Repository 'tripal_expression_get_biomaterials'
hg clone https://toolshed.g2.bx.psu.edu/repos/gga/tripal_expression_get_biomaterials

Changeset 0:de7d91ce970b (2019-02-25)
Next changeset 1:387ea73ea3cf (2019-03-05)
Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a
added:
README.rst
expression_get_biomaterials.xml
macros.xml
test-data/blast.xml
test-data/blast2go.gaf
test-data/citrus_genome.fasta
test-data/interpro.xml
test-data/sample.gff3
tripal.py
b
diff -r 000000000000 -r de7d91ce970b README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Feb 25 06:33:51 2019 -0500
b
@@ -0,0 +1,45 @@
+Galaxy-tripal
+=============
+
+Galaxy tools to interface with Tripal using python-tripal
+
+Dependencies
+------------
+
+You will need to install some python modules in the Galaxy virtualenv for these
+tools to be fully functional:
+
+.. code:: bash
+
+    . /path/to/galaxy/.venv/bin/activate
+    pip install future tripal
+    deactivate
+
+Environment
+-----------
+
+The following environment variables must be set:
+
++--------------------------------+-----------------------------------------------------------+
+| ENV                            | Use                                                       |
++================================+===========================================================+
+| ``$GALAXY_TRIPAL_URL``         | The URL at which Tripal is accessible, internal to Galaxy |
+|                                | and where the tools run. Must be absolute, with FQDN and  |
+|                                | protocol.                                                 |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_TRIPAL_USER``        | The admin user which Galaxy should use to talk to Tripal. |
+|                                |                                                           |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_TRIPAL_PASSWORD``    | The password for the admin user.                          |
+|                                |                                                           |
+|                                |                                                           |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_TRIPAL_SHARED_DIR``  | Directory shared between Galaxy and Tripal, used to       |
+|                                | exchange data files.                                      |
++--------------------------------+-----------------------------------------------------------+
+
+
+License
+-------
+
+All python scripts and wrappers are licensed under MIT license.
b
diff -r 000000000000 -r de7d91ce970b expression_get_biomaterials.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/expression_get_biomaterials.xml Mon Feb 25 06:33:51 2019 -0500
[
@@ -0,0 +1,49 @@
+<?xml version="1.0"?>
+<tool id="expression_get_biomaterials" name="Get biomaterials" version="@WRAPPER_VERSION@.0">
+ <description>from Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.5">jq</requirement>
+    </expand>
+    <code file="tripal.py"/>
+    <command detect_errors="aggressive"><![CDATA[
+@AUTH@
+
+tripaille expression get_biomaterials
+
+#if $provider_id:
+  --provider_id '$provider_id'
+#end if
+#if $biomaterial_id:
+  --biomaterial_id '$biomaterial_id'
+#end if
+#if $organism_id:
+  --organism_id '$organism_id'
+#end if
+#if $dbxref_id:
+  --dbxref_id '$dbxref_id'
+#end if
+
+| jq -S . > $results
+]]></command>
+    <inputs>
+        <!-- arguments -->
+
+        <!-- options -->
+        <param argument="--organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
+        <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" />
+        <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial" />
+        <param name="dbxref_id" label="Dbxref Id" argument="dbxref_id" type="text" help="Limit query to the selected ref" />
+
+    </inputs>
+    <outputs>
+        <data format="json" name="results"/>
