| Previous changeset 10:d8de5b627c88 (2013-09-13) Next changeset 12:b7c85bb42d87 (2014-06-13) |
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Commit message:
Uploaded v0.1.0, handles extended tabular input. |
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modified:
test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular |
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added:
test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.py tools/blastxml_to_top_descr/blastxml_to_top_descr.xml tools/blastxml_to_top_descr/repository_dependencies.xml |
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removed:
blastxml_to_top_descr/README.rst blastxml_to_top_descr/blastxml_to_top_descr.py blastxml_to_top_descr/blastxml_to_top_descr.xml blastxml_to_top_descr/repository_dependencies.xml |
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| diff -r d8de5b627c88 -r 6f623a9718f1 blastxml_to_top_descr/README.rst --- a/blastxml_to_top_descr/README.rst Fri Sep 13 06:30:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,121 +0,0 @@ -Galaxy tool to extract top BLAST hit descriptions from BLAST XML -================================================================ - -This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -This tool is a short Python script to parse a BLAST XML file, and extract the -identifiers with description for the top matches (by default the top 3), and -output these as a simple tabular file along with the query identifiers. - -It is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr - -This requires the 'blast_datatypes' repository from the Galaxy Tool Shed -to provide the 'blastxml' file format definition. - - -Automated Installation -====================== - -This should be straightforward, Galaxy should automatically install the -'blast_datatypes' dependency. - - -Manual Installation -=================== - -If you haven't done so before, first install the 'blast_datatypes' repository. - -There are just two files to install (if doing this manually): - -* blastxml_to_top_descr.py (the Python script) -* blastxml_to_top_descr.xml (the Galaxy tool definition) - -The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to -the NCBI BLAST+ tool wrappers. - -You will also need to modify the tools_conf.xml file to tell Galaxy to offer -the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:: - - <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" /> - -To run the tool's tests, also add this line to tools_conf.xml.sample then:: - - $ sh run_functional_tests.sh -id blastxml_to_top_descr - - -History -======= - -======= ====================================================================== -Version Changes -------- ---------------------------------------------------------------------- -v0.0.1 - Initial version. -v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency - on the 'blast_datatypes' repository in the Tool Shed. -v0.0.3 - Include the test files required to run the unit tests -v0.0.4 - Quote filenames in case they contain spaces (internal change) -v0.0.5 - Include number of queries with BLAST matches in stdout (peek text) -v0.0.6 - Check for errors via the script's return code (internal change) -v0.0.7 - Link to Tool Shed added to help text and this documentation. - - Tweak dependency on blast_datatypes to also work on Test Tool Shed - - Adopt standard MIT License. -v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast -v0.0.9 - Updated citation information (Cock et al. 2013). -======= ====================================================================== - - -Bug Reports -=========== - -You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask -us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev - - -Developers -========== - -This script and related tools were originally developed on the 'tools' branch of -the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/ - -As of July 2013, development is continuing on a dedicated GitHub repository: -https://github.com/peterjc/galaxy_blast - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the GitHub repository root folder:: - - $ tar -czf blastxml_to_top_descr.tar.gz blastxml_to_top_descr/README.rst blastxml_to_top_descr/blastxml_to_top_descr.* blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular - -Check this worked:: - - $ tar -tzf blastxml_to_top_descr.tar.gz - blastxml_to_top_descr/README.rst - blastxml_to_top_descr/blastxml_to_top_descr.py - blastxml_to_top_descr/blastxml_to_top_descr.xml - blastxml_to_top_descr/repository_dependencies.xml - test-data/blastp_four_human_vs_rhodopsin.xml - test-data/blastp_four_human_vs_rhodopsin_top3.tabular - - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. |
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| diff -r d8de5b627c88 -r 6f623a9718f1 blastxml_to_top_descr/blastxml_to_top_descr.py --- a/blastxml_to_top_descr/blastxml_to_top_descr.py Fri Sep 13 06:30:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,122 +0,0 @@ -#!/usr/bin/env python -"""Convert a BLAST XML file to a top hits description table. - -Takes three command line options, input BLAST XML filename, output tabular -BLAST filename, number of hits to collect the descriptions of. -""" -import sys -import re - -if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.5" - sys.exit(0) - -if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as ElementTree -else: - from galaxy import eggs - import pkg_resources; pkg_resources.require( "elementtree" ) - from elementtree import ElementTree - -def stop_err( msg ): - sys.stderr.write("%s\n" % msg) - sys.exit(1) - -#Parse Command Line -try: - in_file, out_file, topN = sys.argv[1:] -except: - stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, number of hits") - - -try: - topN = int(topN) -except ValueError: - stop_err("Number of hits argument should be an integer (at least 1)") -if topN < 1: - stop_err("Number of hits argument should be an integer (at least 1)") - -# get an iterable -try: - context = ElementTree.iterparse(in_file, events=("start", "end")) -except: - stop_err("Invalid data format.") -# turn it into an iterator -context = iter(context) -# get the root element -try: - event, root = context.next() -except: - stop_err( "Invalid data format." ) - - -re_default_query_id = re.compile("^Query_\d+$") -assert re_default_query_id.match("Query_101") -assert not re_default_query_id.match("Query_101a") -assert not re_default_query_id.match("MyQuery_101") -re_default_subject_id = re.compile("^Subject_\d+$") -assert re_default_subject_id.match("Subject_1") -assert not re_default_subject_id.match("Subject_") -assert not re_default_subject_id.match("Subject_12a") -assert not re_default_subject_id.match("TheSubject_1") - - -count = 0 -pos_count = 0 -outfile = open(out_file, 'w') -outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) -for event, elem in context: - # for every <Iteration> tag - if event == "end" and elem.tag == "Iteration": - #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA - # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - # <Iteration_query-len>406</Iteration_query-len> - # <Iteration_hits></Iteration_hits> - # - #Or, from BLAST 2.2.24+ run online - # <Iteration_query-ID>Query_1</Iteration_query-ID> - # <Iteration_query-def>Sample</Iteration_query-def> - # <Iteration_query-len>516</Iteration_query-len> - # <Iteration_hits>... - qseqid = elem.findtext("Iteration_query-ID") - if qseqid is None: - stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)") - if re_default_query_id.match(qseqid): - #Place holder ID, take the first word of the query definition - qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] - # for every <Hit> within <Iteration> - hit_descrs = [] - for hit in elem.findall("Iteration_hits/Hit"): - #Expecting either this, - # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> - # <Hit_def>RecName: Full=Rhodopsin</Hit_def> - # <Hit_accession>P56514</Hit_accession> - #or, - # <Hit_id>Subject_1</Hit_id> - # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> - # <Hit_accession>Subject_1</Hit_accession> - # - #apparently depending on the parse_deflines switch - sseqid = hit.findtext("Hit_id").split(None,1)[0] - hit_def = sseqid + " " + hit.findtext("Hit_def") - if re_default_subject_id.match(sseqid) \ - and sseqid == hit.findtext("Hit_accession"): - #Place holder ID, take the first word of the subject definition - hit_def = hit.findtext("Hit_def") - sseqid = hit_def.split(None,1)[0] - assert hit_def not in hit_descrs - hit_descrs.append(hit_def) - #print "%r has %i hits" % (qseqid, len(hit_descrs)) - if hit_descrs: - pos_count += 1 - hit_descrs = hit_descrs[:topN] - while len(hit_descrs) < topN: - hit_descrs.append("") - outfile.write("%s\t%s\n" % (qseqid, "\t".join(hit_descrs))) - count += 1 - # prevents ElementTree from growing large datastructure - root.clear() - elem.clear() -outfile.close() -print "Of %i queries, %i had BLAST results" % (count, pos_count) |
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| diff -r d8de5b627c88 -r 6f623a9718f1 blastxml_to_top_descr/blastxml_to_top_descr.xml --- a/blastxml_to_top_descr/blastxml_to_top_descr.xml Fri Sep 13 06:30:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,66 +0,0 @@ -<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.9"> - <description>Make a table from BLAST XML</description> - <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> - <command interpreter="python"> - blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN} - </command> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <inputs> - <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> - <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> - </inputs> - <outputs> - <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" /> - </outputs> - <requirements> - </requirements> - <tests> - <test> - <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="topN" value="3" /> - <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> - </test> - </tests> - <help> - -**What it does** - -NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of -formats including text, tabular and a more detailed XML format. You can -do a lot of things with tabular files in Galaxy (sorting, filtering, joins, -etc) however currently the BLAST tabular output omits the hit descriptions -found in the other output formats. - -This tool turns a BLAST XML file into a simple tabular file containing -one row per query sequence, containing the query identifier and then -the three (by default) top hit descriptions. If a query doesn't have -that many hits, then these entries are left blank. - -**Example Usage** - -One simple usage would be to take a transcriptome assembly or set of -gene predictions, run a BLAST search against the NCBI NR database, and -then use this tool to make a table of the top three BLAST hits. This -can give you a 'quick and dirty' crude annotation, potentially enough -to spot some problems (e.g. bacterial contaimination could be very -obvious). - -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite: - -Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). -Galaxy tools and workflows for sequence analysis with applications -in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 - -This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr - - </help> -</tool> |
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| diff -r d8de5b627c88 -r 6f623a9718f1 blastxml_to_top_descr/repository_dependencies.xml --- a/blastxml_to_top_descr/repository_dependencies.xml Fri Sep 13 06:30:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Requires BLAST XML and database datatype definitions."> -<repository changeset_revision="a44a7a5456e1" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> -</repositories> |
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| diff -r d8de5b627c88 -r 6f623a9718f1 test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Fri Sep 13 06:30:16 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Tue May 13 06:32:42 2014 -0400 |
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| b'@@ -2,7 +2,7 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>blastp</BlastOutput_program>\n- <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>\n+ <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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>\n <BlastOutput_db></BlastOutput_db>\n <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>\n@@ -17,630 +17,649 @@\n <Parameters_filter>F</Parameters_filter>\n </Parameters>\n </BlastOutput_param>\n- <BlastOutput_iterations>\n- <Iteration>\n- <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>3</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>4</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteratio'..b'q>\n+ <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>29</Statistics_hsp-len>\n+ <Statistics_eff-space>101761</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>24</Iteration_iter-num>\n+ <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>\n+ <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>\n+ <Iteration_query-len>348</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>\n+ <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>\n+ <Hit_accession>BAB21486</Hit_accession>\n+ <Hit_len>354</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>599.356</Hsp_bit-score>\n+ <Hsp_score>1544</Hsp_score>\n+ <Hsp_evalue>0</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>341</Hsp_query-to>\n+ <Hsp_hit-from>1</Hsp_hit-from>\n+ <Hsp_hit-to>342</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>281</Hsp_identity>\n+ <Hsp_positive>314</Hsp_positive>\n+ <Hsp_gaps>1</Hsp_gaps>\n+ <Hsp_align-len>342</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>29</Statistics_hsp-len>\n+ <Statistics_eff-space>101761</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
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| diff -r d8de5b627c88 -r 6f623a9718f1 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Tue May 13 06:32:42 2014 -0400 |
| [ |
| @@ -0,0 +1,6 @@ +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 rhodopsin [Felis catus] +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 RecName: Full=Rhodopsin +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Cynopterus brachyotis] +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Myotis pilosus] +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 rhodopsin [Bos taurus] +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 fresh water form rod opsin [Conger myriaster] |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 test-data/blastp_four_human_vs_rhodopsin_top3.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Fri Sep 13 06:30:16 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Tue May 13 06:32:42 2014 -0400 |
| [ |
| @@ -1,25 +1,5 @@ #Query BLAST hit 1 BLAST hit 2 BLAST hit 3 sp|Q9BS26|ERP44_HUMAN -sp|Q9BS26|ERP44_HUMAN -sp|Q9BS26|ERP44_HUMAN -sp|Q9BS26|ERP44_HUMAN -sp|Q9BS26|ERP44_HUMAN -sp|Q9BS26|ERP44_HUMAN sp|Q9NSY1|BMP2K_HUMAN -sp|Q9NSY1|BMP2K_HUMAN -sp|Q9NSY1|BMP2K_HUMAN -sp|Q9NSY1|BMP2K_HUMAN -sp|Q9NSY1|BMP2K_HUMAN -sp|Q9NSY1|BMP2K_HUMAN sp|P06213|INSR_HUMAN -sp|P06213|INSR_HUMAN -sp|P06213|INSR_HUMAN -sp|P06213|INSR_HUMAN -sp|P06213|INSR_HUMAN -sp|P06213|INSR_HUMAN -sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] -sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin -sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] -sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus] -sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A rhodopsin [Bos taurus] -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster] +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular Tue May 13 06:32:42 2014 -0400 |
| [ |
| @@ -0,0 +1,2 @@ +#Query BLAST hit 1 BLAST hit 2 BLAST hit 3 +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 tools/blastxml_to_top_descr/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blastxml_to_top_descr/README.rst Tue May 13 06:32:42 2014 -0400 |
| b |
| @@ -0,0 +1,128 @@ +Galaxy tool to extract top BLAST hit descriptions from BLAST XML +================================================================ + +This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script to parse a BLAST XML file, and extract the +identifiers with description for the top matches (by default the top 3), and +output these as a simple tabular file along with the query identifiers. + +It is available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr + +This requires the 'blast_datatypes' repository from the Galaxy Tool Shed +to provide the 'blastxml' file format definition. + + +Automated Installation +====================== + +This should be straightforward, Galaxy should automatically install the +'blast_datatypes' dependency. + + +Manual Installation +=================== + +If you haven't done so before, first install the 'blast_datatypes' repository. + +There are just two files to install (if doing this manually): + +* blastxml_to_top_descr.py (the Python script) +* blastxml_to_top_descr.xml (the Galaxy tool definition) + +The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to +the NCBI BLAST+ tool wrappers. + +You will also need to modify the tools_conf.xml file to tell Galaxy to offer +the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line:: + + <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" /> + +To run the tool's tests, also add this line to tools_conf.xml.sample then:: + + $ sh run_functional_tests.sh -id blastxml_to_top_descr + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version. +v0.0.2 - Since BLAST+ was moved out of the Galaxy core, now have a dependency + on the 'blast_datatypes' repository in the Tool Shed. +v0.0.3 - Include the test files required to run the unit tests +v0.0.4 - Quote filenames in case they contain spaces (internal change) +v0.0.5 - Include number of queries with BLAST matches in stdout (peek text) +v0.0.6 - Check for errors via the script's return code (internal change) +v0.0.7 - Link to Tool Shed added to help text and this documentation. + - Tweak dependency on blast_datatypes to also work on Test Tool Shed + - Adopt standard MIT License. +v0.0.8 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast +v0.0.9 - Updated citation information (Cock et al. 2013). +v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files + including the description/title (via the salltitles field). +v0.1.0 - Switch to using an optparse based API for Python script internally. + - Support BLAST XML with multiple ``<Iteration>`` blocks per query. + - Support the default 25 column extended tabular BLAST output. +======= ====================================================================== + + +Bug Reports +=========== + +You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Developers +========== + +This script and related tools were originally developed on the 'tools' branch of +the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/ + +As of July 2013, development is continuing on a dedicated GitHub repository: +https://github.com/peterjc/galaxy_blast + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the GitHub repository root folder:: + + $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular + +Check this worked:: + + $ tar -tzf blastxml_to_top_descr.tar.gz + tools/blastxml_to_top_descr/README.rst + tools/blastxml_to_top_descr/blastxml_to_top_descr.py + tools/blastxml_to_top_descr/blastxml_to_top_descr.xml + tools/blastxml_to_top_descr/repository_dependencies.xml + test-data/blastp_four_human_vs_rhodopsin.xml + test-data/blastp_four_human_vs_rhodopsin_top3.tabular + test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular + test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 tools/blastxml_to_top_descr/blastxml_to_top_descr.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py Tue May 13 06:32:42 2014 -0400 |
| [ |
| b'@@ -0,0 +1,255 @@\n+#!/usr/bin/env python\n+"""Convert a BLAST XML file to a top hits description table.\n+\n+Takes three command line options, input BLAST XML filename, output tabular\n+BLAST filename, number of hits to collect the descriptions of.\n+\n+Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits.\n+"""\n+import os\n+import sys\n+import re\n+from optparse import OptionParser\n+\n+if "-v" in sys.argv or "--version" in sys.argv:\n+ print "v0.1.0"\n+ sys.exit(0)\n+\n+if sys.version_info[:2] >= ( 2, 5 ):\n+ import xml.etree.cElementTree as ElementTree\n+else:\n+ from galaxy import eggs\n+ import pkg_resources; pkg_resources.require( "elementtree" )\n+ from elementtree import ElementTree\n+\n+def stop_err( msg ):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit(1)\n+\n+usage = """Use as follows:\n+\n+$ blastxml_to_top_descr.py [-t 3] -o example.tabular input.xml\n+\n+Or,\n+\n+$ blastxml_to_top_descr.py [--topN 3] --output example.tabular input.xml\n+\n+This will take the top 3 BLAST descriptions from the input BLAST XML file,\n+writing them to the specified output file in tabular format.\n+"""\n+\n+parser = OptionParser(usage=usage)\n+parser.add_option("-t", "--topN", dest="topN", default=3,\n+ help="Number of descriptions to collect (in order from file)")\n+parser.add_option("-o", "--output", dest="out_file", default=None,\n+ help="Output filename for tabular file",\n+ metavar="FILE")\n+parser.add_option("-f", "--format", dest="format", default="blastxml",\n+ help="Input format (blastxml or tabular)")\n+parser.add_option("-q", "--qseqid", dest="qseqid", default="1",\n+ help="Column for query \'qseqid\' (for tabular input; default 1)")\n+parser.add_option("-s", "--sseqid", dest="sseqid", default="2",\n+ help="Column for subject \'sseqid\' (for tabular input; default 2)")\n+parser.add_option("-d", "--salltitles", dest="salltitles", default="25",\n+ help="Column for descriptions \'salltitles\' (for tabular input; default 25)")\n+(options, args) = parser.parse_args()\n+\n+if len(sys.argv) == 4 and len(args) == 3 and not options.out_file:\n+ stop_err("""The API has changed, replace this:\n+\n+$ python blastxml_to_top_descr.py input.xml output.tab 3\n+\n+with:\n+\n+$ python blastxml_to_top_descr.py -o output.tab -t 3 input.xml\n+\n+Sorry.\n+""")\n+\n+if not args:\n+ stop_err("Input filename missing, try -h")\n+if len(args) > 1:\n+ stop_err("Expects a single argument, one input filename")\n+in_file = args[0]\n+out_file = options.out_file\n+topN = options.topN\n+\n+try:\n+ topN = int(topN)\n+except ValueError:\n+ stop_err("Number of hits argument should be an integer (at least 1)")\n+if topN < 1:\n+ stop_err("Number of hits argument should be an integer (at least 1)")\n+\n+if not os.path.isfile(in_file):\n+ stop_err("Missing input file: %r" % in_file)\n+\n+\n+def get_column(value):\n+ """Convert column number on command line to Python index."""\n+ if value.startswith("c"):\n+ # Ignore c prefix, e.g. "c1" for "1"\n+ value = value[1:]\n+ try:\n+ col = int(value)\n+ except:\n+ stop_err("Expected an integer column number, not %r" % value)\n+ if col < 1:\n+ stop_err("Expect column numbers to be at least one, not %r" % value)\n+ return col - 1 # Python counting!\n+\n+def tabular_hits(in_file, qseqid, sseqid, salltitles):\n+ """Parse key data from tabular BLAST output.\n+\n+ Iterator returning tuples (qseqid, list_of_subject_description)\n+ """\n+ current_query = None\n+ current_hits = []\n+ with open(in_file) as input:\n+ for line in input:\n+ parts = line.rstrip("\\n").split("\\t")\n+ query = parts[qseqid]\n+ descr = "%s %s" % (parts[sseqid], parts[salltitles])\n+ if current_query is None:\n+ # First hit\n+ current_query = query\n+ current_hits = [descr]\n+ elif current_query == query:\n+ # '..b'y-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n+ # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n+ # <Iteration_query-len>406</Iteration_query-len>\n+ # <Iteration_hits></Iteration_hits>\n+ #\n+ # Or, from BLAST 2.2.24+ run online\n+ # <Iteration_query-ID>Query_1</Iteration_query-ID>\n+ # <Iteration_query-def>Sample</Iteration_query-def>\n+ # <Iteration_query-len>516</Iteration_query-len>\n+ # <Iteration_hits>...\n+ qseqid = elem.findtext("Iteration_query-ID")\n+ if qseqid is None:\n+ stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)")\n+ if re_default_query_id.match(qseqid):\n+ #Place holder ID, take the first word of the query definition\n+ qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]\n+ if current_query is None:\n+ # First hit\n+ current_query = qseqid\n+ hit_descrs = []\n+ elif current_query != qseqid:\n+ # New hit\n+ yield current_query, hit_descrs\n+ current_query = qseqid\n+ hit_descrs = []\n+ else:\n+ # Continuation of previous query\n+ # i.e. This BLAST XML did not use one <Iteration> per query\n+ # sys.stderr.write("Multiple <Iteration> blocks for %s\\n" % qseqid)\n+ pass\n+ # for every <Hit> within <Iteration>\n+ for hit in elem.findall("Iteration_hits/Hit"):\n+ # Expecting either this,\n+ # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>\n+ # <Hit_def>RecName: Full=Rhodopsin</Hit_def>\n+ # <Hit_accession>P56514</Hit_accession>\n+ # or,\n+ # <Hit_id>Subject_1</Hit_id>\n+ # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>\n+ # <Hit_accession>Subject_1</Hit_accession>\n+ #\n+ #apparently depending on the parse_deflines switch\n+ sseqid = hit.findtext("Hit_id").split(None,1)[0]\n+ hit_def = sseqid + " " + hit.findtext("Hit_def")\n+ if re_default_subject_id.match(sseqid) \\\n+ and sseqid == hit.findtext("Hit_accession"):\n+ #Place holder ID, take the first word of the subject definition\n+ hit_def = hit.findtext("Hit_def")\n+ sseqid = hit_def.split(None,1)[0]\n+ assert hit_def not in hit_descrs\n+ hit_descrs.append(hit_def)\n+ # prevents ElementTree from growing large datastructure\n+ root.clear()\n+ elem.clear()\n+ if current_query is not None:\n+ # Final query\n+ yield current_query, hit_descrs\n+\n+if options.format == "blastxml":\n+ hits = blastxml_hits(in_file)\n+elif options.format == "tabular":\n+ qseqid = get_column(options.qseqid)\n+ sseqid = get_column(options.sseqid)\n+ salltitles = get_column(options.salltitles)\n+ hits = tabular_hits(in_file, qseqid, sseqid, salltitles)\n+else:\n+ stop_err("Unsupported format: %r" % options.format)\n+\n+\n+def best_hits(descriptions, topN):\n+ if len(descriptions) < topN:\n+ return descriptions + [""] * (topN - len(descriptions))\n+ else:\n+ return descriptions[:topN]\n+\n+count = 0\n+if out_file is None:\n+ outfile = sys.stdout\n+else:\n+ outfile = open(out_file, \'w\')\n+outfile.write("#Query\\t%s\\n" % "\\t".join("BLAST hit %i" % (i+1) for i in range(topN)))\n+for query, descrs in hits:\n+ count += 1\n+ outfile.write("%s\\t%s\\n" % (query, "\\t".join(best_hits(descrs, topN))))\n+if out_file is not None:\n+ outfile.close()\n+# Queries with no hits are not present in tabular BLAST output\n+print("%i queries with BLAST results" % count)\n' |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 tools/blastxml_to_top_descr/blastxml_to_top_descr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml Tue May 13 06:32:42 2014 -0400 |
| b |
| @@ -0,0 +1,111 @@ +<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.0"> + <description>Make a table from BLAST XML</description> + <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> + <command interpreter="python"> +blastxml_to_top_descr.py +-f "$input.in_format" +#if $input.in_format == "tabular": + --qseqid $input.qseqid + --sseqid $input.sseqid + --salltitles $input.salltitles +#end if +-o "${tabular_file}" +-t ${topN} +"${in_file}" + </command> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <conditional name="input"> + <param name="in_format" type="select" label="Input format"> + <option value="blastxml" select="True">BLAST XML</option> + <option value="tabular">Tabular</option> + </param> + <when value="blastxml"> + <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/> + </when> + <when value="tabular"> + <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/> + <param name="qseqid" type="data_column" data_ref="in_file" + multiple="False" numerical="False" default_value="1" value="1" + label="Column containing query ID (qseqid)" + help="This is column 1 in standard BLAST tabular output" /> + <param name="sseqid" type="data_column" data_ref="in_file" + multiple="False" numerical="False" default_value="2" value="2" + label="Column containing match ID (sseqid)" + help="This is column 2 in standard BLAST tabular output"/> + <param name="salltitles" type="data_column" data_ref="in_file" + multiple="False" numerical="False" default_value="25" value="25" + label="Column containing containing descriptions (salltitles)" + help="This is column 25 in the default extended BLAST tabular output"/> + </when> + </conditional> + <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> + </inputs> + <outputs> + <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + <param name="in_format" value="blastxml" /> + <param name="in_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> + <param name="topN" value="3" /> + <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" /> + </test> + <test> + <param name="in_format" value="tabular" /> + <param name="in_file" value="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> + <param name="topN" value="3" /> + <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3_positive.tabular" ftype="tabular" /> + </test> + </tests> + <help> + +**What it does** + +NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of +formats including text, tabular and a more detailed XML format. You can +do a lot of things with tabular files in Galaxy (sorting, filtering, joins, +etc), however until BLAST+ 2.2.28 the tabular output never included the +hit descriptions (titles) found in the other output formats + +This tool turns a BLAST XML file into a simple tabular file containing +one row per query sequence, containing the query identifier and then +the three (by default) top hit descriptions (i.e. the first three). If +a query doesn't have that many hits, then these entries are left blank. + +This tool can also be used with the tabular output from BLAST+ instead, +provided the relevant columns are provided. The default settings will +work with the default 25 column extended output from the BLAST+ tools +wrapped in Galaxy. Note if a query has not hits, it does not appear in +the BLAST tabular output. + +**Example Usage** + +One simple usage would be to take a transcriptome assembly or set of +gene predictions, run a BLAST search against the NCBI NR database, and +then use this tool to make a table of the top three BLAST hits. This +can give you a 'quick and dirty' crude annotation, potentially enough +to spot some problems (e.g. bacterial contaimination could be very +obvious). + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr + + </help> +</tool> |
| b |
| diff -r d8de5b627c88 -r 6f623a9718f1 tools/blastxml_to_top_descr/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/blastxml_to_top_descr/repository_dependencies.xml Tue May 13 06:32:42 2014 -0400 |
| b |
| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Requires BLAST XML and database datatype definitions."> +<repository changeset_revision="939a600f45e9" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +</repositories> |