Mercurial > repos > peterjc > blast_rbh
changeset 24:986673e8d32c draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty
| author | peterjc |
|---|---|
| date | Fri, 03 Feb 2017 12:38:10 -0500 |
| parents | eaabeeb00e10 |
| children | 8b34c3e1d20b |
| files | tools/blast_rbh/blast_rbh.py tools/blast_rbh/tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/tools/blast_rbh/blast_rbh.py Mon Dec 05 13:55:14 2016 -0500 +++ b/tools/blast_rbh/blast_rbh.py Fri Feb 03 12:38:10 2017 -0500 @@ -296,7 +296,8 @@ 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))) + 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) @@ -333,7 +334,8 @@ count = 0 outfile = open(out_file, 'w') outfile.write("#A_id\tB_id\tA_length\tB_length\tA_qcovhsp\tB_qcovhsp\tlength\tpident\tbitscore\n") -for a, (b, a_score_float, a_score_str, a_identity_str, a_coverage_str, a_qlen, a_length) in best_hits(a_vs_b, self_comparison): +for a, (b, a_score_float, a_score_str, + a_identity_str, a_coverage_str, a_qlen, a_length) in best_hits(a_vs_b, self_comparison): if b not in best_b_vs_a: # Match b has no best hit continue
--- a/tools/blast_rbh/tool_dependencies.xml Mon Dec 05 13:55:14 2016 -0500 +++ b/tools/blast_rbh/tool_dependencies.xml Fri Feb 03 12:38:10 2017 -0500 @@ -4,6 +4,6 @@ <repository changeset_revision="bc1d7fa4ad08" name="package_biopython_1_64" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <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>