| Previous changeset 3:de803005027f (2017-02-01) Next changeset 5:2c32e8a8990f (2017-05-11) |
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Commit message:
v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package |
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modified:
tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml |
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| diff -r de803005027f -r c8469274d136 tools/align_back_trans/README.rst --- a/tools/align_back_trans/README.rst Wed Feb 01 06:55:27 2017 -0500 +++ b/tools/align_back_trans/README.rst Wed May 10 12:05:28 2017 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy tool to back-translate a protein alignment to nucleotides ================================================================ -This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute +This tool is copyright 2012-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -70,6 +70,15 @@ - Use ``format_source=...`` tag. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.7 - Minor Python code style improvements (internal change only). +v0.0.8 - Python coding style change to avoid lamba (internal change only). + - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. + - Added two recent NCBI genetic code tables, + + - Table 24, *Pterobranchia* Mitochondrial Code, + - Table 25, Candidate Division SR1 and *Gracilibacteria*. + + - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== @@ -86,17 +95,17 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + $ planemo shed_update -t testtoolshed --check_diff tools/align_back_trans/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ + $ planemo shed_update -t toolshed --check_diff tools/align_back_trans/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/ + $ planemo shed_upload --tar_only tools/align_back_trans/ ... $ tar -tzf shed_upload.tar.gz test-data/demo_nucs.fasta |
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| diff -r de803005027f -r c8469274d136 tools/align_back_trans/align_back_trans.py --- a/tools/align_back_trans/align_back_trans.py Wed Feb 01 06:55:27 2017 -0500 +++ b/tools/align_back_trans/align_back_trans.py Wed May 10 12:05:28 2017 -0400 |
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| @@ -18,12 +18,14 @@ """ import sys -from Bio.Seq import Seq -from Bio.Alphabet import generic_protein + +from Bio import AlignIO +from Bio import SeqIO + from Bio.Align import MultipleSeqAlignment -from Bio import SeqIO -from Bio import AlignIO +from Bio.Alphabet import generic_protein from Bio.Data.CodonTable import ambiguous_generic_by_id +from Bio.Seq import Seq if "-v" in sys.argv or "--version" in sys.argv: print "v0.0.7" @@ -130,19 +132,23 @@ def alignment_back_translate(protein_alignment, nucleotide_records, key_function=None, gap=None, table=0): """Thread nucleotide sequences onto a protein alignment.""" # TODO - Separate arguments for protein and nucleotide gap characters? - if key_function is None: - key_function = lambda x: x if gap is None: gap = "-" aligned = [] - for protein in protein_alignment: - try: - nucleotide = nucleotide_records[key_function(protein.id)] - except KeyError: - raise ValueError("Could not find nucleotide sequence for protein %r" - % protein.id) - aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + try: + if key_function is None: + for protein in protein_alignment: + nucleotide = nucleotide_records[protein.id] + aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + else: + for protein in protein_alignment: + nucleotide = nucleotide_records[key_function(protein.id)] + aligned.append(sequence_back_translate(protein, nucleotide, gap, table)) + except KeyError: + raise ValueError("Could not find nucleotide sequence for protein %r" + % protein.id) + return MultipleSeqAlignment(aligned) |
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| diff -r de803005027f -r c8469274d136 tools/align_back_trans/align_back_trans.xml --- a/tools/align_back_trans/align_back_trans.xml Wed Feb 01 06:55:27 2017 -0500 +++ b/tools/align_back_trans/align_back_trans.xml Wed May 10 12:05:28 2017 -0400 |
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| @@ -1,17 +1,13 @@ -<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.7"> +<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.8"> <description>Gives a codon aware alignment</description> <requirements> - <requirement type="package" version="1.63">biopython</requirement> - <requirement type="python-module">Bio</requirement> + <requirement type="package" version="1.67">biopython</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">align_back_trans.py --version</version_command> - <command interpreter="python"> -align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table" + <version_command> +python $__tool_directory__/align_back_trans.py --version +</version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table' </command> <inputs> <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." /> @@ -33,6 +29,16 @@ <option value="21">21. Trematode Mitochondrial</option> <option value="22">22. Scenedesmus obliquus</option> <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia Mitochondrial</option> + <option value="25">25. Candidate Division SR1 and Gracilibacteria</option> + <!-- TODO, these are not in Biopython 1.67 + <option value="26">26. Pachysolen tannophilus Nuclear</option> + <option value="26">27. Karyorelict Nuclear</option> + <option value="26">28. Condylostoma Nuclear</option> + <option value="26">29. Mesodinium Nuclear</option> + <option value="26">30. Peritrich Nuclear</option> + <option value="26">31. Blastocrithidia Nuclear</option> + --> <option value="0">Don't check the translation</option> </param> <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> |
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| diff -r de803005027f -r c8469274d136 tools/align_back_trans/tool_dependencies.xml --- a/tools/align_back_trans/tool_dependencies.xml Wed Feb 01 06:55:27 2017 -0500 +++ b/tools/align_back_trans/tool_dependencies.xml Wed May 10 12:05:28 2017 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="biopython" version="1.63"> - <repository changeset_revision="ec55b787a0e1" name="package_biopython_1_63" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="biopython" version="1.67"> + <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |