test sequence not as expected?

[KewinOgink]

Related to the #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?

[alexsweeten]

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

[KewinOgink]

thanks a lot!

[KewinOgink]

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.