# HG changeset patch # User peterjc # Date 1402657655 14400 # Node ID 98f8431dab44174d0c33765caff1af3e27ea4043 # Parent 09a68a90d552671a80608953205c2f311e00e367 Uploaded v0.1.0, now also handles extended tabular BLAST output. diff -r 09a68a90d552 -r 98f8431dab44 blastxml_to_top_descr/README.rst --- a/blastxml_to_top_descr/README.rst Wed Sep 18 06:07:53 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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:: - - - -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. diff -r 09a68a90d552 -r 98f8431dab44 blastxml_to_top_descr/blastxml_to_top_descr.py --- a/blastxml_to_top_descr/blastxml_to_top_descr.py Wed Sep 18 06:07:53 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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 tag - if event == "end" and elem.tag == "Iteration": - #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA - # sp|Q9BS26|ERP44_HUMAN - # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - # 406 - # - # - #Or, from BLAST 2.2.24+ run online - # Query_1 - # Sample - # 516 - # ... - qseqid = elem.findtext("Iteration_query-ID") - if qseqid is None: - stop_err("Missing (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 within - hit_descrs = [] - for hit in elem.findall("Iteration_hits/Hit"): - #Expecting either this, - # gi|3024260|sp|P56514.1|OPSD_BUFBU - # RecName: Full=Rhodopsin - # P56514 - #or, - # Subject_1 - # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] - # Subject_1 - # - #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) diff -r 09a68a90d552 -r 98f8431dab44 blastxml_to_top_descr/blastxml_to_top_descr.xml --- a/blastxml_to_top_descr/blastxml_to_top_descr.xml Wed Sep 18 06:07:53 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ - - Make a table from BLAST XML - blastxml_to_top_descr.py --version - - blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN} - - - - - - - - - - - - - - - - - - - - - - - - -**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 - - - diff -r 09a68a90d552 -r 98f8431dab44 blastxml_to_top_descr/repository_dependencies.xml --- a/blastxml_to_top_descr/repository_dependencies.xml Wed Sep 18 06:07:53 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r 09a68a90d552 -r 98f8431dab44 test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Wed Sep 18 06:07:53 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Fri Jun 13 07:07:35 2014 -0400 @@ -2,7 +2,7 @@ blastp - BLASTP 2.2.26+ + BLASTP 2.2.29+ 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. sp|Q9BS26|ERP44_HUMAN @@ -17,630 +17,649 @@ F - - - 1 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 2 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 3 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 4 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 5 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 6 - sp|Q9BS26|ERP44_HUMAN - Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 - 406 - - - - 0 - 0 - 30 - 119568 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 7 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 8 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 9 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 10 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 11 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 12 - sp|Q9NSY1|BMP2K_HUMAN - BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 - 1161 - - - - 0 - 0 - 38 - 348130 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 13 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 14 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 15 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 16 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 17 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 18 - sp|P06213|INSR_HUMAN - Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 - 1382 - - - - 0 - 0 - 39 - 414987 - 0.041 - 0.267 - 0.14 - - - No hits found - - - 19 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|57163783|ref|NP_001009242.1| - rhodopsin [Felis catus] - NP_001009242 - 348 - - - 1 - 701.049 - 1808 - 0 - 1 - 348 - 1 - 348 - 0 - 0 - 336 - 343 - 0 - 348 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA - MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA - MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 20 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|3024260|sp|P56514.1|OPSD_BUFBU - RecName: Full=Rhodopsin - P56514 - 354 - - - 1 - 619.002 - 1595 - 0 - 1 - 341 - 1 - 342 - 0 - 0 - 290 - 322 - 1 - 342 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE - MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE - MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 21 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|283855846|gb|ADB45242.1| - rhodopsin [Cynopterus brachyotis] - ADB45242 - 328 - - - 1 - 653.284 - 1684 - 0 - 11 - 338 - 1 - 328 - 0 - 0 - 311 - 321 - 0 - 328 - VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS - VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS - VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 22 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|283855823|gb|ADB45229.1| - rhodopsin [Myotis pilosus] - ADB45229 - 328 - - - 1 - 631.328 - 1627 - 0 - 11 - 338 - 1 - 328 - 0 - 0 - 311 - 323 - 0 - 328 - VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS - VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS - VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 23 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|223523|prf||0811197A - rhodopsin [Bos taurus] - 0811197A - 347 - - - 1 - 673.315 - 1736 - 0 - 1 - 348 - 1 - 347 - 0 - 0 - 324 - 336 - 1 - 348 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA - MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA - MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - 24 - sp|P08100|OPSD_HUMAN - Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 - 348 - - - 1 - gi|12583665|dbj|BAB21486.1| - fresh water form rod opsin [Conger myriaster] - BAB21486 - 354 - - - 1 - 599.356 - 1544 - 0 - 1 - 341 - 1 - 342 - 0 - 0 - 281 - 314 - 1 - 342 - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE - MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE - 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 - - - - - - - 0 - 0 - 29 - 101761 - 0.041 - 0.267 - 0.14 - - - - - \ No newline at end of file + + + 1 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|57163783|ref|NP_001009242.1| + rhodopsin [Felis catus] + NP_001009242 + 348 + + + 1 + 701.049 + 1808 + 0 + 1 + 348 + 1 + 348 + 0 + 0 + 336 + 343 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 20 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|3024260|sp|P56514.1|OPSD_BUFBU + RecName: Full=Rhodopsin + P56514 + 354 + + + 1 + 619.002 + 1595 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 290 + 322 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE + MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE + MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 21 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|283855846|gb|ADB45242.1| + rhodopsin [Cynopterus brachyotis] + ADB45242 + 328 + + + 1 + 653.284 + 1684 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 321 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 22 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|283855823|gb|ADB45229.1| + rhodopsin [Myotis pilosus] + ADB45229 + 328 + + + 1 + 631.328 + 1627 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 323 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 23 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|223523|prf||0811197A + rhodopsin [Bos taurus] + 0811197A + 347 + + + 1 + 673.315 + 1736 + 0 + 1 + 348 + 1 + 347 + 0 + 0 + 324 + 336 + 1 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 24 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|12583665|dbj|BAB21486.1| + fresh water form rod opsin [Conger myriaster] + BAB21486 + 354 + + + 1 + 599.356 + 1544 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 281 + 314 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE + 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 + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + + diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 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] diff -r 09a68a90d552 -r 98f8431dab44 test-data/blastp_four_human_vs_rhodopsin_top3.tabular --- a/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Wed Sep 18 06:07:53 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular Fri Jun 13 07:07:35 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] diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 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] diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 2014 -0400 @@ -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:: + + + +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 ```` 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. diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 2014 -0400 @@ -0,0 +1,255 @@ +#!/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. + +Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits. +""" +import os +import sys +import re +from optparse import OptionParser + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.1.0" + 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) + +usage = """Use as follows: + +$ blastxml_to_top_descr.py [-t 3] -o example.tabular input.xml + +Or, + +$ blastxml_to_top_descr.py [--topN 3] --output example.tabular input.xml + +This will take the top 3 BLAST descriptions from the input BLAST XML file, +writing them to the specified output file in tabular format. +""" + +parser = OptionParser(usage=usage) +parser.add_option("-t", "--topN", dest="topN", default=3, + help="Number of descriptions to collect (in order from file)") +parser.add_option("-o", "--output", dest="out_file", default=None, + help="Output filename for tabular file", + metavar="FILE") +parser.add_option("-f", "--format", dest="format", default="blastxml", + help="Input format (blastxml or tabular)") +parser.add_option("-q", "--qseqid", dest="qseqid", default="1", + help="Column for query 'qseqid' (for tabular input; default 1)") +parser.add_option("-s", "--sseqid", dest="sseqid", default="2", + help="Column for subject 'sseqid' (for tabular input; default 2)") +parser.add_option("-d", "--salltitles", dest="salltitles", default="25", + help="Column for descriptions 'salltitles' (for tabular input; default 25)") +(options, args) = parser.parse_args() + +if len(sys.argv) == 4 and len(args) == 3 and not options.out_file: + stop_err("""The API has changed, replace this: + +$ python blastxml_to_top_descr.py input.xml output.tab 3 + +with: + +$ python blastxml_to_top_descr.py -o output.tab -t 3 input.xml + +Sorry. +""") + +if not args: + stop_err("Input filename missing, try -h") +if len(args) > 1: + stop_err("Expects a single argument, one input filename") +in_file = args[0] +out_file = options.out_file +topN = options.topN + +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)") + +if not os.path.isfile(in_file): + stop_err("Missing input file: %r" % in_file) + + +def get_column(value): + """Convert column number on command line to Python index.""" + if value.startswith("c"): + # Ignore c prefix, e.g. "c1" for "1" + value = value[1:] + try: + col = int(value) + except: + stop_err("Expected an integer column number, not %r" % value) + if col < 1: + stop_err("Expect column numbers to be at least one, not %r" % value) + return col - 1 # Python counting! + +def tabular_hits(in_file, qseqid, sseqid, salltitles): + """Parse key data from tabular BLAST output. + + Iterator returning tuples (qseqid, list_of_subject_description) + """ + current_query = None + current_hits = [] + with open(in_file) as input: + for line in input: + parts = line.rstrip("\n").split("\t") + query = parts[qseqid] + descr = "%s %s" % (parts[sseqid], parts[salltitles]) + if current_query is None: + # First hit + current_query = query + current_hits = [descr] + elif current_query == query: + # Another hit + current_hits.append(descr) + else: + # New query + yield current_query, current_hits + current_query = query + current_hits = [descr] + if current_query is not None: + # Final query + yield current_query, current_hits + +def blastxml_hits(in_file): + """Parse key data from BLAST XML output. + + Iterator returning tuples (qseqid, list_of_subject_description) + """ + try: + context = ElementTree.iterparse(in_file, events=("start", "end")) + except: + with open(in_file) as handle: + header = handle.read(100) + stop_err("Invalid data format in XML file %r which starts: %r" % (in_file, header)) + # turn it into an iterator + context = iter(context) + # get the root element + try: + event, root = context.next() + except: + with open(in_file) as handle: + header = handle.read(100) + stop_err("Unable to get root element from XML file %r which starts: %r" % (in_file, header)) + + 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 + current_query = None + hit_descrs = [] + for event, elem in context: + # for every tag + if event == "end" and elem.tag == "Iteration": + # Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA + # sp|Q9BS26|ERP44_HUMAN + # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + # 406 + # + # + # Or, from BLAST 2.2.24+ run online + # Query_1 + # Sample + # 516 + # ... + qseqid = elem.findtext("Iteration_query-ID") + if qseqid is None: + stop_err("Missing (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] + if current_query is None: + # First hit + current_query = qseqid + hit_descrs = [] + elif current_query != qseqid: + # New hit + yield current_query, hit_descrs + current_query = qseqid + hit_descrs = [] + else: + # Continuation of previous query + # i.e. This BLAST XML did not use one per query + # sys.stderr.write("Multiple blocks for %s\n" % qseqid) + pass + # for every within + for hit in elem.findall("Iteration_hits/Hit"): + # Expecting either this, + # gi|3024260|sp|P56514.1|OPSD_BUFBU + # RecName: Full=Rhodopsin + # P56514 + # or, + # Subject_1 + # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] + # Subject_1 + # + #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) + # prevents ElementTree from growing large datastructure + root.clear() + elem.clear() + if current_query is not None: + # Final query + yield current_query, hit_descrs + +if options.format == "blastxml": + hits = blastxml_hits(in_file) +elif options.format == "tabular": + qseqid = get_column(options.qseqid) + sseqid = get_column(options.sseqid) + salltitles = get_column(options.salltitles) + hits = tabular_hits(in_file, qseqid, sseqid, salltitles) +else: + stop_err("Unsupported format: %r" % options.format) + + +def best_hits(descriptions, topN): + if len(descriptions) < topN: + return descriptions + [""] * (topN - len(descriptions)) + else: + return descriptions[:topN] + +count = 0 +if out_file is None: + outfile = sys.stdout +else: + outfile = open(out_file, 'w') +outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN))) +for query, descrs in hits: + count += 1 + outfile.write("%s\t%s\n" % (query, "\t".join(best_hits(descrs, topN)))) +if out_file is not None: + outfile.close() +# Queries with no hits are not present in tabular BLAST output +print("%i queries with BLAST results" % count) diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 2014 -0400 @@ -0,0 +1,111 @@ + + Make a table from BLAST output + blastxml_to_top_descr.py --version + +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}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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 *no* 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 + + + diff -r 09a68a90d552 -r 98f8431dab44 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 Fri Jun 13 07:07:35 2014 -0400 @@ -0,0 +1,4 @@ + + + +