ModDotPlot
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marbl
test sequence not as expected?
Related to the https://github.com/marbl/ModDotPlot/issues/29 I thought to investigate by using test sequences.
I take a sequence from arabidopsis chr1 and copy paste a sequence 3 times,
%%writefile ../tmp/seq1.fa
>seq1
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT
CTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTT
CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA
GCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTT
ATCTCAAGAATCTTATTAATTGTTTGGACTGTTTATGTTTGGACATTTATTGTCATTCTT
ACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATTTAGTTG
TAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGG
GATGGTCCTTTAGCATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAA
AGGATTGGTGGTTTGAAGACACATCATATCAAAAAAGCTATCGCCTCGACGATGCTCTAT
TTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGTTTGTTTTGC
TTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTC
AAGACTTCTCGGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCG
TAGATATTAGGTAATCTGTAAGTCAACTCATATACAACTCATAATTTAAAATAAAATTAT
GATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCCGTTATTCCCACA
ATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGT
TTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCC
CCCCCCCCCCACCCCCCAAATTGAGAAGTCAATTTTATATAATTTAATCAAATAAATAAG
TTTATGGTTAAGAGTTTTTTACTCTCTTTATTTTTCTTTTTCTTTTTGAGACATACTGAA
AAAAGTTGTAATTATTAATGATAGTTCTGTGATTCCTCCATGAATCACATCTGCTTGATT
TTTCTTTCATAAATTTATAAGTAATACATTCTTATAAAATGGTCAGAGAAACACCAAAGA
TCCCGAGATTTCTTCTCACTTACTTTTTTTCTATCTATCTAGATTATATAAATGAGATGT
TGAATTAGAGGAACCTTTGATTCAATGATCATAGAAAAATTAGGTAAAGAGTCAGTGTCG
TTATGTTATGGAAGATGTGAATGAAGTTTGACTTCTCATTGTATATGAGTAAAATCTTTT
CTTACAAGGGAAGTCCCCAATTGGTCAACATGTGAAAGCACGTGTCATGTTCTTACTTTT
GTTTGGGTAATCTTCTAATTACTGTATATGGAAGATGTGAATGAAGTTTTGGTCCTGAAT
GTGGCCAAGGTTCCGTCATTTGGAGATACGAAATCAAATCTCCTTTAAGATTTTGTTTTT
ATAATGTGTTCTTCCATCCACATCTATCTCCATATGATATGGACCATATCATACATCATC
ATTTGTCCAAATGCATGAATGAATTTGGAAATAGGTACGAGAATGCCAACAATGACAAGA
AGGGATCAAAGACAGTTTTTAAAACAATATTTTACAGGGTTTTAATCTAATTCTAAGTTT
TGGTCACTCACTTTGTTAAAAGAATAATTCAGTGTCTGGACACTAAAATCTTCCAAAAAC
CCCATATACATATATGCTATTTCGATACTTATATTTATTTACTCAGCATAAAAAATATTA
ACCATGTATTCATAGTAAAATGTTTCATGTGATATCAAACCAGCGACAACAAAAGTATTA
TTCCCCTCATTATGTTTGACTCCTATTATATTTTTATTTTAATTTTTTTCACTATCATCT
TTCTTGCAATGAAAGTCCCATATATTGGTCAACATTTCAAACCACTTGTTCTCTTTTATG
TTTTGGTAAGAGCTATCTTCTAAATTTATAATACGCATAAATTCAAAAGTAAAAGAAAAT
TTTGGTCATGAATGTTGTTTAAGTCATTTGGAGATACGAAATCAAATCTCCTTGTAGATT
%%writefile ../tmp/seq2.fa
>seq2
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAAT
CTTTAAATCCTACATCCATGAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTT
CTCTGGTTGAAAATCATTGTGTATATAATGATAATTTTATCGTTTTTATGTAATTGCTTA
TTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCTTGT
GGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAA
GCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTT
ATCTCAAGAATCTTATTAATTGTTTGGACTGTTTATGTTTGGACATTTATTGTCATTCTT
ACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATTTAGTTG
TAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGG
GATGGTCCTTTAGCATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAA
AGGATTGGTGGTTTGAAGACACATCATATCAAAAAAGCTATCGCCTCGACGATGCTCTAT
TTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGTTTGTTTTGC
TTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTC
AAGACTTCTCGGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCG
TAGATATTAGGTAATCTGTAAGTCAACTCATATACAACTCATAATTTAAAATAAAATTAT
GATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCCGTTATTCCCACA
ATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGT
TTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCC
ACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATTTAGTTG
TAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGG
GATGGTCCTTTAGCATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAA
AGGATTGGTGGTTTGAAGACACATCATATCAAAAAAGCTATCGCCTCGACGATGCTCTAT
TTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGTTTGTTTTGC
TTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTC
AAGACTTCTCGGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCG
