Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads

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 (MIT licence).

This tool is a short Python script (using the Galaxy library functions and Biopython). It is available from the Galaxy Tool Shed here: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip

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:

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

The suggested location is a new tools/seq_primer_clip/ folder. You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool:

<tool file="seq_primer_clip/seq_primer_clip.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_primer_clip

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

History

Version	Changes
v0.0.1	Initial version (not publicly released)
v0.0.2	Sort primers by length (longest and therefore most specific first)
v0.0.3	Consider missing bases at start/end of read as mismatches
v0.0.4	Apply minimum length to sequences with no match too
v0.0.5	Count clipped & non-matched short reads separately, length bug fixes
v0.0.6	Added some functional tests
v0.0.7	Added error check for bad filename arguments
v0.0.8	Record version of Python script when run from Galaxy. Check for errors using Python script's return code.
v0.0.9	Moved test data to workaround Galaxy Tool Shed limititation.
v0.0.10	Include links to Tool Shed in help text and this README file. Use reStructuredText for this README file. Adopted standard MIT licence. Automated installation of Biopython dependency. Development moved to GitHub, https://github.com/peterjc/pico_galaxy Renamed folder and adopted README.rst naming.
v0.0.11	Correct automated dependency definition.
v0.0.12	Simplified XML to apply input format to output data. Tool definition now embeds citation information.
v0.0.13	Use format_source=... tag. Reorder XML elements (internal change only). Planemo for Tool Shed upload (.shed.yml, internal change only). Fixed input file help text.
v0.0.14	Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. Explicit dependency on galaxy_sequence_utils.
v0.0.15	Use <command detect_errors="aggressive"> (internal change only). Single quote command line arguments (internal change only)
v0.0.16	Python 3 compatible print function.
v0.0.17	Use Python 3 style dictionary iteration.
v0.0.18	Fix file open mode for Python 3.11 onwards.

Developers

This script and related tools were initially developed on the following hg branches: http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy

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_primer_clip/
...

or:

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

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/seq_primer_clip/
...
$ tar -tzf shed_upload.tar.gz
test-data/MID4_GLZRM4E04_rnd30.fasta
test-data/MID4_GLZRM4E04_rnd30.fastqsanger
test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
test-data/MID4_GLZRM4E04_rnd30_fclip.sff
test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
test-data/MID4_GLZRM4E04_rnd30_frclip.sff
test-data/MID4_GLZRM4E04_rnd30.sff
test-data/dop_primers.fasta
tools/seq_primer_clip/README.rst
tools/seq_primer_clip/seq_primer_clip.py
tools/seq_primer_clip/seq_primer_clip.xml
tools/seq_primer_clip/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.