| Next changeset 1:43bb9308b52d (2017-09-19) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268 |
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added:
analysis_load_fasta.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 |
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| diff -r 000000000000 -r ca1eb54c95d6 analysis_load_fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/analysis_load_fasta.xml Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -0,0 +1,191 @@ +<?xml version="1.0"?> +<tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta file" version="@WRAPPER_VERSION@.0"> + <description>into Tripal</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <code file="tripal.py"/> + <expand macro="stdio"/> + <command><![CDATA[ + tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}" + + && + + cp '${fasta}' "\${tmp_dir}/content.fasta" + + && + + @AUTH@ + + tripaille analysis load_fasta + + --organism_id '${organism}' + + --analysis_id '${analysis}' + + --sequence_type '${sequence_type}' + + --method '${loading.method}' + + --match_type '${loading.match_type}' + + #if str($naming.re_name): + --re_name '${naming.re_name}' + #end if + + #if str($naming.re_uniquename): + --re_uniquename '${naming.re_uniquename}' + #end if + + #if str($relationships.rel_type) != "none": + --rel_type '${relationships.rel_type}' + --rel_subject_re '${relationships.rel_subject_re}' + --rel_subject_type '${relationships.rel_subject_type}' + #end if + + #if str($ext_db.db_ext_id): + --db_ext_id '${ext_db.db_ext_id}' + #end if + + #if str($ext_db.re_accession): + --re_accession '${ext_db.re_accession}' + #end if + + "\${tmp_dir}/content.fasta" + + && + + echo "Data loaded" > $results + ]]></command> + <inputs> + <param name="fasta" + type="data" + format="fasta" + label="Fasta file to load" /> + + <param argument="--organism" + type="select" + dynamic_options="list_organisms()" + label="Organism" /> + + <param argument="--analysis" + type="select" + dynamic_options="list_analyses()" + label="Analysis" /> + + <param name="sequence_type" + argument="--sequence_type" + type="text" + label="Sequence type" + value="contig" + help="this should be a Sequence Ontology term" /> + + <conditional name="loading"> + <param name="method" + argument="--method" + type="select" + label="Loading method" + help="select wether you expect feature to be already existing or not"> + <option value="insup" selected="true">Insert and update</option> + <option value="insert">Insert only</option> + <option value="update">Update only</option> + </param> + <when value="insup"> + <expand macro="match_type" /> + </when> + <when value="insert"/> + <when value="update"> + <expand macro="match_type" /> + </when> + </conditional> + + <section name="naming" title="Feature naming"> + <param name="re_name" + argument="--re_name" + type="text" + optional="true" + label="Regular expression to extract feature name" + help="this regex will be applied on the fasta definition line to generate the feature name"> + <expand macro="sanitized"/> + </param> + + <param name="re_uniquename" + argument="--re_uniquename" + type="text" + optional="true" + label="Regular expression to extract feature uniquename" + help="this regex will be applied on the fasta definition line to generate the feature uniquename"> + <expand macro="sanitized"/> + </param> + </section> + + <conditional name="relationships"> + <param name="rel_type" + argument="--rel_type" + type="select" + label="Relationship type" + help="Use this when inserting features that should be associated to other already existing features"> + <option value="none" selected="true">No relationship</option> + <option value="part_of">Part of (for CDS sequences)</option> + <option value="derives_from">Derives from (for peptide sequences)</option> + </param> + <when value="none"/> + <when value="part_of"> + <expand macro="feature_rel" /> + </when> + <when value="derives_from"> + <expand macro="feature_rel" /> + </when> + </conditional> + + <section name="ext_db" title="Cross references to external database"> + <param name="db_ext_id" + argument="--db_ext_id" + type="integer" + optional="true" + label="External Database ID" + help="Numeric ID from the Chado database" /> + + <param name="re_accession" + argument="--re_accession" + type="text" + optional="true" + label="Regular expression to extract the accession from external DB" + help="this regex will be applied on the fasta definition line to generate the accession from external DB" /> + </section> + </inputs> + <outputs> + <data format="txt" name="results" label="Load Fasta into Tripal" /> + </outputs> + <tests> + <test expect_failure="true" expect_exit_code="1"> + <param name="fasta" value="citrus_genome.fasta" /> + <param name="organism" value="Testus testus" /> + <param name="analysis" value="Annotation xx" /> + <param name="sequence_type" value="mRNA" /> + <conditional name="loading"> + <param name="method" value="insup" /> + <param name="match_type" value="uniquename" /> + </conditional> + <section name="naming"> + <param name="re_name" value="([a-z]{4}[0-9]+)_suffix" /> + <param name="re_uniquename" value="([a-z]{4}[0-9]+_suffix)" /> + </section> + + <expand macro="test_result" /> + </test> + </tests> + <help><![CDATA[ + @HELP_OVERVIEW@ + + **Load Fasta** + + With this tool, you can load sequences from a Fasta file into the Tripal/Chado database. + + Corresponding features can be created if needed. + + @HELP@ + ]]></help> + <expand macro="citation"/> +</tool> |
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| diff -r 000000000000 -r ca1eb54c95d6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -0,0 +1,215 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.0.4">python-tripal</requirement> + <yield/> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <regex level="fatal" match="Exception:" source="stderr" /> + <regex level="fatal" match="error" source="stderr" /> + <exit_code range="1:" /> + </stdio> + </xml> + + <token name="@WRAPPER_VERSION@">2.0.4</token> + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/database/bat075</citation> + </citations> + </xml> + + <token name="@HELP_OVERVIEW@"><![CDATA[ + **Python-tripal Overview** + + Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database. + The tripal_rest_api Tripal module must be installed on the remote server to use these tools. + ]]></token> + + <token name="@HELP@"><![CDATA[ + **Useful Links** + + `Tripal project website <http://tripal.info/>`_ + + `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools + ]]></token> + + <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token> + + <token name="@AUTH@"><![CDATA[ + echo "__default: local" > '.auth.yml' && + echo "local:" >> '.auth.yml' && + echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' && + echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' && + echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' && + + TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml' + ]]></token> + + <xml name="test_result"> + <assert_stderr> + <has_text text="MissingSchema" /> + </assert_stderr> + </xml> + + <xml name="analysis"> + <section name="analysis" title="Analysis" expanded="True"> + <param name="name" + type="text" + label="The analysis name [mandatory]"> + <expand macro="sanitized"/> + </param> + + <param name="program" + type="text" + label="Program name [mandatory]" + help="Name of the program that was used to perform this analysis"> + <expand macro="sanitized"/> + </param> + <param name="program_version" + type="text" + label="Program version [mandatory]" + help="Version of the program that was used to perform this analysis"/> + <param name="source" + type="text" + label="Source name [mandatory]" + help="Where this analysis comes from"> + <expand macro="sanitized"/> + </param> + + <param name="source_version" + argument="--sourceversion" + type="text" + optional="True" + label="Source version" /> + <param name="source_uri" + argument="--sourceuri" + type="text" + optional="True" + label="Source URI" + help="URI where source data was retrieved" /> + <param name="algorithm" + argument="--algorithm" + type="text" + label="Algorithm" + optional="True" + help="Algorithm of the program that was used to perform this analysis" /> + <param name="description" + argument="--description" + type="text" + optional="True" + label="Analysis description"> + <expand macro="sanitized"/> + </param> + <param name="date" + argument="--date_executed" + type="text" + optional="True" + label="Execution date" + help="Format: yyyy-mm-dd Default: Today"> + <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator> + </param> + </section> + </xml> + + <xml name="feature_rel"> + <param name="rel_subject_re" + argument="--rel-subject-re" + type="text" + label="Regular expression to extract the unique name of the parent feature" + help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature"> + <expand macro="sanitized"/> + </param> + + <param name="rel_subject_type" + argument="--rel-subject-type" + type="text" + label="Sequence type of the parent" + help="this should be a Sequence Ontology term" /> + </xml> + + <xml name="match_type"> + <param name="match_type" + argument="--match-type" + type="select" + label="Match type for already loaded features"> + <option value="uniquename" selected="true">Unique name</option> + <option value="name">Name</option> + </param> + </xml> + + <xml name="matching"> + <section name="matching" title="Feature matching" expanded="True"> + <param name="query_type" + type="text" + label="The feature type of the blast query" + help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" /> + + <param name="query_uniquename" + type="boolean" + checked="false" + truevalue="--query_uniquename" + falsevalue="" + label="Find blast query features using their Unique name" + help="Feature name will be used otherwise" /> + + <param name="query_re" + type="text" + optional="true" + label="Regular expression to extract the feature name from the blast query name" + help="leave empty if the first word in query name is sufficient"> + <expand macro="sanitized"/> + </param> + </section> + </xml> + + <xml name="sanitized"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="'"'"'"/> + <add source="(" target="\("/> + <add source=")" target="\)"/> + </mapping> + </sanitizer> + </xml> + + <token name="@MATCHING@"><![CDATA[ + #if str($matching.query_re): + --query_re '${matching.query_re}' + #end if + + $matching.query_uniquename + + --query_type '$matching.query_type' + ]]></token> + + <token name="@ANALYSIS@"><![CDATA[ + #if $analysis.algorithm: + --algorithm '$analysis.algorithm' + #end if + #if $analysis.source_version: + --sourceversion '$analysis.source_version' + #end if + #if $analysis.source_uri: + --sourceuri '$analysis.source_uri' + #end if + #if $analysis.description: + --description '$analysis.description' + #end if + #if $analysis.date: + --date_executed '$analysis.date' + #end if + + '$analysis.name' + '$analysis.program' + '$analysis.program_version' + '$analysis.source' + ]]></token> +</macros> |
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| diff -r 000000000000 -r ca1eb54c95d6 test-data/blast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast.xml Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -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), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", 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] >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> |
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| diff -r 000000000000 -r ca1eb54c95d6 test-data/blast2go.gaf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast2go.gaf Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r ca1eb54c95d6 test-data/citrus_genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/citrus_genome.fasta Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -0,0 +1,10 @@ +>scaffold00001 length=5927163 +TTTTGTATTCTATGTCCTCTGATCTTTATACTTCTTCATTTTGTCTTTGCAAGAACCGGA +ATTATGGGTACATCACAAATTCTCTAGGTGTGACTTGTGTTGTGGGGCCTTTTTTTtACA +TTTCCATATTGCAAGTATTTTTTTGCTACCATTGGTATATTTGTCTGTTAAAATCAATCT +GCTTTCACTTATGTTCGTGCGTTCTTGTTCCCTCGCCTTGCAATTGCATATCTCAAATTA +TCTTTCTTACTTTGATTTAGATGGCCAAGGTTTTAAGCTAACTTTTTACAATGCCAATTT +TTAAATGGTTTTCTAATGCTGTTCAAAGTTGCAGCCTTTACTTCGTATATTTGTCAGGTT +CTGACGGGTGCGGTCGGCGGCGGGGGCTATAGCATGCGGTCTCGAGAGCCGCAAAGAAAA +ATGGGTGGTTTTCCCGGTTTCGGCCATAACTCGTGATCGGGGCCTCCGATTCTGGTTCCG +TTTCGTCCCACGGGACCAGCCGGGCGGGGGCATCGGATTGCAAAAGTCTTTAAATTTGAA |
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| diff -r 000000000000 -r ca1eb54c95d6 test-data/interpro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interpro.xml Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r ca1eb54c95d6 test-data/sample.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.gff3 Mon Sep 11 05:50:45 2017 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r ca1eb54c95d6 tripal.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tripal.py Mon Sep 11 05:50:45 2017 -0400 |
| [ |
| b'@@ -0,0 +1,503 @@\n+import collections\n+import os\n+import time\n+\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' |