Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences

This tool is copyright 2011-2023 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_length

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_length.py (the Python script)
• seq_length.xml (the Galaxy tool definition)

The suggested location is in a dedicated tools/seq_length folder.

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_length/seq_length.xml" />

If you wish to run the unit tests, also move/copy the test-data/ files under Galaxy's test-data/ folder. Then:

$ ./run_tests.sh -id seq_length

You will also need to install Biopython 1.54 or later. That's it.

History

Developers

Development is here:

https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length

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 tools/seq_length/
...

or:

$ planemo shed_update -t toolshed --check_diff tools/seq_length/
...

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/seq_length/
...
$ tar -tzf shed_upload.tar.gz
test-data/MID4_GLZRM4E04_rnd30.length.tabular
test-data/MID4_GLZRM4E04_rnd30.sff
test-data/SRR639755_sample_strict.fastq
test-data/SRR639755_sample_strict.length.tabular
test-data/four_human_proteins.fasta
test-data/four_human_proteins.length.tabular
tools/seq_length/README.rst
tools/seq_length/seq_length.py
tools/seq_length/seq_length.xml
tools/seq_length/tool_dependencies.xml

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.