TAGATATTAGGTAATCTGTAAGTCAACTCATATACAACTCATAATTTAAAATAAAATTAT
GATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCCGTTATTCCCACA
ATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGT
TTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCC
ACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATTTAGTTG
TAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGG
GATGGTCCTTTAGCATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAA
AGGATTGGTGGTTTGAAGACACATCATATCAAAAAAGCTATCGCCTCGACGATGCTCTAT
TTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGTTTGTTTTGC
TTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTC
AAGACTTCTCGGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCG
TAGATATTAGGTAATCTGTAAGTCAACTCATATACAACTCATAATTTAAAATAAAATTAT
GATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCCGTTATTCCCACA
ATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGT
TTTCCACTTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCC
CCCCCCCCCCACCCCCCAAATTGAGAAGTCAATTTTATATAATTTAATCAAATAAATAAG
TTTATGGTTAAGAGTTTTTTACTCTCTTTATTTTTCTTTTTCTTTTTGAGACATACTGAA
AAAAGTTGTAATTATTAATGATAGTTCTGTGATTCCTCCATGAATCACATCTGCTTGATT
TTTCTTTCATAAATTTATAAGTAATACATTCTTATAAAATGGTCAGAGAAACACCAAAGA
TCCCGAGATTTCTTCTCACTTACTTTTTTTCTATCTATCTAGATTATATAAATGAGATGT
TGAATTAGAGGAACCTTTGATTCAATGATCATAGAAAAATTAGGTAAAGAGTCAGTGTCG
TTATGTTATGGAAGATGTGAATGAAGTTTGACTTCTCATTGTATATGAGTAAAATCTTTT
CTTACAAGGGAAGTCCCCAATTGGTCAACATGTGAAAGCACGTGTCATGTTCTTACTTTT
GTTTGGGTAATCTTCTAATTACTGTATATGGAAGATGTGAATGAAGTTTTGGTCCTGAAT
GTGGCCAAGGTTCCGTCATTTGGAGATACGAAATCAAATCTCCTTTAAGATTTTGTTTTT
ATAATGTGTTCTTCCATCCACATCTATCTCCATATGATATGGACCATATCATACATCATC
ATTTGTCCAAATGCATGAATGAATTTGGAAATAGGTACGAGAATGCCAACAATGACAAGA
AGGGATCAAAGACAGTTTTTAAAACAATATTTTACAGGGTTTTAATCTAATTCTAAGTTT
TGGTCACTCACTTTGTTAAAAGAATAATTCAGTGTCTGGACACTAAAATCTTCCAAAAAC
CCCATATACATATATGCTATTTCGATACTTATATTTATTTACTCAGCATAAAAAATATTA
ACCATGTATTCATAGTAAAATGTTTCATGTGATATCAAACCAGCGACAACAAAAGTATTA
TTCCCCTCATTATGTTTGACTCCTATTATATTTTTATTTTAATTTTTTTCACTATCATCT
TTCTTGCAATGAAAGTCCCATATATTGGTCAACATTTCAAACCACTTGTTCTCTTTTATG
TTTTGGTAAGAGCTATCTTCTAAATTTATAATACGCATAAATTCAAAAGTAAAAGAAAAT
TTTGGTCATGAATGTTGTTTAAGTCATTTGGAGATACGAAATCAAATCTCCTTGTAGATT
so I would expect a dotplot like
However, I get this
why?
Hi @KewinOgink,
Apologies for the late reply. There has been a version update (v0.8.4) that addresses some of the issues that lead up to this.
When running moddotplot static -f seq1.fa seq2.fa --identity 80 -w 10 --compare-only under the latest version, and using seq1 and seq2 you've linked above, this is my result:
This is what you expected to see. As a heads up, ModDotPlot is recommended to be used only with sequences > 10kb. You should also not set --identity below 80, nor set -w below 10.
Best, Alex
Hi I actually didn't make time to test this. Now I find out it still doesn't work for me after re-installing moddotplot: not sure what is going on. I'll have time to actually test now.
moddotplot static -f seq1.fa seq2.fa --identity 80 -w 10 --compare-only
__ __ _ _____ _ _____ _ _
| \/ | | | | __ \ | | | __ \| | | |
| \ / | ___ __| | | | | | ___ | |_ | |__) | | ___ | |_
| |\/| |/ _ \ / _` | | | | |/ _ \| __| | ___/| |/ _ \| __|
| | | | (_) | (_| | | |__| | (_) | |_ | | | | (_) | |_
|_| |_|\___/ \__,_| |_____/ \___/ \__| |_| |_|\___/ \__|
v0.8.4
Running ModDotPlot in static mode
Retrieving k-mers from seq1....
Progress: |████████████████████████████████████████| 100.0% Completed
seq1 k-mers retrieved!
Retrieving k-mers from seq2....
Progress: |████████████████████████████████████████| 100.0% Completed
seq2 k-mers retrieved!
Computing pairwise identity matrix for seq2 and seq1...
Sequence length seq2: 700
Sequence length seq1: 500
Window size w: 10
Modimizer sketch size: 10
Plot Resolution r: 48
Progress: |████████████████████████████████████████| 100.0% Completed
Saved bed file to seq1.bed
Creating plots and saving to ./seq1_seq2...
./seq1_seq2.pdf, ./seq1_seq2.png, ./seq1_seq2_HIST.pdf and ./seq1_seq2_HIST.png saved sucessfully.
Apologies @KewinOgink for not getting to this a second time around. Testing on v0.9.7 shows that this is is working as expected
Closing to cleanup issue backlog.