| Previous changeset 0:b828ca44a313 (2014-08-04) Next changeset 2:14b2e159b310 (2015-09-04) |
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Commit message:
Uploaded v0.1.5, NCBI BLAST+ 2.2.30 etc |
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modified:
test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.py tools/blast_rbh/blast_rbh.xml tools/blast_rbh/tool_dependencies.xml |
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| diff -r b828ca44a313 -r ff0b814c1320 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular --- a/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Mon Aug 04 08:13:39 2014 -0400 +++ b/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular Fri Nov 21 06:57:14 2014 -0500 |
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| @@ -1,2 +1,2 @@ #A_id B_id A_length B_length A_qcovhsp B_qcovhsp length pident bitscore -gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 66 57 230 97.39 559 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 1047 1213 22 19 230 97.39 559 |
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| diff -r b828ca44a313 -r ff0b814c1320 tools/blast_rbh/README.rst --- a/tools/blast_rbh/README.rst Mon Aug 04 08:13:39 2014 -0400 +++ b/tools/blast_rbh/README.rst Fri Nov 21 06:57:14 2014 -0500 |
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| @@ -1,16 +1,19 @@ -Galaxy tool to find BLAST Reciprocal Best Hits (RBH) -==================================================== +Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper +========================================================== This tool is copyright 2011-2014 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 run reciprocal BLAST searches on a -pair of sequence files, and extract the reciprocal best hits. +pair of sequence files, and extract the reciprocal best hits. The script +``blast_rbh.py`` can be used directly (without Galaxy) as long as NCBI +BLAST+ is installed. -This is a work in progress, and builds on an earlier implementation which -prequired the two BLAST searches be prepared in advance. Integration allows -a much simpler user experience, and can ensure sensible filters are used. +It comes with an optional Galaxy tool definition file ``blast_rbh.xml`` +allowing the Python script to be run from within Galaxy. It is available +from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Automated Installation @@ -34,11 +37,10 @@ <tool file="blast_rbh/blast_rbh.xml" /> -If you want to run the functional tests, include the same line in your -``tool_conf.xml.sample`` file, and the sample test files under Galaxy's -``test-data/`` directory. Then:: +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then:: - ./run_functional_tests.sh -id blast_reciprocal_best_hits + ./run_tests.sh -id blast_reciprocal_best_hits You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. @@ -52,7 +54,14 @@ v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates. v0.1.2 - Using optparse for command line API. + - Tool definition now embeds citation information. - Fixed Tool Shed dependency definition. +v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency). + - Avoid extra database and BLAST search in self-comparison mode. +v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb + not treating this as an error, leading to confusing RBH output). +v0.1.5 - Clarify documentation for using the Python script outside Galaxy. + - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install. ======= ====================================================================== |
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| diff -r b828ca44a313 -r ff0b814c1320 tools/blast_rbh/blast_rbh.py --- a/tools/blast_rbh/blast_rbh.py Mon Aug 04 08:13:39 2014 -0400 +++ b/tools/blast_rbh/blast_rbh.py Fri Nov 21 06:57:14 2014 -0500 |
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| @@ -1,14 +1,16 @@ #!/usr/bin/env python """BLAST Reciprocal Best Hit (RBH) from two FASTA input files. -Takes the following command line options, -1. FASTA filename of species A -2. FASTA filename of species B -3. Sequence type (prot/nucl) -4. BLAST type (e.g. blastn, or blastp) consistent with sequence type -5. Minimum BLAST Percentage identity -6. Minimum BLAST query coverage -7. Output filename +Run "blast_rbh.py -h" to see the help text, or read the associated +README.rst file which is also available on GitHub at: +https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh + +This requires Python and the NCBI BLAST+ tools to be installed +and on the $PATH. + +You can also run this tool via Galaxy using the "blast_rbh.xml" +definition file. This is available as a package on the Galaxy +Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh """ # TODO - Output more columns, e.g. pident, qcovs, descriptions? @@ -30,7 +32,7 @@ if "--version" in sys.argv[1:]: #TODO - Capture version of BLAST+ binaries too? - print "BLAST RBH v0.1.2" + print "BLAST RBH v0.1.5" sys.exit(0) #Parse Command Line @@ -47,11 +49,14 @@ default=None, help="BLAST task (e.g. blastp, blastn, megablast)") parser.add_option("-i","--identity", dest="min_identity", - default="0", - help="Minimum percentage identity (optional, default 0)") + default="70", + help="Minimum percentage identity (optional, default 70)") parser.add_option("-c", "--coverage", dest="min_coverage", - default="0", - help="Minimum HSP coverage (optional, default 0)") + default="50", + help="Minimum HSP coverage (optional, default 50)") +parser.add_option("--nr", dest="nr", default=False, action="store_true", + help="Preprocess FASTA files to collapse identifical " + "entries (make sequences non-redundant)") parser.add_option("-o", "--output", dest="output", default=None, metavar="FILE", help="Output filename") @@ -117,10 +122,17 @@ makeblastdb_exe = "makeblastdb" base_path = tempfile.mkdtemp() +tmp_a = os.path.join(base_path, "SpeciesA.fasta") db_a = os.path.join(base_path, "SpeciesA") -db_b = os.path.join(base_path, "SpeciesB") a_vs_b = os.path.join(base_path, "A_vs_B.tabular") -b_vs_a = os.path.join(base_path, "B_vs_A.tabular") +if self_comparison: + tmp_b = tmp_a + db_b = db_a + b_vs_a = a_vs_b +else: + tmp_b = os.path.join(base_path, "SpeciesB.fasta") + db_b = os.path.join(base_path, "SpeciesB") + b_vs_a = os.path.join(base_path, "B_vs_A.tabular") log = os.path.join(base_path, "blast.log") cols = "qseqid sseqid bitscore pident qcovhsp qlen length" #Or qcovs? @@ -202,18 +214,87 @@ #print("%s has %i equally good hits: %s" % (a, len(best), ", ".join(best))) tie_warning += 1 +def check_duplicate_ids(filename): + # Copied from tools/ncbi_blast_plus/check_no_duplicates.py + # TODO - just use Biopython's FASTA parser? + if not os.path.isfile(filename): + stop_err("Missing FASTA file %r" % filename, 2) + identifiers = set() + handle = open(filename) + for line in handle: + if line.startswith(">"): + # The split will also take care of the new line character, + # e.g. ">test\n" and ">test description here\n" both give "test" + seq_id = line[1:].split(None, 1)[0] + if seq_id in identifiers: + handle.close() + stop_err("Repeated identifiers, e.g. %r" % seq_id, 3) + identifiers.add(seq_id) + handle.close() + +def make_nr(input_fasta, output_fasta, sep=";"): + #TODO - seq-hash based to avoid loading everything into RAM? + by_seq = dict() + try: + from Bio import SeqIO + except KeyError: + stop_err("Missing Biopython") + for record in SeqIO.parse(input_fasta, "fasta"): + s = str(record.seq).upper() + try: + by_seq[s].append(record.id) + except KeyError: + by_seq[s] = [record.id] + unique = 0 + representatives = dict() + duplicates = set() + for cluster in by_seq.values(): + if len(cluster) > 1: + representatives[cluster[0]] = cluster + duplicates.update(cluster[1:]) + else: + unique += 1 + del by_seq + if duplicates: + #TODO - refactor as a generator with single SeqIO.write(...) call + with open(output_fasta, "w") as handle: + for record in SeqIO.parse(input_fasta, "fasta"): + if record.id in representatives: + cluster = representatives[record.id] + record.id = sep.join(cluster) + record.description = "representing %i records" % len(cluster) + elif record.id in duplicates: + continue + SeqIO.write(record, handle, "fasta") + print("%i unique entries; removed %i duplicates leaving %i representative records" % (unique, len(duplicates), len(representatives))) + else: + os.symlink(os.path.abspath(input_fasta), output_fasta) + print("No perfect duplicates in file, %i unique entries" % unique) #print("Starting...") +check_duplicate_ids(fasta_a) +if not self_comparison: + check_duplicate_ids(fasta_b) + +if options.nr: + make_nr(fasta_a, tmp_a) + if not self_comparison: + make_nr(fasta_b, tmp_b) + fasta_a = tmp_a + fasta_b = tmp_b + #TODO - Report log in case of error? run('%s -dbtype %s -in "%s" -out "%s" -logfile "%s"' % (makeblastdb_exe, dbtype, fasta_a, db_a, log)) -run('%s -dbtype %s -in "%s" -out "%s" -logfile "%s"' % (makeblastdb_exe, dbtype, fasta_b, db_b, log)) +if not self_comparison: + run('%s -dbtype %s -in "%s" -out "%s" -logfile "%s"' % (makeblastdb_exe, dbtype, fasta_b, db_b, log)) #print("BLAST databases prepared.") run('%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i' % (blast_cmd, fasta_a, db_b, a_vs_b, cols, threads)) #print("BLAST species A vs species B done.") -run('%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i' - % (blast_cmd, fasta_b, db_a, b_vs_a, cols, threads)) -#print("BLAST species B vs species A done.") +if not self_comparison: + run('%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i' + % (blast_cmd, fasta_b, db_a, b_vs_a, cols, threads)) + #print("BLAST species B vs species A done.") best_b_vs_a = dict(best_hits(b_vs_a, self_comparison)) |
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| diff -r b828ca44a313 -r ff0b814c1320 tools/blast_rbh/blast_rbh.xml --- a/tools/blast_rbh/blast_rbh.xml Mon Aug 04 08:13:39 2014 -0400 +++ b/tools/blast_rbh/blast_rbh.xml Fri Nov 21 06:57:14 2014 -0500 |
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| @@ -1,10 +1,12 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.2"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.5"> <description>from two FASTA files</description> <requirements> - <requirement type="binary">makeblastdb</requirement> - <requirement type="binary">blastp</requirement> - <requirement type="binary">blastn</requirement> - <requirement type="package" version="2.2.29">blast+</requirement> + <requirement type="package" version="1.64">biopython</requirement> + <requirement type="python-module">Bio</requirement> + <requirement type="binary">makeblastdb</requirement> + <requirement type="binary">blastp</requirement> + <requirement type="binary">blastn</requirement> + <requirement type="package" version="2.2.30">blast+</requirement> </requirements> <version_command interpreter="python"> blast_rbh.py --version @@ -17,6 +19,7 @@ #else -t $seq.prot_type #end if +$make_nr -i $identity -c $q_cover -o "$output" @@ -61,6 +64,9 @@ <param name="q_cover" type="float" value="50" min="0" max="100" label="Minimum percentage query coverage for BLAST matches" help="Default is 50%, use 0 for no filtering." /> + <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue="" + label="Process input FASTA files to collapse identical sequences" + help="i.e. First make the input non-redundant" /> </inputs> <outputs> <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" /> @@ -201,6 +207,13 @@ can happen following gene duplication, or for (near) identical gene duplicates. +The tool can optionally make the FASTA files non-redundant by replacing +repeated identical sequences with a single representative before building +the databases and running BLAST. + +Finally, the tool can be run using the same FASTA input file to look for +RBH within the dataset. In this case, self matches are discarded. + .. class:: warningmark **Note** |
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| diff -r b828ca44a313 -r ff0b814c1320 tools/blast_rbh/tool_dependencies.xml --- a/tools/blast_rbh/tool_dependencies.xml Mon Aug 04 08:13:39 2014 -0400 +++ b/tools/blast_rbh/tool_dependencies.xml Fri Nov 21 06:57:14 2014 -0500 |
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| @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="blast+" version="2.2.29"> - <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.64"> + <repository changeset_revision="5477a05cc158" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="blast+" version="2.2.30"> + <repository changeset_revision="0fe5d5c28ea2" name="package_blast_plus_2_2_30" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |