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| SEQMAGICK(1) |
User Commands |
SEQMAGICK(1) |
NAME¶
seqmagick - Manipulate sequence files
SYNOPSIS¶
usage: seqmagick [-h] [-V] [-v] [-q]
- {help,convert,info,mogrify,primer-trim,quality-filter,extract-ids,backtrans-align}
...
DESCIPTION¶
Seqmagick is a little utility to expose the file format conversion in BioPython
in a convenient way.
OPTIONS¶
positional arguments:¶
- {help,convert,info,mogrify,primer-trim,quality-filter,extract-ids,backtrans-align}
- help
- Detailed help for actions using help <action>
- convert
- Convert between sequence formats
- info
- Info action
- mogrify
- Modify sequence file(s) in place.
- primer-trim
- Find a primer sequence in a gapped alignment, trim to amplicon
- quality-filter
- Filter reads based on quality scores
- extract-ids
- Extract the sequence IDs from a file
- backtrans-align
- Given a protein alignment and unaligned nucleotides, align the nucleotides
using the protein alignment. Protein and nucleotide sequence files must
contain the same number of sequences, in the same order, with the same
IDs.
optional arguments:¶
- -h, --help
- show this help message and exit
- -V, --version
- Print the version number and exit
- -v, --verbose
- Be more verbose. Specify -vv or -vvv for even more
- -q, --quiet
- Suppress output
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.
