| Previous changeset 14:61cec46f6be5 (2013-11-20) Next changeset 16:e279ed332c8e (2015-05-13) |
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Commit message:
Uploaded v0.0.6, handle white space in identifier columns, embed citation, simpler XML |
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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 tools/seq_rename/tool_dependencies.xml |
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| diff -r 61cec46f6be5 -r ba3ec1b3e635 test-data/four_human_proteins.rename.tabular --- a/test-data/four_human_proteins.rename.tabular Wed Nov 20 12:11:32 2013 -0500 +++ b/test-data/four_human_proteins.rename.tabular Thu Nov 27 08:20:54 2014 -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 61cec46f6be5 -r ba3ec1b3e635 tools/seq_rename/README.rst --- a/tools/seq_rename/README.rst Wed Nov 20 12:11:32 2013 -0500 +++ b/tools/seq_rename/README.rst Thu Nov 27 08:20:54 2014 -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 2011-2014 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. @@ -70,7 +70,11 @@ - 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 +v0.0.5 - 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). ======= ====================================================================== |
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| diff -r 61cec46f6be5 -r ba3ec1b3e635 tools/seq_rename/seq_rename.py --- a/tools/seq_rename/seq_rename.py Wed Nov 20 12:11:32 2013 -0500 +++ b/tools/seq_rename/seq_rename.py Thu Nov 27 08:20:54 2014 -0500 |
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| @@ -20,13 +20,11 @@ This script is copyright 2011-2013 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 "v0.0.6" sys.exit(0) def stop_err(msg, err=1): @@ -57,13 +55,38 @@ stop_err("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 rename = dict(parse_ids(tabular_file, old_column, new_column)) |
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| diff -r 61cec46f6be5 -r ba3ec1b3e635 tools/seq_rename/seq_rename.xml --- a/tools/seq_rename/seq_rename.xml Wed Nov 20 12:11:32 2013 -0500 +++ b/tools/seq_rename/seq_rename.xml Thu Nov 27 08:20:54 2014 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="seq_rename" name="Rename sequences" version="0.0.4"> +<tool id="seq_rename" name="Rename sequences" version="0.0.6"> <description>with ID mapping from a tabular file</description> <requirements> <requirement type="package" version="1.62">biopython</requirement> @@ -20,17 +20,7 @@ <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="input" metadata_source="input_file" label="Renamed ${on_string}"/> </outputs> <tests> <test> @@ -55,12 +45,17 @@ 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 +76,8 @@ 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 61cec46f6be5 -r ba3ec1b3e635 tools/seq_rename/tool_dependencies.xml --- a/tools/seq_rename/tool_dependencies.xml Wed Nov 20 12:11:32 2013 -0500 +++ b/tools/seq_rename/tool_dependencies.xml Thu Nov 27 08:20:54 2014 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.62"> - <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |