19152 2.43092 2.26797 3.77243 3.16939 3.97062 1.69754 2.73211 2.88896 3.05024 3.01368 5.15367 3.80747 28 q - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 6 1.96528 5.02402 2.30355 2.05596 4.32542 3.05196 3.65086 3.77327 2.51296 3.33530 4.14888 2.71539 3.78621 2.65549 3.01420 2.66175 2.94409 3.40418 5.54285 4.15135 29 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 7 2.80616 5.09448 2.63904 2.23927 4.35587 3.37371 3.36290 3.83921 2.30093 3.36613 4.20407 2.73502 3.85607 1.67'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n- 1092 2.48411 4.80914 2.38269 2.16541 4.06714 3.19545 3.59049 3.47448 2.36289 3.08014 3.58530 2.86918 3.76448 2.73883 2.86648 2.59333 2.81189 2.86703 5.31779 3.97005 1199 e - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n- 1093 1.24199 4.14570 3.59318 3.27579 3.90565 3.06922 4.23995 2.85564 3.22241 2.82059 3.86698 3.41584 3.78036 3.55807 3.49165 2.52495 2.75938 2.36754 5.42950 4.19313 1200 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.06474 3.88362 3.16732 0.61958 0.77255 0.54401 0.86849\n- 1094 2.97106 4.49154 3.93866 3.46547 2.54041 3.89976 3.77718 2.63214 3.27427 1.57888 3.33399 3.70082 4.26271 3.58207 3.49841 3.23908 3.21105 2.56656 4.22346 1.92820 1201 l - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03209 3.85097 4.57331 0.61958 0.77255 0.57161 0.83152\n- 1095 2.60101 4.65512 3.08558 2.56003 3.93846 3.38076 3.35844 3.37716 2.29364 2.98880 3.84025 3.01919 3.81697 2.81258 2.11081 2.23871 2.85240 2.88090 5.19817 3.90318 1202 r - - -\n- 2.68618 4.42210 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37883 2.77520 2.98519 4.58477 3.61504\n- 0.08263 2.67392 4.57331 0.47744 0.96856 0.57161 0.83152\n- 1096 2.18154 4.62997 2.75539 1.99629 4.09189 3.21947 3.71130 3.44588 2.55475 3.11415 3.95949 2.91659 3.75436 2.89454 2.98369 2.45299 2.43810 3.09910 5.37976 4.06153 1204 e - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03209 3.85097 4.57331 0.61958 0.77255 0.52453 0.89608\n- 1097 2.46358 4.30538 3.37350 2.85594 3.45882 3.46342 3.46832 2.79047 2.73797 1.87351 3.43484 3.24873 3.57204 3.10968 3.06502 2.75631 2.66774 2.52856 4.91799 3.66813 1205 l - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.06381 3.88362 3.18837 0.61958 0.77255 0.54401 0.86849\n- 1098 1.76981 4.22446 3.25481 2.84716 3.91324 3.07102 3.91525 3.24756 2.83205 2.73784 3.84439 3.15656 3.31202 3.16923 3.18419 1.97191 2.69401 2.87700 5.28803 4.03807 1206 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.17726 3.85187 1.95758 0.61958 0.77255 0.57087 0.83249\n- 1099 2.12671 4.27681 2.94823 2.62386 4.02260 3.00213 3.81075 3.41128 2.69615 3.08313 3.92445 2.61229 3.24401 3.03239 3.07499 2.18871 2.34694 2.99753 5.34368 4.07427 1207 a - - -\n- 2.68560 4.42236 2.77531 2.73135 3.46365 2.40517 3.72506 3.29361 2.67747 2.69366 4.24701 2.90355 2.73729 3.18150 2.89812 2.37889 2.77501 2.98510 4.58488 3.61514\n- 0.29451 1.36610 * 1.25311 0.33633 0.00000 *\n-//\n' |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/lengths_cutoff --- a/busco/test-data/arthropoda/lengths_cutoff Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST 1099 16.763712248907 1099.28947368421 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl --- a/busco/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1179 +0,0 @@\n-[name]\n-unknown\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-2\t136\n-\n-[block]\n-# block no. 0 follows, 38 sequences, length 19\n-# corresponding to MSA columns:\n-# 159-177\n-name=unknown_A\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.00849\t0.00611\t0.00840\t0.00857\t0.00923\t0.00669\t0.00611\t0.00985\t0.00961\t0.01343\t0.01902\t0.11988\t0.02008\t0.26734\t0.45119\t0.00764\t0.01148\t0.00842\t0.00363\t0.00479\n-1\t0.04698\t0.19994\t0.01897\t0.01402\t0.05388\t0.40529\t0.01057\t0.01996\t0.01473\t0.02840\t0.01285\t0.12269\t0.01254\t0.00774\t0.00537\t0.00165\t0.00826\t0.00573\t0.00343\t0.00702\n-2\t0.10059\t0.05592\t0.04037\t0.12369\t0.03571\t0.33917\t0.01177\t0.05040\t0.04291\t0.12639\t0.01235\t0.01357\t0.00924\t0.00633\t0.00543\t0.00172\t0.00824\t0.00453\t0.00392\t0.00774\n-3\t0.00726\t0.00551\t0.00670\t0.00765\t0.00853\t0.00495\t0.00526\t0.00846\t0.01222\t0.01564\t0.04202\t0.55279\t0.26594\t0.01769\t0.00750\t0.00231\t0.00335\t0.01570\t0.00558\t0.00495\n-4\t0.01515\t0.01282\t0.01932\t0.01411\t0.01942\t0.01141\t0.20122\t0.08029\t0.06461\t0.07934\t0.01338\t0.01496\t0.01020\t0.00535\t0.00554\t0.00143\t0.00624\t0.00509\t0.00412\t0.41602\n-5\t0.01058\t0.00786\t0.01056\t0.13305\t0.01554\t0.00789\t0.00807\t0.01432\t0.07133\t0.05518\t0.29599\t0.18162\t0.03460\t0.01123\t0.00661\t0.00194\t0.00427\t0.02125\t0.02469\t0.08341\n-6\t0.05178\t0.16631\t0.50028\t0.01491\t0.02246\t0.01521\t0.03686\t0.01844\t0.01252\t0.01860\t0.01027\t0.01208\t0.00775\t0.00547\t0.00520\t0.00170\t0.00786\t0.00415\t0.00271\t0.08546\n-7\t0.01705\t0.01432\t0.01620\t0.01348\t0.01711\t0.07518\t0.07737\t0.22677\t0.26217\t0.05482\t0.04993\t0.11213\t0.01834\t0.00888\t0.00635\t0.00197\t0.00608\t0.00758\t0.00556\t0.00869\n-8\t0.01317\t0.01251\t0.02070\t0.15609\t0.52474\t0.01281\t0.01616\t0.01652\t0.01342\t0.01844\t0.01838\t0.02129\t0.11604\t0.00690\t0.00613\t0.00186\t0.00670\t0.00642\t0.00330\t0.00841\n-9\t0.01162\t0.00686\t0.00910\t0.00862\t0.01050\t0.00629\t0.00674\t0.01414\t0.01595\t0.14470\t0.42875\t0.11434\t0.07208\t0.01284\t0.00715\t0.00207\t0.00368\t0.11180\t0.00647\t0.00632\n-10\t0.01274\t0.01372\t0.12068\t0.01259\t0.01636\t0.01187\t0.04762\t0.04955\t0.31522\t0.02196\t0.05626\t0.13802\t0.02193\t0.00996\t0.00649\t0.00206\t0.00548\t0.07423\t0.00517\t0.05810\n-11\t0.00985\t0.00796\t0.01067\t0.01037\t0.01075\t0.00947\t0.00786\t0.01102\t0.01014\t0.01418\t0.01964\t0.14789\t0.02183\t0.26045\t0.10775\t0.00446\t0.21652\t0.11018\t0.00389\t0.00511\n-12\t0.00789\t0.00529\t0.00678\t0.00798\t0.00848\t0.00499\t0.00539\t0.00919\t0.01168\t0.01638\t0.03120\t0.67455\t0.03627\t0.01714\t0.00718\t0.00229\t0.00339\t0.01544\t0.12352\t0.00499\n-13\t0.00773\t0.00552\t0.00742\t0.00873\t0.00928\t0.00522\t0.00618\t0.00911\t0.01211\t0.01615\t0.06621\t0.64670\t0.03983\t0.01822\t0.00774\t0.00246\t0.00376\t0.11699\t0.00563\t0.00502\n-14\t0.23475\t0.01397\t0.01501\t0.05417\t0.12272\t0.06638\t0.01071\t0.11816\t0.17197\t0.11209\t0.01510\t0.01554\t0.01116\t0.00661\t0.00538\t0.00187\t0.00596\t0.00510\t0.00478\t0.00858\n-15\t0.01774\t0.01310\t0.01239\t0.01066\t0.01380\t0.13284\t0.00829\t0.12299\t0.12073\t0.17836\t0.04824\t0.03777\t0.12169\t0.04898\t0.00726\t0.00202\t0.00564\t0.00710\t0.08255\t0.00785\n-16\t0.00774\t0.00594\t0.00698\t0.00734\t0.00855\t0.00550\t0.00526\t0.00913\t0.01231\t0.01568\t0.07962\t0.21341\t0.34318\t0.13048\t0.08206\t0.00342\t0.00490\t0.04842\t0.00514\t0.00491\n-17\t0.01499\t0.01157\t0.01661\t0.08113\t0.01840\t0.01286\t0.11905\t0.12120\t0.08357\t0.07287\t0.05034\t0.01918\t0.01402\t0.00762\t0.00806\t0.00193\t0.13253\t0.00612\t0.20034\t0.00760\n-18\t0.02074\t0.06499\t0.01691\t0.01445\t0.01751\t0.60356\t0.01097\t0.07075\t0.01705\t0.01634\t0.01185\t0.08393\t0.01094\t0.00741\t0.00560\t0.00164\t0.00964\t0.00519\t0.00351\t0.00704\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-0\t1\n-\n-[block]\n-# block no. 1 follows, 38 sequences, length 22\n-# corresponding to MSA columns:\n-# 179-200\n-name=unknown_B\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.08270\t0.19710\t0.02137\t0.01349\t0.01801\t0.06215\t0.13254\t0.04863\t0.19656\t0.08108\t0.01574\t0.01622\t0.02523\t0.00640\t0.00542\t0.00172\t0.00649\t0.00534\t0.00432\t0.05948\n-1\t0.01139\t0.00879\t0.01512\t0.01313\t0.01560\t0.00826\t0.17794\t0.01415\t0.01395\t0.08259\t0.12369\t0.26603\t0.03144\t0.01318\t0.00747\t0.00230\t0.00560\t0.17772\t0.0'..b'01399\t0.02763\t0.59409\t0.01622\t0.02410\t0.01459\t0.01966\t0.15312\t0.01578\t0.02277\t0.03493\t0.01405\t0.00968\t0.00621\t0.00582\t0.00189\t0.00827\t0.00483\t0.00333\t0.00904\n-17\t0.01558\t0.61804\t0.05875\t0.01338\t0.01885\t0.02182\t0.14636\t0.01829\t0.01261\t0.01530\t0.00917\t0.01100\t0.00798\t0.00515\t0.00454\t0.00145\t0.00722\t0.00399\t0.00266\t0.00784\n-18\t0.03107\t0.12435\t0.21748\t0.02929\t0.04145\t0.01280\t0.01239\t0.04101\t0.05280\t0.01971\t0.03883\t0.03793\t0.01160\t0.00601\t0.00512\t0.00147\t0.00610\t0.00477\t0.00351\t0.30232\n-19\t0.01371\t0.36393\t0.29683\t0.15693\t0.02425\t0.01821\t0.01591\t0.01790\t0.01236\t0.01619\t0.00970\t0.01198\t0.00774\t0.00552\t0.00495\t0.00165\t0.00764\t0.00407\t0.00258\t0.00796\n-20\t0.16658\t0.02744\t0.61619\t0.01540\t0.02332\t0.01388\t0.01926\t0.01879\t0.01224\t0.02055\t0.01034\t0.01215\t0.00741\t0.00569\t0.00534\t0.00190\t0.00809\t0.00422\t0.00276\t0.00844\n-21\t0.02417\t0.01022\t0.01334\t0.01041\t0.01471\t0.00913\t0.00853\t0.08055\t0.01774\t0.60573\t0.05239\t0.02435\t0.08388\t0.00832\t0.00618\t0.00187\t0.00496\t0.00679\t0.00713\t0.00960\n-22\t0.01677\t0.01205\t0.08140\t0.01031\t0.01522\t0.00893\t0.00905\t0.02045\t0.05274\t0.25615\t0.06649\t0.04544\t0.01557\t0.00678\t0.00547\t0.00148\t0.00495\t0.00560\t0.00513\t0.36003\n-23\t0.16683\t0.01180\t0.01496\t0.01290\t0.01423\t0.01516\t0.01064\t0.01467\t0.00977\t0.01725\t0.00928\t0.01378\t0.00863\t0.01340\t0.10939\t0.00321\t0.46410\t0.00488\t0.00300\t0.08213\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-7\t16\n-\n-[block]\n-# block no. 22 follows, 38 sequences, length 6\n-# corresponding to MSA columns:\n-# 1247-1252\n-name=unknown_W\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.00733\t0.00524\t0.00698\t0.00838\t0.00873\t0.00489\t0.00558\t0.00838\t0.01152\t0.01536\t0.03316\t0.78466\t0.03979\t0.01885\t0.00768\t0.00244\t0.00349\t0.01710\t0.00558\t0.00489\n-1\t0.01041\t0.00709\t0.00808\t0.00738\t0.00993\t0.00599\t0.00575\t0.01235\t0.01441\t0.11123\t0.12398\t0.04824\t0.47386\t0.01304\t0.00680\t0.00193\t0.00356\t0.05072\t0.00575\t0.07949\n-2\t0.01430\t0.02608\t0.54722\t0.01765\t0.02555\t0.01352\t0.13402\t0.02039\t0.01351\t0.11246\t0.01266\t0.01425\t0.00878\t0.00583\t0.00598\t0.00192\t0.00861\t0.00507\t0.00324\t0.00894\n-3\t0.26692\t0.01203\t0.01543\t0.01222\t0.01656\t0.01225\t0.10707\t0.07068\t0.07963\t0.29248\t0.01726\t0.01826\t0.01233\t0.00696\t0.00558\t0.00193\t0.00575\t0.03264\t0.00543\t0.00857\n-4\t0.19703\t0.02395\t0.01536\t0.01387\t0.01690\t0.55243\t0.01062\t0.02202\t0.01505\t0.01736\t0.00901\t0.01077\t0.00749\t0.00635\t0.00600\t0.00169\t0.06019\t0.00383\t0.00320\t0.00685\n-5\t0.01450\t0.01539\t0.01823\t0.01575\t0.01620\t0.12585\t0.01294\t0.01585\t0.01034\t0.01451\t0.00810\t0.01283\t0.00788\t0.00991\t0.01768\t0.00248\t0.66716\t0.00506\t0.00270\t0.00664\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-0\t1\n-\n-[block]\n-# block no. 23 follows, 38 sequences, length 6\n-# corresponding to MSA columns:\n-# 1254-1259\n-name=unknown_X\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.01343\t0.01028\t0.01283\t0.00977\t0.01415\t0.00866\t0.03490\t0.04640\t0.05049\t0.08028\t0.16725\t0.02064\t0.01996\t0.00666\t0.00539\t0.00132\t0.00449\t0.00567\t0.00472\t0.48271\n-1\t0.04265\t0.10015\t0.01305\t0.00922\t0.01226\t0.00970\t0.00754\t0.01866\t0.03805\t0.26240\t0.27072\t0.05409\t0.09335\t0.00992\t0.00664\t0.00187\t0.02797\t0.00820\t0.00606\t0.00751\n-2\t0.00774\t0.00584\t0.00715\t0.00741\t0.00866\t0.00525\t0.00533\t0.00963\t0.01433\t0.01908\t0.32409\t0.28450\t0.24864\t0.01522\t0.00729\t0.00211\t0.00311\t0.01338\t0.00600\t0.00525\n-3\t0.01099\t0.00669\t0.00941\t0.09845\t0.01363\t0.00652\t0.00742\t0.01259\t0.01250\t0.13528\t0.02900\t0.57076\t0.03203\t0.01550\t0.00722\t0.00230\t0.00428\t0.01393\t0.00554\t0.00596\n-4\t0.69880\t0.01184\t0.00961\t0.00861\t0.01228\t0.01373\t0.00700\t0.02000\t0.12855\t0.02669\t0.01099\t0.01183\t0.00844\t0.00600\t0.00411\t0.00189\t0.00467\t0.00383\t0.00411\t0.00700\n-5\t0.01499\t0.01161\t0.03484\t0.10038\t0.03814\t0.03077\t0.00958\t0.01979\t0.11229\t0.14220\t0.06861\t0.04057\t0.01539\t0.00673\t0.00552\t0.00153\t0.00526\t0.00563\t0.00467\t0.33149\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-12\t79\n-\n-# created by:\n-# /software/SequenceAnalysis/GenePrediction/augustus/3.0.1/scripts/msa2prfl.pl ./aligns/BUSCOaEOG7B0HST.fas\n' |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/arthropoda/scores_cutoff --- a/busco/test-data/arthropoda/scores_cutoff Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST 996.48 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/genome.fa --- a/busco/test-data/genome.fa Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ ->sample -TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG -GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA -GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG -TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC -AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC -AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG -TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC -GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT -GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA -AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT -ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT -TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC -AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/genome_results/full_table --- a/busco/test-data/genome_results/full_table Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG73JZBF Missing |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/genome_results/missing_buscos_list --- a/busco/test-data/genome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG73JZBF |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/genome_results/short_summary --- a/busco/test-data/genome_results/short_summary Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,11 +0,0 @@ -#BUSCO was run in mode: genome - -Summarized benchmarks in BUSCO notation: - C:0.0%[D:0.0%],F:0.0%,M:10%,n:2675 - -Representing: - 0 Complete Single-Copy BUSCOs - 0 Complete Duplicated BUSCOs - 0 Fragmented BUSCOs - 2675 Missing BUSCOs - 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/proteome.fa --- a/busco/test-data/proteome.fa Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ ->BUSCOaEOG7B0HST -MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA -VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE -DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED -TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID -LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI -VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE -AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN -AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY -LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI -IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT -SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS -LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT -AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG -AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK -VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/proteome_results/full_table --- a/busco/test-data/proteome_results/full_table Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 1877.5 900 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/proteome_results/missing_buscos_list --- a/busco/test-data/proteome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7VF93N |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/proteome_results/short_summary --- a/busco/test-data/proteome_results/short_summary Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,11 +0,0 @@ -#BUSCO was run in mode: OGS - -Summarized benchmarks in BUSCO notation: - C:0.0%[D:0.0%],F:0.0%,M:99%,n:2675 - -Representing: - 0 Complete Single-copy BUSCOs - 0 Complete Duplicated BUSCOs - 1 Fragmented BUSCOs - 2674 Missing BUSCOs - 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/transcriptome.fa --- a/busco/test-data/transcriptome.fa Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,46 +0,0 @@ ->BUSCOaEOG7B0HST -atggcggcggatcaggcgcagtttcagcagctgctggtgagcctgctgagcaccgataac -gaagtgcgcaaacaggcggaagaagcgtataacaacctgccggtggaaagcaaagtgacc -tttctgctgggcgcgattgcgaacggccagctgagcgaagaagtgcgccagctggcggcg -gtgctgctgcgccgcctgtttagcagcgaatttctggaattttataaaaaactgccggcg -gaagcgcaggcgcagctgaaagaacagattctgctggcggtgcagcaggaagtgagcgaa -cagctgcgccgcaaagtgtgcgaagtggtggcggaagtggcgcgcaacctgattgatgaa -gatggcaacaaccagtggccggaatttctgcagtttctgtttcagtgcgcgaacagcccg -agcccgcagctgaaagaaagcgcgctgcgcatttttaccagcgtgccgggcatttttggc -aaccaggaagcgcagtatctggatctgattaaacagatgctggcgaaaagcctggaagat -accgaagatgcggaagtgcgcctgcaggcggtgcgcgcggtgggcgcgtttattctgctg -catgataaagaaaaagaaattcagaaacattttgcggatctgctgccggcgctgctgcag -gtggtggcggaaagcattgaaaaacaggatgatgatgcgctgctgaaagtgctgattgat -ctggcggaagcgaccccgaaatttctgcgcccgcagctggaaaccattctggaactgtgc -ctgaaagtgctgagcgaagaagatgtggaagatagctggcgccatctggcgctggaagtg -ctggtgaccctggcggaaaccgcgccggcgatggtgcgcaaacgcgcggaaaaatatatt -gtggcgctggtgccgctggtgctgaaaatgatgaccgatctggaagaagatgaagattgg -agcgtggcggatgaaattaccgaagatgataacgatagcaacaacgtggtggcggaaagc -gcgctggatcgcctggcgtgcggcctgggcggcaaagtggtgctgccgctggtggtggaa -gcgattccggcgatgctgagcagcagcgattggaaaaaacgccatgcggcgctgatggcg -attagcgcgattggcgaaggctgccataaacagatggaagcgctgctggatcaggtgctg -gatggcgtgctgaaatatctgcaggatccgcatccgcgcgtgcgctatgcggcgtgcaac -gcgattggccagatgagcaccgattttgcgccgatttttgaaaaaaaatttcatgataaa -gtgattccgggcctgctgctgctgctggatgatgaagcgaacccgcgcgtgcaggcgcat -gcgggcgcggcgctggtgaactttagcgaagattgcccgaaaaacattctgacccgctat -ctggatgcgattatggcgaaactggaagcgattctgaccagcaaatttaaagaactggtg -gaaaaaggcaccaaactggtgctggaacaggtggtgaccaccattgcgagcgtggcggat -accgcggaagaagaatttgtggcgtattatgatcgcctgatgccgtgcctgaaatatatt -attcagaacgcgaacagcgaagaactgaaactgctgcgcggcaaaaccattgaatgcgtg -agcctgattggcctggcggtgggccgcgaaaaatttattgcggatgcgagcgaagtgatg -gatctgctgctgaaaacccataccgaaggcgcggaactgccggatgatgatccgcagacc -agctatctgattagcgcgtgggcgcgcatttgcaaaattctgggcaaacagtttgaacag -tatctgccgctggtgatgggcccggtgctgcgcaccgcgagcctgaaaccggaagtggcg -ctgctggataacgaagatctggaagatattgaaggcgatgtggattggcagtttgtgagc -ctgggcgaacagcagaactttggcattcgcaccgcgggcctggaagataaagcgagcgcg -tgcgaaatgctggtgtgctatgcgcgcgaactgaaagaaggctttgcggaatatgcggaa -gaagtggtgcgcctgatggtgccgctgctgaaattttattttcatgatggcgtgcgcacc -gcggcggcggaaagcctgccgtatctgctggattgcgcgaaaattaaaggcccgcagtat -ctggaaggcatgtgggcgtatatttgcccggaactgctgaaagcgattgataccgaaccg -gaaaaagaagtgctgagcgaactgctgagcagcctggcgaaatgcattgaaaccctgggc -gcgggctgcctgagcgaagaagcgctgaaagaactgctgcgcattctggataaactgctg -aaagaacattttgaacgcgcggaaaaacgcctggaaaaacgcaaagatgaagattatgat -gaagtggtggaagaagaactggcggaagaagatgatgaagatgtgtatattctgagcaaa -gtggcggatattctgcatgcgctgtttgcgacctataaagaagcgtttctgccggcgttt -gatcaggtggtgccgcattttgtgaaactgctggaaccggaacgcccgctggcggatcgc -cagtgggcgctgtgcgtgtttgatgatgtgattgaatttggcggcccggcgtgcgtgaaa |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/transcriptome_results/full_table --- a/busco/test-data/transcriptome_results/full_table Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 0 7700 1874.8 898 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/transcriptome_results/missing_buscos_list --- a/busco/test-data/transcriptome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7XHK44 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/test-data/transcriptome_results/short_summary --- a/busco/test-data/transcriptome_results/short_summary Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,11 +0,0 @@ -#BUSCO was run in mode: genome - -Summarized benchmarks in BUSCO notation: - C:0.0%[D:0.0%],F:0.0%,M:99%,n:2675 - -Representing: - 0 Complete Single-Copy BUSCOs - 0 Complete Duplicated BUSCOs - 1 Fragmented BUSCOs - 2674 Missing BUSCOs - 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f busco/tool_dependencies.xml --- a/busco/tool_dependencies.xml Mon Jan 18 10:59:40 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="busco" version="1.1b1"> - <repository changeset_revision="5bf6666ef8a3" name="package_busco_1_1b1" owner="abretaud" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="augustus" version="3.1"> - <repository changeset_revision="24009970003a" name="package_augustus_3_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="blast+" version="2.2.31"> - <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="hmmer" version="3.1b2"> - <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="python" version="3.4"> - <repository changeset_revision="aca5076020ea" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/ancestral --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/ancestral Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>BUSCOaEOG7B0HST +MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA +VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE +DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED +TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID +LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI +VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE +AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN +AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY +LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI +IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT +SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS +LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT +AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG +AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK +VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK +YQEIFLRALLQYVSDKSAEVRQAAAYGCGVLGQFGGEQFAEACAEALPKLVEVINDPESR +ELENINATENAISAVTKILKYNKSAITNVDELLAVWLSWLPVVEDEEEAAHVYGYLCDLI +EANHPVVLGANNANLPRIVSILAEAFLREVVEAESAVAKRLLSIVKQIESNEELLQACIS +ELSAEQQQALKEALRELAA |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/clade_parameters --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/clade_parameters Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +#ARTHROPODA Clade parameters for BUSCOS +Z 102785 +sp1 fly +sp2 nasonia +sp3 generic +flank 5000 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm Mon Jan 18 11:00:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,3319 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME BUSCOaEOG7B0HST\n+LENG 1099\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Tue Apr 15 12:38:52 2014\n+NSEQ 23\n+EFFN 0.603638\n+CKSUM 3500044453\n+STATS LOCAL MSV -12.8285 0.69537\n+STATS LOCAL VITERBI -13.9416 0.69537\n+STATS LOCAL FORWARD -6.9634 0.69537\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.48078 4.06146 2.86181 2.63028 3.29447 3.05836 3.78580 2.74928 2.73520 2.31160 3.52187 3.11102 3.40692 3.07770 2.99944 2.73817 2.93658 2.56860 4.67180 3.56430\n+ 2.68613 4.42194 2.77509 2.73133 3.46348 2.40518 3.72504 3.29351 2.67743 2.69350 4.24642 2.90347 2.73745 3.18156 2.89802 2.37884 2.77522 2.98518 4.58487 3.61513\n+ 0.08969 2.57172 4.66890 1.68962 0.20406 0.00000 *\n+ 1 2.57261 4.35167 3.86119 3.40692 3.39776 3.63900 4.23782 2.41302 3.22676 2.05613 1.62924 3.68308 4.13489 3.59563 3.47552 3.02060 2.87665 2.31461 5.12383 3.92328 24 m - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 2 1.67850 4.50203 3.03694 2.37498 3.89784 3.30262 3.77719 3.19331 2.62660 2.92462 3.55380 3.06800 3.81401 2.99279 3.01679 2.53568 2.82599 2.89438 5.25006 3.96735 25 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 3 1.72593 4.51596 3.03450 2.62358 3.94870 3.02850 3.77178 3.31742 2.58759 2.83773 3.85577 3.06024 3.80166 2.49425 2.96418 2.62424 2.82773 2.99569 5.27761 3.99238 26 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 4 3.06989 5.20867 0.81737 2.38286 4.59580 3.26742 3.99737 4.20098 3.09568 3.79622 4.77615 2.94287 3.92548 3.23679 3.62179 3.02404 3.41012 3.83236 5.74996 4.45674 27 d - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 5 2.80194 4.77013 3.14922 2.71763 3.71311 3.52519 3.75923 3.19152 2.43092 2.26797 3.77243 3.16939 3.97062 1.69754 2.73211 2.88896 3.05024 3.01368 5.15367 3.80747 28 q - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 6 1.96528 5.02402 2.30355 2.05596 4.32542 3.05196 3.65086 3.77327 2.51296 3.33530 4.14888 2.71539 3.78621 2.65549 3.01420 2.66175 2.94409 3.40418 5.54285 4.15135 29 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n+ 7 2.80616 5.09448 2.63904 2.23927 4.35587 3.37371 3.36290 3.83921 2.30093 3.36613 4.20407 2.73502 3.85607 1.67'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n+ 1092 2.48411 4.80914 2.38269 2.16541 4.06714 3.19545 3.59049 3.47448 2.36289 3.08014 3.58530 2.86918 3.76448 2.73883 2.86648 2.59333 2.81189 2.86703 5.31779 3.97005 1199 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n+ 1093 1.24199 4.14570 3.59318 3.27579 3.90565 3.06922 4.23995 2.85564 3.22241 2.82059 3.86698 3.41584 3.78036 3.55807 3.49165 2.52495 2.75938 2.36754 5.42950 4.19313 1200 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06474 3.88362 3.16732 0.61958 0.77255 0.54401 0.86849\n+ 1094 2.97106 4.49154 3.93866 3.46547 2.54041 3.89976 3.77718 2.63214 3.27427 1.57888 3.33399 3.70082 4.26271 3.58207 3.49841 3.23908 3.21105 2.56656 4.22346 1.92820 1201 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03209 3.85097 4.57331 0.61958 0.77255 0.57161 0.83152\n+ 1095 2.60101 4.65512 3.08558 2.56003 3.93846 3.38076 3.35844 3.37716 2.29364 2.98880 3.84025 3.01919 3.81697 2.81258 2.11081 2.23871 2.85240 2.88090 5.19817 3.90318 1202 r - - -\n+ 2.68618 4.42210 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37883 2.77520 2.98519 4.58477 3.61504\n+ 0.08263 2.67392 4.57331 0.47744 0.96856 0.57161 0.83152\n+ 1096 2.18154 4.62997 2.75539 1.99629 4.09189 3.21947 3.71130 3.44588 2.55475 3.11415 3.95949 2.91659 3.75436 2.89454 2.98369 2.45299 2.43810 3.09910 5.37976 4.06153 1204 e - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03209 3.85097 4.57331 0.61958 0.77255 0.52453 0.89608\n+ 1097 2.46358 4.30538 3.37350 2.85594 3.45882 3.46342 3.46832 2.79047 2.73797 1.87351 3.43484 3.24873 3.57204 3.10968 3.06502 2.75631 2.66774 2.52856 4.91799 3.66813 1205 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06381 3.88362 3.18837 0.61958 0.77255 0.54401 0.86849\n+ 1098 1.76981 4.22446 3.25481 2.84716 3.91324 3.07102 3.91525 3.24756 2.83205 2.73784 3.84439 3.15656 3.31202 3.16923 3.18419 1.97191 2.69401 2.87700 5.28803 4.03807 1206 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.17726 3.85187 1.95758 0.61958 0.77255 0.57087 0.83249\n+ 1099 2.12671 4.27681 2.94823 2.62386 4.02260 3.00213 3.81075 3.41128 2.69615 3.08313 3.92445 2.61229 3.24401 3.03239 3.07499 2.18871 2.34694 2.99753 5.34368 4.07427 1207 a - - -\n+ 2.68560 4.42236 2.77531 2.73135 3.46365 2.40517 3.72506 3.29361 2.67747 2.69366 4.24701 2.90355 2.73729 3.18150 2.89812 2.37889 2.77501 2.98510 4.58488 3.61514\n+ 0.29451 1.36610 * 1.25311 0.33633 0.00000 *\n+//\n' |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/lengths_cutoff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/lengths_cutoff Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST 1099 16.763712248907 1099.28947368421 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl Mon Jan 18 11:00:29 2016 -0500 |
| [ |
| b'@@ -0,0 +1,1179 @@\n+[name]\n+unknown\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+2\t136\n+\n+[block]\n+# block no. 0 follows, 38 sequences, length 19\n+# corresponding to MSA columns:\n+# 159-177\n+name=unknown_A\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.00849\t0.00611\t0.00840\t0.00857\t0.00923\t0.00669\t0.00611\t0.00985\t0.00961\t0.01343\t0.01902\t0.11988\t0.02008\t0.26734\t0.45119\t0.00764\t0.01148\t0.00842\t0.00363\t0.00479\n+1\t0.04698\t0.19994\t0.01897\t0.01402\t0.05388\t0.40529\t0.01057\t0.01996\t0.01473\t0.02840\t0.01285\t0.12269\t0.01254\t0.00774\t0.00537\t0.00165\t0.00826\t0.00573\t0.00343\t0.00702\n+2\t0.10059\t0.05592\t0.04037\t0.12369\t0.03571\t0.33917\t0.01177\t0.05040\t0.04291\t0.12639\t0.01235\t0.01357\t0.00924\t0.00633\t0.00543\t0.00172\t0.00824\t0.00453\t0.00392\t0.00774\n+3\t0.00726\t0.00551\t0.00670\t0.00765\t0.00853\t0.00495\t0.00526\t0.00846\t0.01222\t0.01564\t0.04202\t0.55279\t0.26594\t0.01769\t0.00750\t0.00231\t0.00335\t0.01570\t0.00558\t0.00495\n+4\t0.01515\t0.01282\t0.01932\t0.01411\t0.01942\t0.01141\t0.20122\t0.08029\t0.06461\t0.07934\t0.01338\t0.01496\t0.01020\t0.00535\t0.00554\t0.00143\t0.00624\t0.00509\t0.00412\t0.41602\n+5\t0.01058\t0.00786\t0.01056\t0.13305\t0.01554\t0.00789\t0.00807\t0.01432\t0.07133\t0.05518\t0.29599\t0.18162\t0.03460\t0.01123\t0.00661\t0.00194\t0.00427\t0.02125\t0.02469\t0.08341\n+6\t0.05178\t0.16631\t0.50028\t0.01491\t0.02246\t0.01521\t0.03686\t0.01844\t0.01252\t0.01860\t0.01027\t0.01208\t0.00775\t0.00547\t0.00520\t0.00170\t0.00786\t0.00415\t0.00271\t0.08546\n+7\t0.01705\t0.01432\t0.01620\t0.01348\t0.01711\t0.07518\t0.07737\t0.22677\t0.26217\t0.05482\t0.04993\t0.11213\t0.01834\t0.00888\t0.00635\t0.00197\t0.00608\t0.00758\t0.00556\t0.00869\n+8\t0.01317\t0.01251\t0.02070\t0.15609\t0.52474\t0.01281\t0.01616\t0.01652\t0.01342\t0.01844\t0.01838\t0.02129\t0.11604\t0.00690\t0.00613\t0.00186\t0.00670\t0.00642\t0.00330\t0.00841\n+9\t0.01162\t0.00686\t0.00910\t0.00862\t0.01050\t0.00629\t0.00674\t0.01414\t0.01595\t0.14470\t0.42875\t0.11434\t0.07208\t0.01284\t0.00715\t0.00207\t0.00368\t0.11180\t0.00647\t0.00632\n+10\t0.01274\t0.01372\t0.12068\t0.01259\t0.01636\t0.01187\t0.04762\t0.04955\t0.31522\t0.02196\t0.05626\t0.13802\t0.02193\t0.00996\t0.00649\t0.00206\t0.00548\t0.07423\t0.00517\t0.05810\n+11\t0.00985\t0.00796\t0.01067\t0.01037\t0.01075\t0.00947\t0.00786\t0.01102\t0.01014\t0.01418\t0.01964\t0.14789\t0.02183\t0.26045\t0.10775\t0.00446\t0.21652\t0.11018\t0.00389\t0.00511\n+12\t0.00789\t0.00529\t0.00678\t0.00798\t0.00848\t0.00499\t0.00539\t0.00919\t0.01168\t0.01638\t0.03120\t0.67455\t0.03627\t0.01714\t0.00718\t0.00229\t0.00339\t0.01544\t0.12352\t0.00499\n+13\t0.00773\t0.00552\t0.00742\t0.00873\t0.00928\t0.00522\t0.00618\t0.00911\t0.01211\t0.01615\t0.06621\t0.64670\t0.03983\t0.01822\t0.00774\t0.00246\t0.00376\t0.11699\t0.00563\t0.00502\n+14\t0.23475\t0.01397\t0.01501\t0.05417\t0.12272\t0.06638\t0.01071\t0.11816\t0.17197\t0.11209\t0.01510\t0.01554\t0.01116\t0.00661\t0.00538\t0.00187\t0.00596\t0.00510\t0.00478\t0.00858\n+15\t0.01774\t0.01310\t0.01239\t0.01066\t0.01380\t0.13284\t0.00829\t0.12299\t0.12073\t0.17836\t0.04824\t0.03777\t0.12169\t0.04898\t0.00726\t0.00202\t0.00564\t0.00710\t0.08255\t0.00785\n+16\t0.00774\t0.00594\t0.00698\t0.00734\t0.00855\t0.00550\t0.00526\t0.00913\t0.01231\t0.01568\t0.07962\t0.21341\t0.34318\t0.13048\t0.08206\t0.00342\t0.00490\t0.04842\t0.00514\t0.00491\n+17\t0.01499\t0.01157\t0.01661\t0.08113\t0.01840\t0.01286\t0.11905\t0.12120\t0.08357\t0.07287\t0.05034\t0.01918\t0.01402\t0.00762\t0.00806\t0.00193\t0.13253\t0.00612\t0.20034\t0.00760\n+18\t0.02074\t0.06499\t0.01691\t0.01445\t0.01751\t0.60356\t0.01097\t0.07075\t0.01705\t0.01634\t0.01185\t0.08393\t0.01094\t0.00741\t0.00560\t0.00164\t0.00964\t0.00519\t0.00351\t0.00704\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+0\t1\n+\n+[block]\n+# block no. 1 follows, 38 sequences, length 22\n+# corresponding to MSA columns:\n+# 179-200\n+name=unknown_B\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.08270\t0.19710\t0.02137\t0.01349\t0.01801\t0.06215\t0.13254\t0.04863\t0.19656\t0.08108\t0.01574\t0.01622\t0.02523\t0.00640\t0.00542\t0.00172\t0.00649\t0.00534\t0.00432\t0.05948\n+1\t0.01139\t0.00879\t0.01512\t0.01313\t0.01560\t0.00826\t0.17794\t0.01415\t0.01395\t0.08259\t0.12369\t0.26603\t0.03144\t0.01318\t0.00747\t0.00230\t0.00560\t0.17772\t0.0'..b'01399\t0.02763\t0.59409\t0.01622\t0.02410\t0.01459\t0.01966\t0.15312\t0.01578\t0.02277\t0.03493\t0.01405\t0.00968\t0.00621\t0.00582\t0.00189\t0.00827\t0.00483\t0.00333\t0.00904\n+17\t0.01558\t0.61804\t0.05875\t0.01338\t0.01885\t0.02182\t0.14636\t0.01829\t0.01261\t0.01530\t0.00917\t0.01100\t0.00798\t0.00515\t0.00454\t0.00145\t0.00722\t0.00399\t0.00266\t0.00784\n+18\t0.03107\t0.12435\t0.21748\t0.02929\t0.04145\t0.01280\t0.01239\t0.04101\t0.05280\t0.01971\t0.03883\t0.03793\t0.01160\t0.00601\t0.00512\t0.00147\t0.00610\t0.00477\t0.00351\t0.30232\n+19\t0.01371\t0.36393\t0.29683\t0.15693\t0.02425\t0.01821\t0.01591\t0.01790\t0.01236\t0.01619\t0.00970\t0.01198\t0.00774\t0.00552\t0.00495\t0.00165\t0.00764\t0.00407\t0.00258\t0.00796\n+20\t0.16658\t0.02744\t0.61619\t0.01540\t0.02332\t0.01388\t0.01926\t0.01879\t0.01224\t0.02055\t0.01034\t0.01215\t0.00741\t0.00569\t0.00534\t0.00190\t0.00809\t0.00422\t0.00276\t0.00844\n+21\t0.02417\t0.01022\t0.01334\t0.01041\t0.01471\t0.00913\t0.00853\t0.08055\t0.01774\t0.60573\t0.05239\t0.02435\t0.08388\t0.00832\t0.00618\t0.00187\t0.00496\t0.00679\t0.00713\t0.00960\n+22\t0.01677\t0.01205\t0.08140\t0.01031\t0.01522\t0.00893\t0.00905\t0.02045\t0.05274\t0.25615\t0.06649\t0.04544\t0.01557\t0.00678\t0.00547\t0.00148\t0.00495\t0.00560\t0.00513\t0.36003\n+23\t0.16683\t0.01180\t0.01496\t0.01290\t0.01423\t0.01516\t0.01064\t0.01467\t0.00977\t0.01725\t0.00928\t0.01378\t0.00863\t0.01340\t0.10939\t0.00321\t0.46410\t0.00488\t0.00300\t0.08213\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+7\t16\n+\n+[block]\n+# block no. 22 follows, 38 sequences, length 6\n+# corresponding to MSA columns:\n+# 1247-1252\n+name=unknown_W\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.00733\t0.00524\t0.00698\t0.00838\t0.00873\t0.00489\t0.00558\t0.00838\t0.01152\t0.01536\t0.03316\t0.78466\t0.03979\t0.01885\t0.00768\t0.00244\t0.00349\t0.01710\t0.00558\t0.00489\n+1\t0.01041\t0.00709\t0.00808\t0.00738\t0.00993\t0.00599\t0.00575\t0.01235\t0.01441\t0.11123\t0.12398\t0.04824\t0.47386\t0.01304\t0.00680\t0.00193\t0.00356\t0.05072\t0.00575\t0.07949\n+2\t0.01430\t0.02608\t0.54722\t0.01765\t0.02555\t0.01352\t0.13402\t0.02039\t0.01351\t0.11246\t0.01266\t0.01425\t0.00878\t0.00583\t0.00598\t0.00192\t0.00861\t0.00507\t0.00324\t0.00894\n+3\t0.26692\t0.01203\t0.01543\t0.01222\t0.01656\t0.01225\t0.10707\t0.07068\t0.07963\t0.29248\t0.01726\t0.01826\t0.01233\t0.00696\t0.00558\t0.00193\t0.00575\t0.03264\t0.00543\t0.00857\n+4\t0.19703\t0.02395\t0.01536\t0.01387\t0.01690\t0.55243\t0.01062\t0.02202\t0.01505\t0.01736\t0.00901\t0.01077\t0.00749\t0.00635\t0.00600\t0.00169\t0.06019\t0.00383\t0.00320\t0.00685\n+5\t0.01450\t0.01539\t0.01823\t0.01575\t0.01620\t0.12585\t0.01294\t0.01585\t0.01034\t0.01451\t0.00810\t0.01283\t0.00788\t0.00991\t0.01768\t0.00248\t0.66716\t0.00506\t0.00270\t0.00664\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+0\t1\n+\n+[block]\n+# block no. 23 follows, 38 sequences, length 6\n+# corresponding to MSA columns:\n+# 1254-1259\n+name=unknown_X\n+#\n+# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n+#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n+0\t0.01343\t0.01028\t0.01283\t0.00977\t0.01415\t0.00866\t0.03490\t0.04640\t0.05049\t0.08028\t0.16725\t0.02064\t0.01996\t0.00666\t0.00539\t0.00132\t0.00449\t0.00567\t0.00472\t0.48271\n+1\t0.04265\t0.10015\t0.01305\t0.00922\t0.01226\t0.00970\t0.00754\t0.01866\t0.03805\t0.26240\t0.27072\t0.05409\t0.09335\t0.00992\t0.00664\t0.00187\t0.02797\t0.00820\t0.00606\t0.00751\n+2\t0.00774\t0.00584\t0.00715\t0.00741\t0.00866\t0.00525\t0.00533\t0.00963\t0.01433\t0.01908\t0.32409\t0.28450\t0.24864\t0.01522\t0.00729\t0.00211\t0.00311\t0.01338\t0.00600\t0.00525\n+3\t0.01099\t0.00669\t0.00941\t0.09845\t0.01363\t0.00652\t0.00742\t0.01259\t0.01250\t0.13528\t0.02900\t0.57076\t0.03203\t0.01550\t0.00722\t0.00230\t0.00428\t0.01393\t0.00554\t0.00596\n+4\t0.69880\t0.01184\t0.00961\t0.00861\t0.01228\t0.01373\t0.00700\t0.02000\t0.12855\t0.02669\t0.01099\t0.01183\t0.00844\t0.00600\t0.00411\t0.00189\t0.00467\t0.00383\t0.00411\t0.00700\n+5\t0.01499\t0.01161\t0.03484\t0.10038\t0.03814\t0.03077\t0.00958\t0.01979\t0.11229\t0.14220\t0.06861\t0.04057\t0.01539\t0.00673\t0.00552\t0.00153\t0.00526\t0.00563\t0.00467\t0.33149\n+\n+[dist]\n+# distance from previous block\n+# <min> <max>\n+12\t79\n+\n+# created by:\n+# /software/SequenceAnalysis/GenePrediction/augustus/3.0.1/scripts/msa2prfl.pl ./aligns/BUSCOaEOG7B0HST.fas\n' |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/arthropoda/scores_cutoff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arthropoda/scores_cutoff Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST 996.48 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>sample +TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG +GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA +GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG +TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC +AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC +AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG +TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC +GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT +GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA +AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT +ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT +TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC +AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/genome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/full_table Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG73JZBF Missing |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/genome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/missing_buscos_list Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG73JZBF |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/genome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results/short_summary Mon Jan 18 11:00:29 2016 -0500 |
| [ |
| @@ -0,0 +1,11 @@ +#BUSCO was run in mode: genome + +Summarized benchmarks in BUSCO notation: + C:0.0%[D:0.0%],F:0.0%,M:10%,n:2675 + +Representing: + 0 Complete Single-Copy BUSCOs + 0 Complete Duplicated BUSCOs + 0 Fragmented BUSCOs + 2675 Missing BUSCOs + 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/proteome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome.fa Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,16 @@ +>BUSCOaEOG7B0HST +MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA +VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE +DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED +TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID +LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI +VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE +AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN +AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY +LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI +IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT +SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS +LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT +AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG +AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK +VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/proteome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/full_table Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 1877.5 900 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/proteome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/missing_buscos_list Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7VF93N |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/proteome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proteome_results/short_summary Mon Jan 18 11:00:29 2016 -0500 |
