usage: align.py [-h] [--columns N] [--max-dist N] [--min-score N]
ACTG|path[:id] ACTG|path[:id]
Align sequences and show them vertically interleaved
positional arguments:
ACTG|path[:id] First input. Either a literal sequence or a path to a fasta
or fastq file. If a path, optionally include a colon-
separated id to refer to identify a specific record in the
file.
ACTG|path[:id] Same as first input.
optional arguments:
-h, --help show this help message and exit
--columns N How many columns to wrap at. If unspecified, autodetects.
--max-dist N How hard to try to avoid over-alignment when blocks have
been substituted out.
--min-score N Minimum score of alignment to print.
usage: seqdsp.py [-h] [--colorize-quality] [--columns N] [--skip-lines]
[--highlighted-only] [--show-quality]
[--show-quality-when-highlighted] [--id-matches REGEX]
[--seq-matches [rc]ACTG[:COLOR]] [--max-quality CHAR]
[--min-score N]
[fname[:id] ...]
Display seqence files in a human-readable way.
positional arguments:
fname[:id]
optional arguments:
-h, --help show this help message and exit
--colorize-quality Color the quality line to show the quality visually.
Order, lowest to highest, is black, magenta, red,
yellow, white, green, blue, cyan.
--columns N How many columns to wrap at. If unspecified,
autodetects.
--skip-lines Leave extra space between lines for readability.
--highlighted-only Only print sequences that have colored portions. For
example, the output of fuzzy_highlighter.
--show-quality Print quality lines.
--show-quality-when-highlighted
Print quality lines corresponding to sequence lines
that have colored portions.
--id-matches REGEX Only print sequences whose id line matches the regex.
--seq-matches [rc]ACTG[:COLOR]
Only print matching sequence, or reverse complement if
"rc" prefix is present. May bespecified multiple
times, and sequences that match any will be printed.
Colors are red, yellow, green, blue, magenta, cyan,
white, and black.
--max-quality CHAR If your sequencer doesn't use the whole quality range,
set this to something smaller than '~' to make better
use of the available colors. Ignored when --colorize-
quality is false.
--min-score N Minimum score of alignment to print.
Highlight matching subsequences with fuzzy matching. Handles substitutions but not insertions or deletions.
- Install rust
cargo build --release- Put
target/release/fuzzy_highlightersomewhere on your path.
cat input | fuzzy_highlighter pattern1 pattern2
Run fuzzy_highlighter --help for more details.