| Previous changeset 2:7c0642fc57ad (2013-10-11) |
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Commit message:
v0.0.8 galaxy_sequence_utils dependency etc |
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modified:
test-data/four_human_proteins.rename.tabular tools/seq_rename/README.rst tools/seq_rename/seq_rename.py tools/seq_rename/seq_rename.xml |
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added:
tools/seq_rename/tool_dependencies.xml |
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removed:
tools/seq_rename/repository_dependencies.xml |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe test-data/four_human_proteins.rename.tabular --- a/test-data/four_human_proteins.rename.tabular Fri Oct 11 04:39:16 2013 -0400 +++ b/test-data/four_human_proteins.rename.tabular Thu Feb 02 11:49:03 2017 -0500 |
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| @@ -1,5 +1,5 @@ #FASTA ID -sp|Q9BS26|ERP44_HUMAN Q9BS26 +sp|Q9BS26|ERP44_HUMAN Q9BS26 and ignore this description sp|Q9NSY1|BMP2K_HUMAN Q9NSY1 -sp|P06213|INSR_HUMAN P06213 +sp|P06213|INSR_HUMAN and ignore this description P06213 sp|P08100|OPSD_HUMAN P08100 |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe tools/seq_rename/README.rst --- a/tools/seq_rename/README.rst Fri Oct 11 04:39:16 2013 -0400 +++ b/tools/seq_rename/README.rst Thu Feb 02 11:49:03 2017 -0500 |
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| @@ -1,7 +1,7 @@ Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences ========================================================= -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -35,20 +35,20 @@ There are just two files to install to use this tool from within Galaxy: -* seq_rename.py (the Python script) -* seq_rename.xml (the Galaxy tool definition) +* ``seq_rename.py`` (the Python script) +* ``seq_rename.xml`` (the Galaxy tool definition) -The suggested location is in a dedicated tools/seq_rename folder. +The suggested location is in a dedicated ``tools/seq_rename`` folder. -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool. One suggested location is in the filters section. Simply add the line:: <tool file="seq_rename/seq_rename.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id seq_rename + $ ./run_tests.sh -id seq_rename You will also need to install Biopython 1.54 or later. That's it. @@ -70,6 +70,18 @@ - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy - Renamed folder and adopted README.rst naming. +v0.0.5 - Correct automated dependency definition. +v0.0.6 - Simplified XML to apply input format to output data. + - Tool definition now embeds citation information. + - If white space is found in the requested tabular field then only + the first word is used as the identifier (with a warning to stderr). +v0.0.7 - Use the ``format_source=...`` tag. + - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Capture the tool version via Galaxy (bug fix). +v0.0.8 - Updated to point at Biopython 1.67 (latest version in Tool Shed). + - Explicit dependency on ``galaxy_sequence_utils``. + - Python style updates (internal change only). ======= ====================================================================== @@ -82,21 +94,30 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +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/seq_rename/ + ... + +or:: - $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_rename/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf seq_rename.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_rename/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/four_human_proteins.fasta + test-data/four_human_proteins.rename.fasta + test-data/four_human_proteins.rename.tabular tools/seq_rename/README.rst tools/seq_rename/seq_rename.py tools/seq_rename/seq_rename.xml - tools/seq_rename/repository_dependencies.xml - test-data/four_human_proteins.fasta - test-data/four_human_proteins.rename.tabular - test-data/four_human_proteins.rename.fasta + tools/seq_rename/tool_dependencies.xml Licence (MIT) |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe tools/seq_rename/repository_dependencies.xml --- a/tools/seq_rename/repository_dependencies.xml Fri Oct 11 04:39:16 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires Biopython as a dependency."> -<!-- Leave out the tool shed and revision to get the current - tool shed and latest revision at the time of upload --> -<repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" /> -</repositories> |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe tools/seq_rename/seq_rename.py --- a/tools/seq_rename/seq_rename.py Fri Oct 11 04:39:16 2013 -0400 +++ b/tools/seq_rename/seq_rename.py Thu Feb 02 11:49:03 2017 -0500 |
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| @@ -17,64 +17,85 @@ molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. -This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute UK. +This script is copyright 2011-2017 by Peter Cock, The James Hutton Institute UK. All rights reserved. See accompanying text file for licence details (MIT license). - -This is version 0.0.4 of the script. """ import sys if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.4" + print "v0.0.8" sys.exit(0) -def stop_err(msg, err=1): - sys.stderr.write(msg.rstrip() + "\n") - sys.exit(err) - -#Parse Command Line +# Parse Command Line try: tabular_file, old_col_arg, new_col_arg, in_file, seq_format, out_file = sys.argv[1:] except ValueError: - stop_err("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv))) + sys.exit("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv) - 1, " ".join(sys.argv))) try: if old_col_arg.startswith("c"): - old_column = int(old_col_arg[1:])-1 + old_column = int(old_col_arg[1:]) - 1 else: - old_column = int(old_col_arg)-1 + old_column = int(old_col_arg) - 1 except ValueError: - stop_err("Expected column number, got %s" % old_col_arg) + sys.exit("Expected column number, got %s" % old_col_arg) try: if old_col_arg.startswith("c"): - new_column = int(new_col_arg[1:])-1 + new_column = int(new_col_arg[1:]) - 1 else: - new_column = int(new_col_arg)-1 + new_column = int(new_col_arg) - 1 except ValueError: - stop_err("Expected column number, got %s" % new_col_arg) + sys.exit("Expected column number, got %s" % new_col_arg) if old_column == new_column: - stop_err("Old and new column arguments are the same!") + sys.exit("Old and new column arguments are the same!") + def parse_ids(tabular_file, old_col, new_col): - """Read tabular file and record all specified ID mappings.""" + """Read tabular file and record all specified ID mappings. + + Will print a single warning to stderr if any of the old/new column + entries have non-trailing white space (only the first word will + be used as the identifier). + + Internal white space in the new column is taken as desired output. + """ handle = open(tabular_file, "rU") + old_warn = False + new_warn = False for line in handle: + if not line.strip(): + # Ignore blank lines + continue if not line.startswith("#"): parts = line.rstrip("\n").split("\t") - yield parts[old_col].strip(), parts[new_col].strip() + old = parts[old_col].strip().split(None, 1) + new = parts[new_col].strip().split(None, 1) + if not old_warn and len(old) > 1: + old_warn = "WARNING: Some of your old identifiers had white space in them, " + \ + "using first word only. e.g.:\n%s\n" % parts[old_col].strip() + if not new_warn and len(new) > 1: + new_warn = "WARNING: Some of your new identifiers had white space in them, " + \ + "using first word only. e.g.:\n%s\n" % parts[new_col].strip() + yield old[0], new[0] handle.close() + if old_warn: + sys.stderr.write(old_warn) + if new_warn: + sys.stderr.write(new_warn) -#Load the rename mappings + +# Load the rename mappings rename = dict(parse_ids(tabular_file, old_column, new_column)) print "Loaded %i ID mappings" % len(rename) - -#Rewrite the sequence file -if seq_format.lower()=="sff": - #Use Biopython for this format + +# Rewrite the sequence file +if seq_format.lower() == "sff": + # Use Biopython for this format renamed = 0 + def rename_seqrecords(records, mapping): - global renamed #nasty, but practical! + global renamed # nasty, but practical! for record in records: try: record.id = mapping[record.id] @@ -82,33 +103,33 @@ except KeyError: pass yield record - + try: from Bio.SeqIO.SffIO import SffIterator, SffWriter except ImportError: - stop_err("Requires Biopython 1.54 or later") + sys.exit("Requires Biopython 1.54 or later") try: from Bio.SeqIO.SffIO import ReadRocheXmlManifest except ImportError: - #Prior to Biopython 1.56 this was a private function + # Prior to Biopython 1.56 this was a private function from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest - in_handle = open(in_file, "rb") #must be binary mode! + in_handle = open(in_file, "rb") # must be binary mode! try: manifest = ReadRocheXmlManifest(in_handle) except ValueError: manifest = None out_handle = open(out_file, "wb") writer = SffWriter(out_handle, xml=manifest) - in_handle.seek(0) #start again after getting manifest + in_handle.seek(0) # start again after getting manifest count = writer.write_file(rename_seqrecords(SffIterator(in_handle), rename)) out_handle.close() in_handle.close() else: - #Use Galaxy for FASTA, QUAL or FASTQ + # Use Galaxy for FASTA, QUAL or FASTQ if seq_format.lower() in ["fasta", "csfasta"] \ - or seq_format.lower().startswith("qual"): + or seq_format.lower().startswith("qual"): from galaxy_utils.sequence.fasta import fastaReader, fastaWriter reader = fastaReader(open(in_file, "rU")) writer = fastaWriter(open(out_file, "w")) @@ -119,13 +140,13 @@ writer = fastqWriter(open(out_file, "w")) marker = "@" else: - stop_err("Unsupported file type %r" % seq_format) - #Now do the renaming + sys.exit("Unsupported file type %r" % seq_format) + # Now do the renaming count = 0 renamed = 0 for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifier, - #likewise the fastqReader leaves the @ on the identifier + # The [1:] is because the fastaReader leaves the > on the identifier, + # likewise the fastqReader leaves the @ on the identifier try: idn, descr = record.identifier[1:].split(None, 1) except ValueError: |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe tools/seq_rename/seq_rename.xml --- a/tools/seq_rename/seq_rename.xml Fri Oct 11 04:39:16 2013 -0400 +++ b/tools/seq_rename/seq_rename.xml Thu Feb 02 11:49:03 2017 -0500 |
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| @@ -1,18 +1,19 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.4"> +<tool id="seq_rename" name="Rename sequences" version="0.0.8"> <description>with ID mapping from a tabular file</description> <requirements> - <requirement type="package" version="1.62">biopython</requirement> + <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> + <requirement type="package" version="1.67">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> - <version_commmand interpreter="python">seq_rename.py --version</version_commmand> - <command interpreter="python"> -seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file - </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> + <version_command interpreter="python">seq_rename.py --version</version_command> + <command interpreter="python"> +seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file + </command> <inputs> <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> @@ -20,17 +21,7 @@ <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/> </inputs> <outputs> - <data name="output_file" format="fasta" label="Renamed ${on_string}"> - <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> - <change_format> - <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> - <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> - <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> - <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> - <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> - <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> - </change_format> - </data> + <data name="output_file" format_source="input_file" metadata_source="input_file" label="Renamed ${on_string}"/> </outputs> <tests> <test> @@ -55,12 +46,17 @@ new sequence file (of the same format) where the sequence identifiers have been renamed according to the specified columns in your tabular file. +Any original description is preserved (N/A for the SFF file format). + WARNING: If you have any duplicates in the input sequence file, you will still have duplicate sequences in the output. WARNING: If the tabular file has more than one new name for any old ID, the last one is used. +WARNING: The old and new names in your tabular file should not contain white space. +If they do, only the first word is used as the identifier. + **References** If you use this Galaxy tool in work leading to a scientific publication please @@ -81,4 +77,8 @@ This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </citations> </tool> |
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| diff -r 7c0642fc57ad -r e1398f2ba9fe tools/seq_rename/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/seq_rename/tool_dependencies.xml Thu Feb 02 11:49:03 2017 -0500 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <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> + <package name="galaxy_sequence_utils" version="1.0.1"> + <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |