14.04.2019
[Major bugfixes]:
We corrected a few bugs, including a bug introduced in version 1.05, affecting dotplots with substitutions allowed. We reverted (for now) to the pattern matching algorithm of version 1.04.
14.12.2018
[Faster run time]:
We modified word match recognition, speeding up FlexiDot's runtime.
[New feature] New option for pairwise dotplot collages:
With the new -O, --only_vs_first_seq option, it is now possible to limit the output of the pairwise dotplots. Instead of printing all possible pairwise combinations from a multi-fasta-sequence, only the pairwise comparisons against the first sequence are generated, if switched on (-O y). We use this feature to compare a new/unknown sequence against a batch of references.
[Changed default wordsize]:
The default wordsize has been changed from 7 to 10 in order to prevent people from running FlexiDot with small word sizes on large datasets, as this presumably takes a very long time.
[Bugfixes]:
We fixed a few bugs with the dotplot shading legends.
29.06.2018
[New feature] Graphic formatting options for all-against-all dotplots:
On request we added two parameters:
- With
-M/--mirrorit is now possible to mirror the middle diagonal.
Basic commands:
python flexidot.py -i test-seqs.fas -p 2 -M n
python flexidot.py -i test-seqs.fas -p 2 -M y
Command plus aesthetics as shown here (as described in version update 1.03):
python flexidot.py -i test-seqs.fas -p 2 -M n -g example2.gff3 -G gff_color.config -x y -k 10 -F 0.06 -A 1.5
python flexidot.py -i test-seqs.fas -p 2 -M y -g example2.gff3 -G gff_color.config -x y -k 10 -F 0.06 -A 1.5
- The
-R/--representationparameter allows partial dotplotting, either printing the complete-R 0, the top-R 1, or the bottom dotplot-R 2.
Basic commands:
python flexidot.py -i test-seqs.fas -p 2 -R 0
python flexidot.py -i test-seqs.fas -p 2 -R 1
python flexidot.py -i test-seqs.fas -p 2 -R 2
Command plus aesthetics as shown here (as described in version update 1.03):
python flexidot.py -i test-seqs.fas -p 2 -R 0 -g example2.gff3 -G gff_color.config -x y -k 10 -F 0.06 -A 1.5
python flexidot.py -i test-seqs.fas -p 2 -R 1 -g example2.gff3 -G gff_color.config -x y -k 10 -F 0.06 -A 1.5
python flexidot.py -i test-seqs.fas -p 2 -R 2 -g example2.gff3 -G gff_color.config -x y -k 10 -F 0.06 -A 1.5
[Bugfix]:
We also fixed a distortion issue in -p/--plotting_mode 0 (self dotplots).
17.06.2018
[New feature] Annotation-based shading also available for all-against-all dotplots:
Previously only available for self dotplots, we added annotation-based shading to all-against-all dotplots, allowing for many new visualizations. As before, annotation information is provided as general feature file (GFF3). These features are added to the middle diagonal (see our example below).
Basic command:
python flexidot.py -i test-seqs.fas -g example2.gff3 -G gff_color.config -p 2
Command plus aesthetics as shown here (+ LCS shading, wordsize 10, change of subplot spacing and line width):
python flexidot.py -i test-seqs.fas -g example2.gff3 -G gff_color.config -p 2 -x y -k 10 -F 0.06 -A 1.5
The test files used here are provided:
09.05.2018
Changed handling of -T parameter: The character count of the sequence titles has been limited to 20 by default. This limit can be changed with -T. If an E (end) is added to the limit, the last characters are chosen instead of the first.
-T 20 (the first 20 characters)
-T 20E (the last 20 characters)
21.04.2018
minor bugfixing
21.03.2018
first FlexiDot release