+    </outputs>
+    <help>
+List biomaterials in the database
+
+@HELP@
+    </help>
+</tool>
b
diff -r 000000000000 -r de7d91ce970b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Feb 25 06:33:51 2019 -0500
[
b'@@ -0,0 +1,224 @@\n+<?xml version="1.0"?>\n+<macros>\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="3.2">python-tripal</requirement>\n+            <yield/>\n+        </requirements>\n+    </xml>\n+\n+    <xml name="stdio">\n+        <stdio>\n+            <regex level="fatal" match="Exception:" source="stderr" />\n+            <regex level="fatal" match="error" source="stderr" />\n+            <exit_code range="1:" />\n+        </stdio>\n+    </xml>\n+\n+    <token name="@WRAPPER_VERSION@">3.2</token>\n+\n+    <xml name="citation">\n+        <citations>\n+            <citation type="doi">10.1093/database/bat075</citation>\n+        </citations>\n+    </xml>\n+\n+    <token name="@HELP_OVERVIEW@"><![CDATA[\n+        **Python-tripal Overview**\n+\n+        Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database.\n+        The tripal_rest_api Tripal module must be installed on the remote server to use these tools.\n+    ]]></token>\n+\n+    <token name="@HELP@"><![CDATA[\n+        **Useful Links**\n+\n+        `Tripal project website <http://tripal.info/>`_\n+\n+        `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools\n+    ]]></token>\n+\n+    <token name="@DATA_DIR@">\\$GALAXY_TRIPAL_SHARED_DIR</token>\n+\n+    <token name="@AUTH@"><![CDATA[\n+        echo "__default: local" > \'.auth.yml\' &&\n+        echo "local:" >> \'.auth.yml\' &&\n+        echo "    tripal_url: \\"\\$GALAXY_TRIPAL_URL\\"" >> \'.auth.yml\' &&\n+        echo "    username: \\"\\$GALAXY_TRIPAL_USER\\"" >> \'.auth.yml\' &&\n+        echo "    password: \\"\\$GALAXY_TRIPAL_PASSWORD\\"" >> \'.auth.yml\' &&\n+\n+        TRIPAILLE_GLOBAL_CONFIG_PATH=\'.auth.yml\'\n+    ]]></token>\n+\n+    <xml name="wait_for">\n+        <param name="wait_for"\n+               type="data"\n+               format="data"\n+               optional="true"\n+               label="Run this only after the following dataset is ready"\n+               help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>\n+    </xml>\n+\n+    <xml name="test_result">\n+        <assert_stderr>\n+            <has_text text="MissingSchema" />\n+        </assert_stderr>\n+    </xml>\n+\n+    <xml name="analysis">\n+        <section name="analysis" title="Analysis" expanded="True">\n+            <param name="name"\n+                   type="text"\n+                   label="The analysis name [mandatory]">\n+                <expand macro="sanitized"/>\n+            </param>\n+\n+            <param name="program"\n+                   type="text"\n+                   label="Program name [mandatory]"\n+                   help="Name of the program that was used to perform this analysis">\n+                <expand macro="sanitized"/>\n+            </param>\n+            <param name="program_version"\n+                   type="text"\n+                   label="Program version [mandatory]"\n+                   help="Version of the program that was used to perform this analysis"/>\n+            <param name="source"\n+                   type="text"\n+                   label="Source name [mandatory]"\n+                   help="Where this analysis comes from">\n+                <expand macro="sanitized"/>\n+            </param>\n+\n+            <param name="source_version"\n+                   argument="--sourceversion"\n+                   type="text"\n+                   optional="True"\n+                   label="Source version" />\n+            <param name="source_uri"\n+                   argument="--sourceuri"\n+                   type="text"\n+                   optional="True"\n+                   label="Source URI"\n+                   help="URI where source data was retrieved" />\n+            <param name="algorithm"\n+                   argument="--algorithm"\n+                   type="text"\n+                   label="Algorithm"\n+                   optional="True"\n'..b'scription">\n+                <expand macro="sanitized"/>\n+            </param>\n+            <param name="date"\n+                   argument="--date_executed"\n+                   type="text"\n+                   optional="True"\n+                   label="Execution date"\n+                   help="Format: yyyy-mm-dd  Default: Today">\n+                <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>\n+            </param>\n+        </section>\n+    </xml>\n+\n+    <xml name="feature_rel">\n+        <param name="rel_subject_re"\n+               argument="--rel-subject-re"\n+               type="text"\n+               label="Regular expression to extract the unique name of the parent feature"\n+               help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">\n+            <expand macro="sanitized"/>\n+        </param>\n+\n+        <param name="rel_subject_type"\n+               argument="--rel-subject-type"\n+               type="text"\n+               label="Sequence type of the parent"\n+               help="this should be a Sequence Ontology term" />\n+    </xml>\n+\n+    <xml name="match_type">\n+        <param name="match_type"\n+               argument="--match-type"\n+               type="select"\n+               label="Match type for already loaded features">\n+            <option value="uniquename" selected="true">Unique name</option>\n+            <option value="name">Name</option>\n+        </param>\n+    </xml>\n+\n+    <xml name="matching">\n+        <section name="matching" title="Feature matching" expanded="True">\n+            <param name="query_type"\n+                   type="text"\n+                   label="The feature type of the blast query"\n+                   help="It must be a valid Sequence Ontology term. e.g. \'contig\', \'gene\', \'mRNA\', \'polypeptide\'" />\n+\n+            <param name="query_uniquename"\n+                   type="boolean"\n+                   checked="false"\n+                   truevalue="--query_uniquename"\n+                   falsevalue=""\n+                   label="Find blast query features using their Unique name"\n+                   help="Feature name will be used otherwise" />\n+\n+            <param name="query_re"\n+                   type="text"\n+                   optional="true"\n+                   label="Regular expression to extract the feature name from the blast query name"\n+                   help="leave empty if the first word in query name is sufficient">\n+                <expand macro="sanitized"/>\n+            </param>\n+        </section>\n+    </xml>\n+\n+    <xml name="sanitized">\n+        <sanitizer>\n+            <valid initial="string.printable">\n+                <remove value="&apos;"/>\n+            </valid>\n+            <mapping initial="none">\n+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>\n+                <add source="(" target="\\("/>\n+                <add source=")" target="\\)"/>\n+            </mapping>\n+        </sanitizer>\n+    </xml>\n+\n+    <token name="@MATCHING@"><![CDATA[\n+        #if str($matching.query_re):\n+            --query_re \'${matching.query_re}\'\n+        #end if\n+\n+        $matching.query_uniquename\n+\n+        --query_type \'$matching.query_type\'\n+    ]]></token>\n+\n+    <token name="@ANALYSIS@"><![CDATA[\n+        #if $analysis.algorithm:\n+            --algorithm \'$analysis.algorithm\'\n+        #end if\n+        #if $analysis.source_version:\n+            --sourceversion \'$analysis.source_version\'\n+        #end if\n+        #if $analysis.source_uri:\n+            --sourceuri \'$analysis.source_uri\'\n+        #end if\n+        #if $analysis.description:\n+            --description \'$analysis.description\'\n+        #end if\n+        #if $analysis.date:\n+            --date_executed \'$analysis.date\'\n+        #end if\n+\n+        \'$analysis.name\'\n+        \'$analysis.program\'\n+        \'$analysis.program_version\'\n+        \'$analysis.source\'\n+    ]]></token>\n+</macros>\n'
b
diff -r 000000000000 -r de7d91ce970b test-data/blast.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blast.xml Mon Feb 25 06:33:51 2019 -0500
[
@@ -0,0 +1,68 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastx</BlastOutput_program>
+  <BlastOutput_version>blastx 2.2.25 [Feb-01-2011]</BlastOutput_version>
+  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>/scratch/mainlab/data/lib/nr</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
+  <BlastOutput_query-def>orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis</BlastOutput_query-def>
+  <BlastOutput_query-len>2075</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>1e-06</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>1</Iteration_iter-num>
+      <Iteration_query-ID>lcl|1_0</Iteration_query-ID>
+      <Iteration_query-def>orange1.1g015632m PAC:18136217 (mRNA) Citrus sinensis</Iteration_query-def>
+      <Iteration_query-len>2075</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|224068663|ref|XP_002302794.1|</Hit_id>
+          <Hit_def>predicted protein [Populus trichocarpa] &gt;gi|222844520|gb|EEE82067.1| predicted protein [Populus trichocarpa]</Hit_def>
+          <Hit_accession>XP_002302794</Hit_accession>
+          <Hit_len>409</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>792.727</Hsp_bit-score>
+              <Hsp_score>2046</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>559</Hsp_query-from>
+              <Hsp_query-to>1767</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>409</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_identity>387</Hsp_identity>
+              <Hsp_positive>394</Hsp_positive>
+              <Hsp_gaps>6</Hsp_gaps>
+              <Hsp_align-len>409</Hsp_align-len>
+              <Hsp_qseq>MASVSVVPASG------NTVGVDRLPEEMNDMKIRDDKEMEATVVDGNGTEAGHIIVTTIGGKNGQPKQTISYMAERVVGHGSFGVVFQAKCLETGEAVAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPETVHRVIKHHYKMSQRMPLIYVKLYFYQICRALAYIHNTIGVCHRDIKPQNLLVNPHTHQLKLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYTAAIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIFQKRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPNTRLPNGRFLPPLFNFKPHELKGVPVDMLVKLIPEHARKQCAFLGL</Hsp_qseq>
+              <Hsp_hseq>MASVSVVPASGLRDTLGNTTGVDKLPEEMNDMKISDDKEMEAAVVDGNGTETGHIIVTTIGGKNGQPKQTISYMAERVVGHGSFGLVFQAKCLETGETVAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPETIHRVIKHYYKMSQRMPLIYVKLYFYQICRALAYIHNSIGVCHRDIKPQNLLVNPHTHQVKLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYTTAIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIFHKRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPNARLPNGRILPPLFNFKPHELKGVPVEMLVKLIPEHARKQCAFLGL</Hsp_hseq>
+              <Hsp_midline>MASVSVVPASG      NT GVD+LPEEMNDMKI DDKEMEA VVDGNGTE GHIIVTTIGGKNGQPKQTISYMAERVVGHGSFG+VFQAKCLETGE VAIKKVLQDKRYKNRELQTMRLLDHPNVVSLKHCFFSTTEKDELYLNLVLEYVPET+HRVIKH+YKMSQRMPLIYVKLYFYQICRALAYIHN+IGVCHRDIKPQNLLVNPHTHQ+KLCDFGSAKVLVKGEPNISYICSRYYRAPELIFGATEYT AIDIWSAGCVLAELLLGQPLFPGESGVDQLVEIIKVLGTPTREEIKCMNPNYTEFKFPQIKAHPWHKIF KRMPPEAVDLVSRLLQYSPNLRSTALEALIHPFFDELRDPN RLPNGR LPPLFNFKPHELKGVPV+MLVKLIPEHARKQCAFLGL</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>18996442</Statistics_db-num>
+          <Statistics_db-len>6510958228</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+  </BlastOutput_iterations>
+</BlastOutput>
b
diff -r 000000000000 -r de7d91ce970b test-data/blast2go.gaf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blast2go.gaf Mon Feb 25 06:33:51 2019 -0500
b
@@ -0,0 +1,6 @@
+!gaf-version: 2.1
+ gi|328696447|ref|XP_003240026.1| GO:0016021
+ gi|328696447|ref|XP_003240026.1| GO:0006511
+ gi|328696447|ref|XP_003240026.1| GO:0030145
+ gi|328696447|ref|XP_003240026.1| GO:0004803
+ gi|328696447|ref|XP_003240026.1| GO:0004177
b
diff -r 000000000000 -r de7d91ce970b test-data/citrus_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/citrus_genome.fasta Mon Feb 25 06:33:51 2019 -0500
b
@@ -0,0 +1,10 @@
+>scaffold00001  length=5927163
+TTTTGTATTCTATGTCCTCTGATCTTTATACTTCTTCATTTTGTCTTTGCAAGAACCGGA
+ATTATGGGTACATCACAAATTCTCTAGGTGTGACTTGTGTTGTGGGGCCTTTTTTTtACA
+TTTCCATATTGCAAGTATTTTTTTGCTACCATTGGTATATTTGTCTGTTAAAATCAATCT
+GCTTTCACTTATGTTCGTGCGTTCTTGTTCCCTCGCCTTGCAATTGCATATCTCAAATTA
+TCTTTCTTACTTTGATTTAGATGGCCAAGGTTTTAAGCTAACTTTTTACAATGCCAATTT
+TTAAATGGTTTTCTAATGCTGTTCAAAGTTGCAGCCTTTACTTCGTATATTTGTCAGGTT
+CTGACGGGTGCGGTCGGCGGCGGGGGCTATAGCATGCGGTCTCGAGAGCCGCAAAGAAAA
+ATGGGTGGTTTTCCCGGTTTCGGCCATAACTCGTGATCGGGGCCTCCGATTCTGGTTCCG
+TTTCGTCCCACGGGACCAGCCGGGCGGGGGCATCGGATTGCAAAAGTCTTTAAATTTGAA
b
diff -r 000000000000 -r de7d91ce970b test-data/interpro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interpro.xml Mon Feb 25 06:33:51 2019 -0500
b
@@ -0,0 +1,12 @@
+<interpro_matches>
+
+   <protein id="orange1.1g022799m_6_ORF4" length="79" crc64="D3F0B609CB0B9D28" >
+ <interpro id="noIPR" name="unintegrated" type="unintegrated">
+   <match id="seg" name="seg" dbname="SEG">
+     <location start="11" end="17" score="NA" status="?" evidence="Seg" />
+     <location start="54" end="78" score="NA" status="?" evidence="Seg" />
+   </match>
+ </interpro>
+   </protein>
+
+</interpro_matches>
b
diff -r 000000000000 -r de7d91ce970b test-data/sample.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample.gff3 Mon Feb 25 06:33:51 2019 -0500
b
@@ -0,0 +1,21 @@
+##gff-version 3
+##sequence-region scaffold00001 4058460 4062210
+scaffold00001 phytozome6 supercontig 1 5927163 . . . Name=scaffold00001;ID=scaffold00001
+scaffold00001 phytozome6 gene 4058460 4062210 . + . ID=orange1.1g015632m.g;Name=orange1.1g015632m.g
+scaffold00001 phytozome6 mRNA 4058460 4062210 . + . ID=PAC:18136217;Name=orange1.1g015632m;PACid=18136217;Parent=orange1.1g015632m.g
+scaffold00001 phytozome6 five_prime_UTR 4058460 4058898 . + . Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 five_prime_UTR 4059019 4059074 . + . Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 five_prime_UTR 4059172 4059234 . + . Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4059235 4059330 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4059422 4059514 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4059600 4059659 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4059790 4060062 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4060285 4060359 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4060480 4060536 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4060625 4060765 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4060857 4060907 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4061250 4061345 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4061417 4061500 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4061617 4061719 . + 0 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 CDS 4061823 4061905 . + 2 Parent=PAC:18136217;PACid=18136217
+scaffold00001 phytozome6 three_prime_UTR 4061906 4062210 . + . Parent=PAC:18136217;PACid=18136217
b
diff -r 000000000000 -r de7d91ce970b tripal.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tripal.py Mon Feb 25 06:33:51 2019 -0500
[
b'@@ -0,0 +1,502 @@\n+import collections\n+import os\n+import time\n+from abc import abstractmethod\n+\n+import tripal\n+\n+\n+#############################################\n+#      BEGIN IMPORT OF CACHING LIBRARY      #\n+#############################################\n+# This code is licensed under the MIT       #\n+# License and is a copy of code publicly    #\n+# available in rev.                         #\n+# e27332bc82f4e327aedaec17c9b656ae719322ed  #\n+# of https://github.com/tkem/cachetools/    #\n+#############################################\n+class DefaultMapping(collections.MutableMapping):\n+\n+    __slots__ = ()\n+\n+    @abstractmethod\n+    def __contains__(self, key):  # pragma: nocover\n+        return False\n+\n+    @abstractmethod\n+    def __getitem__(self, key):  # pragma: nocover\n+        if hasattr(self.__class__, \'__missing__\'):\n+            return self.__class__.__missing__(self, key)\n+        else:\n+            raise KeyError(key)\n+\n+    def get(self, key, default=None):\n+        if key in self:\n+            return self[key]\n+        else:\n+            return default\n+\n+    __marker = object()\n+\n+    def pop(self, key, default=__marker):\n+        if key in self:\n+            value = self[key]\n+            del self[key]\n+        elif default is self.__marker:\n+            raise KeyError(key)\n+        else:\n+            value = default\n+        return value\n+\n+    def setdefault(self, key, default=None):\n+        if key in self:\n+            value = self[key]\n+        else:\n+            self[key] = value = default\n+        return value\n+\n+\n+DefaultMapping.register(dict)\n+\n+\n+class _DefaultSize(object):\n+    def __getitem__(self, _):\n+        return 1\n+\n+    def __setitem__(self, _, value):\n+        assert value == 1\n+\n+    def pop(self, _):\n+        return 1\n+\n+\n+class Cache(DefaultMapping):\n+    """Mutable mapping to serve as a simple cache or cache base class."""\n+\n+    __size = _DefaultSize()\n+\n+    def __init__(self, maxsize, missing=None, getsizeof=None):\n+        if missing:\n+            self.__missing = missing\n+        if getsizeof:\n+            self.__getsizeof = getsizeof\n+            self.__size = dict()\n+        self.__data = dict()\n+        self.__currsize = 0\n+        self.__maxsize = maxsize\n+\n+    def __repr__(self):\n+        return \'%s(%r, maxsize=%r, currsize=%r)\' % (\n+            self.__class__.__name__,\n+            list(self.__data.items()),\n+            self.__maxsize,\n+            self.__currsize,\n+        )\n+\n+    def __getitem__(self, key):\n+        try:\n+            return self.__data[key]\n+        except KeyError:\n+            return self.__missing__(key)\n+\n+    def __setitem__(self, key, value):\n+        maxsize = self.__maxsize\n+        size = self.getsizeof(value)\n+        if size > maxsize:\n+            raise ValueError(\'value too large\')\n+        if key not in self.__data or self.__size[key] < size:\n+            while self.__currsize + size > maxsize:\n+                self.popitem()\n+        if key in self.__data:\n+            diffsize = size - self.__size[key]\n+        else:\n+            diffsize = size\n+        self.__data[key] = value\n+        self.__size[key] = size\n+        self.__currsize += diffsize\n+\n+    def __delitem__(self, key):\n+        size = self.__size.pop(key)\n+        del self.__data[key]\n+        self.__currsize -= size\n+\n+    def __contains__(self, key):\n+        return key in self.__data\n+\n+    def __missing__(self, key):\n+        value = self.__missing(key)\n+        try:\n+            self.__setitem__(key, value)\n+        except ValueError:\n+            pass  # value too large\n+        return value\n+\n+    def __iter__(self):\n+        return iter(self.__data)\n+\n+    def __len__(self):\n+        return len(self.__data)\n+\n+    @staticmethod\n+    def __getsizeof(value):\n+        return 1\n+\n+    @staticmethod\n+    def __missing(key):\n+        raise KeyError(key)\n+\n+    @property\n+    def maxsize(self):\n+        """The maximum size of the cache."""\n+        return self.__maxsize\n+\n+   '..b'XY_TRIPAL_USER\'],\n+        os.environ[\'GALAXY_TRIPAL_PASSWORD\']\n+    )\n+\n+\n+def list_organisms(*args, **kwargs):\n+\n+    ti = _get_instance()\n+\n+    # Key for cached data\n+    cacheKey = \'orgs\'\n+    # We don\'t want to trust "if key in cache" because between asking and fetch\n+    # it might through key error.\n+    if cacheKey not in cache:\n+        # However if it ISN\'T there, we know we\'re safe to fetch + put in\n+        # there.\n+        data = _list_organisms(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+    try:\n+        # The cache key may or may not be in the cache at this point, it\n+        # /likely/ is. However we take no chances that it wasn\'t evicted between\n+        # when we checked above and now, so we reference the object from the\n+        # cache in preparation to return.\n+        data = cache[cacheKey]\n+        return data\n+    except KeyError:\n+        # If access fails due to eviction, we will fail over and can ensure that\n+        # data is inserted.\n+        data = _list_organisms(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+\n+\n+def _list_organisms(ti, *args, **kwargs):\n+    # Fetch the orgs.\n+    orgs_data = []\n+    for org in ti.organism.get_organisms():\n+        clean_name = \'%s %s\' % (org[\'genus\'], org[\'species\'])\n+        if org[\'infraspecific_name\']:\n+            clean_name += \' (%s)\' % (org[\'infraspecific_name\'])\n+        orgs_data.append((clean_name, org[\'organism_id\'], False))\n+    return orgs_data\n+\n+\n+def list_analyses(*args, **kwargs):\n+\n+    ti = _get_instance()\n+\n+    # Key for cached data\n+    cacheKey = \'analyses\'\n+    # We don\'t want to trust "if key in cache" because between asking and fetch\n+    # it might through key error.\n+    if cacheKey not in cache:\n+        # However if it ISN\'T there, we know we\'re safe to fetch + put in\n+        # there.<?xml version="1.0"?>\n+\n+        data = _list_analyses(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+    try:\n+        # The cache key may or may not be in the cache at this point, it\n+        # /likely/ is. However we take no chances that it wasn\'t evicted between\n+        # when we checked above and now, so we reference the object from the\n+        # cache in preparation to return.\n+        data = cache[cacheKey]\n+        return data\n+    except KeyError:\n+        # If access fails due to eviction, we will fail over and can ensure that\n+        # data is inserted.\n+        data = _list_analyses(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+\n+\n+def _list_analyses(ti, *args, **kwargs):\n+    ans_data = []\n+    for an in ti.analysis.get_analyses():\n+        ans_data.append((an[\'name\'], an[\'analysis_id\'], False))\n+    return ans_data\n+\n+\n+def list_blastdbs(*args, **kwargs):\n+\n+    ti = _get_instance()\n+\n+    # Key for cached data\n+    cacheKey = \'blastdbs\'\n+    # We don\'t want to trust "if key in cache" because between asking and fetch\n+    # it might through key error.\n+    if cacheKey not in cache:\n+        # However if it ISN\'T there, we know we\'re safe to fetch + put in\n+        # there.\n+        data = _list_blastdbs(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+    try:\n+        # The cache key may or may not be in the cache at this point, it\n+        # /likely/ is. However we take no chances that it wasn\'t evicted between\n+        # when we checked above and now, so we reference the object from the\n+        # cache in preparation to return.\n+        data = cache[cacheKey]\n+        return data\n+    except KeyError:\n+        # If access fails due to eviction, we will fail over and can ensure that\n+        # data is inserted.\n+        data = _list_blastdbs(ti, *args, **kwargs)\n+        cache[cacheKey] = data\n+        return data\n+\n+\n+def _list_blastdbs(ti, *args, **kwargs):\n+    dbs_data = []\n+    for db in ti.db.get_dbs():\n+        dbs_data.append((db[\'name\'], db[\'db_id\'], False))\n+    return dbs_data\n'