Mercurial > repos > peterjc > seq_rename
changeset 6:8b3cd18ab9e1 draft
Uploaded v0.0.4b, README style
| author | peterjc |
|---|---|
| date | Wed, 24 Jul 2013 10:35:43 -0400 |
| parents | 44b2e489e26f |
| children | e440681dd17c |
| files | tools/filters/seq_rename.rst tools/filters/seq_rename.txt |
| diffstat | 2 files changed, 115 insertions(+), 108 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/seq_rename.rst Wed Jul 24 10:35:43 2013 -0400 @@ -0,0 +1,115 @@ +Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences +========================================================= + +This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +This tool is a short Python script (using Biopython library functions) to rename +sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as +two columns of a tabular file. The output order follows that of the sequence file, +and if there are duplicates in the input sequence file, there will be duplicates +in the output sequence file. + +This tool is available from the Galaxy Tool Shed, + +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename + +See also the sister tools to filter or select sequence files according to IDs +from column(s) of tabular file: + +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id +* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id + + +Automated Installation +====================== + +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. + + +Manual Installation +=================== + +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) + +The suggested location is in the Galaxy folder tools/filters next to the tool +for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. + +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="filters/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:: + + $ ./run_functional_tests.sh -id seq_rename + +You will also need to install Biopython 1.54 or later. That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version. +v0.0.2 - Record script version when run from Galaxy. + - Add unit test. + - Check for errors using Python script's return code. +v0.0.3 - Link to Tool Shed added to help text and this documentation. +v0.0.4 - Automated installation of Biopython dependency. + - Use reStructuredText for this README file. +======= ====================================================================== + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder:: + + $ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* tools/filters/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta + +Check this worked:: + + $ tar -tzf seq_rename.tar.gz + tools/filter/seq_rename.py + tools/filter/seq_rename.rst + tools/filter/seq_rename.xml + tools/filters/repository_dependencies.xml + test-data/four_human_proteins.fasta + test-data/four_human_proteins.rename.tabular + test-data/four_human_proteins.rename.fasta + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE.
--- a/tools/filters/seq_rename.txt Mon Jun 24 02:01:15 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,108 +0,0 @@ -Galaxy tool to renamed FASTA, QUAL, FASTQ or SFF sequences -========================================================== - -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -This tool is a short Python script (using Biopython library functions) to rename -sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as -two columns of a tabular file. The output order follows that of the sequence file, -and if there are duplicates in the input sequence file, there will be duplicates -in the output sequence file. - -This tool is available from the Galaxy Tool Shed, -http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - -See also the sister tools to filter or select sequence files according to IDs -from column(s) of tabular file: -http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id -http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id - - -Automated Installation -====================== - -This should be straightforward using the Galaxy Tool Shed, which should be -able to automatically install the dependency on Biopython, and then install -this tool and run its unit tests. - - -Manual Installation -=================== - -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) - -The suggested location is in the Galaxy folder tools/filters next to the tool -for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. - -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="filters/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: - -$ ./run_functional_tests.sh -id seq_rename - -You will also need to install Biopython 1.54 or later. That's it. - - -History -======= - -v0.0.1 - Initial version. -v0.0.2 - Record script version when run from Galaxy. - - Add unit test. - - Check for errors using Python script's return code. -v0.0.3 - Link to Tool Shed added to help text and this documentation. -v0.0.4 - Automated installation of Biopython dependency. - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder: - -$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* tools/filters/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta - -Check this worked: - -$ tar -tzf seq_rename.tar.gz -tools/filter/seq_rename.py -tools/filter/seq_rename.txt -tools/filter/seq_rename.xml -tools/filters/repository_dependencies.xml -test-data/four_human_proteins.fasta -test-data/four_human_proteins.rename.tabular -test-data/four_human_proteins.rename.fasta - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE.