Mercurial > repos > devteam > ncbi_blast_plus
changeset 15:269c5826e86f draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty
| author | peterjc |
|---|---|
| date | Fri, 03 Feb 2017 12:39:01 -0500 |
| parents | db9863278936 |
| children | a7b40298fc89 |
| files | tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/repository_dependencies.xml tools/ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 3 files changed, 19 insertions(+), 16 deletions(-) [+] |
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--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Dec 08 06:31:03 2016 -0500 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Fri Feb 03 12:39:01 2017 -0500 @@ -106,11 +106,16 @@ 'qseqid,sseqid,pident' (space or comma separated). """ parser = OptionParser(usage=usage) -parser.add_option('-o', '--output', dest='output', default=None, help='output filename (defaults to stdout)', metavar="FILE") -parser.add_option("-c", "--columns", dest="columns", default='std', help="[std|ext|col1,col2,...] standard 12 columns, extended 25 columns, or list of column names") +parser.add_option('-o', '--output', dest='output', default=None, + help='output filename (defaults to stdout)', + metavar="FILE") +parser.add_option("-c", "--columns", dest="columns", default='std', + help="[std|ext|col1,col2,...] standard 12 columns, extended 25 columns, or list of column names") (options, args) = parser.parse_args() -colnames = 'qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles'.split(',') +colnames = ('qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,' + 'sstart,send,evalue,bitscore,sallseqid,score,nident,positive,' + 'gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles').split(',') if len(args) < 1: sys.exit("ERROR: No BLASTXML input files given; run with --help to see options.") @@ -176,7 +181,8 @@ 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-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> # @@ -206,17 +212,16 @@ # # Or, with a local database not using -parse_seqids can get this, # <Hit_id>gnl|BL_ORD_ID|2</Hit_id> - # <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence</Hit_def> + # <Hit_def>chrIII gi|240255695|ref|NC_003074.8| Arabidopsis + # thaliana chromosome 3, complete sequence</Hit_def> # <Hit_accession>2</Hit_accession> 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"): + 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] - if sseqid.startswith("gnl|BL_ORD_ID|") \ - and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"): + if sseqid.startswith("gnl|BL_ORD_ID|") and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"): # Alternative place holder ID, again take the first word of hit_def hit_def = hit.findtext("Hit_def") sseqid = hit_def.split(None, 1)[0] @@ -234,13 +239,11 @@ gapopen = str(len(q_seq.replace('-', ' ').split()) - 1 + len(h_seq.replace('-', ' ').split()) - 1) - mismatch = m_seq.count(' ') + m_seq.count('+') \ - - q_seq.count('-') - h_seq.count('-') + mismatch = m_seq.count(' ') + m_seq.count('+') - q_seq.count('-') - h_seq.count('-') # TODO - Remove this alternative mismatch calculation and test # once satisifed there are no problems - expected_mismatch = len(q_seq) \ - - sum(1 for q, h in zip(q_seq, h_seq) - if q == h or q == "-" or h == "-") + expected_mismatch = len(q_seq) - sum(1 for q, h in zip(q_seq, h_seq) + if q == h or q == "-" or h == "-") xx = sum(1 for q, h in zip(q_seq, h_seq) if q == "X" and h == "X") if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx): sys.exit("%s vs %s mismatches, expected %i <= %i <= %i"
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Thu Dec 08 06:31:03 2016 -0500 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Fri Feb 03 12:39:01 2017 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="e96b515847dd" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="623a3fbe5340" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/tools/ncbi_blast_plus/tool_dependencies.xml Thu Dec 08 06:31:03 2016 -0500 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Fri Feb 03 12:39:01 2017 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.31"> - <repository changeset_revision="6e4a0aaa3357" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="803954bd4ff7" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>