Repository 'busco'
hg clone https://toolshed.g2.bx.psu.edu/repos/abretaud/busco

Changeset 2:b74cdbcbdfdc (2016-01-18)
Previous changeset 1:a8ddf9d3c14c (2016-01-18) Next changeset 3:51e3c4a7ce3f (2016-01-18)
Commit message:
Uploaded
added:
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
removed:
busco.xml
tool_dependencies.xml
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco.xml
--- a/busco.xml Mon Jan 18 10:52:35 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -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>
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/.shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/.shed.yml Mon Jan 18 10:59:40 2016 -0500
[
@@ -0,0 +1,7 @@
+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
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/busco.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/busco.xml Mon Jan 18 10:59:40 2016 -0500
[
@@ -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>
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/ancestral
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/ancestral Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/clade_parameters
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/clade_parameters Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/lengths_cutoff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/lengths_cutoff Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7B0HST 1099 16.763712248907 1099.28947368421
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/arthropoda/scores_cutoff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/arthropoda/scores_cutoff Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7B0HST 996.48
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/genome.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/genome.fa Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,14 @@
+>sample
+TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG
+GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA
+GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG
+TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC
+AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC
+AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG
+TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC
+GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT
+GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA
+AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT
+ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT
+TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC
+AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/genome_results/full_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/genome_results/full_table Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG73JZBF Missing
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/genome_results/missing_buscos_list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/genome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG73JZBF
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/genome_results/short_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/genome_results/short_summary Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/proteome.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/proteome.fa Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/proteome_results/full_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/proteome_results/full_table Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 1877.5 900
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/proteome_results/missing_buscos_list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/proteome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7VF93N
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/proteome_results/short_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/proteome_results/short_summary Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/transcriptome.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/transcriptome.fa Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/transcriptome_results/full_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/transcriptome_results/full_table Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7B0HST Fragmented BUSCOaEOG7B0HST 0 7700 1874.8 898
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/transcriptome_results/missing_buscos_list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/transcriptome_results/missing_buscos_list Mon Jan 18 10:59:40 2016 -0500
b
@@ -0,0 +1,1 @@
+BUSCOaEOG7XHK44
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc busco/test-data/transcriptome_results/short_summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/test-data/transcriptome_results/short_summary Mon Jan 18 10:59:40 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 a8ddf9d3c14c -r b74cdbcbdfdc busco/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco/tool_dependencies.xml Mon Jan 18 10:59:40 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>
b
diff -r a8ddf9d3c14c -r b74cdbcbdfdc tool_dependencies.xml
--- a/tool_dependencies.xml Mon Jan 18 10:52:35 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>