| [ |
| @@ -0,0 +1,11 @@ +#BUSCO was run in mode: OGS + +Summarized benchmarks in BUSCO notation: + C:0.0%[D:0.0%],F:0.0%,M:99%,n:2675 + +Representing: + 0 Complete Single-copy BUSCOs + 0 Complete Duplicated BUSCOs + 1 Fragmented BUSCOs + 2674 Missing BUSCOs + 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/transcriptome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome.fa Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,46 @@ +>BUSCOaEOG7B0HST +atggcggcggatcaggcgcagtttcagcagctgctggtgagcctgctgagcaccgataac +gaagtgcgcaaacaggcggaagaagcgtataacaacctgccggtggaaagcaaagtgacc +tttctgctgggcgcgattgcgaacggccagctgagcgaagaagtgcgccagctggcggcg +gtgctgctgcgccgcctgtttagcagcgaatttctggaattttataaaaaactgccggcg +gaagcgcaggcgcagctgaaagaacagattctgctggcggtgcagcaggaagtgagcgaa +cagctgcgccgcaaagtgtgcgaagtggtggcggaagtggcgcgcaacctgattgatgaa +gatggcaacaaccagtggccggaatttctgcagtttctgtttcagtgcgcgaacagcccg +agcccgcagctgaaagaaagcgcgctgcgcatttttaccagcgtgccgggcatttttggc +aaccaggaagcgcagtatctggatctgattaaacagatgctggcgaaaagcctggaagat +accgaagatgcggaagtgcgcctgcaggcggtgcgcgcggtgggcgcgtttattctgctg +catgataaagaaaaagaaattcagaaacattttgcggatctgctgccggcgctgctgcag +gtggtggcggaaagcattgaaaaacaggatgatgatgcgctgctgaaagtgctgattgat +ctggcggaagcgaccccgaaatttctgcgcccgcagctggaaaccattctggaactgtgc +ctgaaagtgctgagcgaagaagatgtggaagatagctggcgccatctggcgctggaagtg +ctggtgaccctggcggaaaccgcgccggcgatggtgcgcaaacgcgcggaaaaatatatt +gtggcgctggtgccgctggtgctgaaaatgatgaccgatctggaagaagatgaagattgg +agcgtggcggatgaaattaccgaagatgataacgatagcaacaacgtggtggcggaaagc +gcgctggatcgcctggcgtgcggcctgggcggcaaagtggtgctgccgctggtggtggaa +gcgattccggcgatgctgagcagcagcgattggaaaaaacgccatgcggcgctgatggcg +attagcgcgattggcgaaggctgccataaacagatggaagcgctgctggatcaggtgctg +gatggcgtgctgaaatatctgcaggatccgcatccgcgcgtgcgctatgcggcgtgcaac +gcgattggccagatgagcaccgattttgcgccgatttttgaaaaaaaatttcatgataaa +gtgattccgggcctgctgctgctgctggatgatgaagcgaacccgcgcgtgcaggcgcat +gcgggcgcggcgctggtgaactttagcgaagattgcccgaaaaacattctgacccgctat +ctggatgcgattatggcgaaactggaagcgattctgaccagcaaatttaaagaactggtg +gaaaaaggcaccaaactggtgctggaacaggtggtgaccaccattgcgagcgtggcggat +accgcggaagaagaatttgtggcgtattatgatcgcctgatgccgtgcctgaaatatatt +attcagaacgcgaacagcgaagaactgaaactgctgcgcggcaaaaccattgaatgcgtg +agcctgattggcctggcggtgggccgcgaaaaatttattgcggatgcgagcgaagtgatg +gatctgctgctgaaaacccataccgaaggcgcggaactgccggatgatgatccgcagacc +agctatctgattagcgcgtgggcgcgcatttgcaaaattctgggcaaacagtttgaacag +tatctgccgctggtgatgggcccggtgctgcgcaccgcgagcctgaaaccggaagtggcg +ctgctggataacgaagatctggaagatattgaaggcgatgtggattggcagtttgtgagc +ctgggcgaacagcagaactttggcattcgcaccgcgggcctggaagataaagcgagcgcg +tgcgaaatgctggtgtgctatgcgcgcgaactgaaagaaggctttgcggaatatgcggaa +gaagtggtgcgcctgatggtgccgctgctgaaattttattttcatgatggcgtgcgcacc +gcggcggcggaaagcctgccgtatctgctggattgcgcgaaaattaaaggcccgcagtat +ctggaaggcatgtgggcgtatatttgcccggaactgctgaaagcgattgataccgaaccg +gaaaaagaagtgctgagcgaactgctgagcagcctggcgaaatgcattgaaaccctgggc +gcgggctgcctgagcgaagaagcgctgaaagaactgctgcgcattctggataaactgctg +aaagaacattttgaacgcgcggaaaaacgcctggaaaaacgcaaagatgaagattatgat +gaagtggtggaagaagaactggcggaagaagatgatgaagatgtgtatattctgagcaaa +gtggcggatattctgcatgcgctgtttgcgacctataaagaagcgtttctgccggcgttt +gatcaggtggtgccgcattttgtgaaactgctggaaccggaacgcccgctggcggatcgc +cagtgggcgctgtgcgtgtttgatgatgtgattgaatttggcggcccggcgtgcgtgaaa |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/transcriptome_results/full_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/full_table Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 0 7700 1874.8 898 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/transcriptome_results/missing_buscos_list --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/missing_buscos_list Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +BUSCOaEOG7XHK44 |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f test-data/transcriptome_results/short_summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcriptome_results/short_summary Mon Jan 18 11:00:29 2016 -0500 |
| [ |
| @@ -0,0 +1,11 @@ +#BUSCO was run in mode: genome + +Summarized benchmarks in BUSCO notation: + C:0.0%[D:0.0%],F:0.0%,M:99%,n:2675 + +Representing: + 0 Complete Single-Copy BUSCOs + 0 Complete Duplicated BUSCOs + 1 Fragmented BUSCOs + 2674 Missing BUSCOs + 2675 Total BUSCO groups searched |
| b |
| diff -r b74cdbcbdfdc -r 51e3c4a7ce3f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 18 11:00:29 2016 -0500 |
| b |
| @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="busco" version="1.1b1"> + <repository changeset_revision="5bf6666ef8a3" name="package_busco_1_1b1" owner="abretaud" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="augustus" version="3.1"> + <repository changeset_revision="24009970003a" name="package_augustus_3_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="blast+" version="2.2.31"> + <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="hmmer" version="3.1b2"> + <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="python" version="3.4"> + <repository changeset_revision="aca5076020ea" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |