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Changeset 3:24e471d13fe9 (2022-06-30)

Previous changeset 2:e53b0473d575 (2022-05-08) Next changeset 4:5e0825476fb7 (2023-04-04)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b

modified:
smudgeplot.xml

added:
static/images/smudge.png
test-data/dump.jf
test-data/my_genome_summary_table.tsv
test-data/my_genome_verbose_summary.txt
test-data/my_genome_warnings.txt
test-data/test_reads.fasta.gz
test-data/test_reads_2.fasta
test-data/test_reads_3.fasta

diff -r e53b0473d575 -r 24e471d13fe9 smudgeplot.xml
--- a/smudgeplot.xml Sun May 08 10:43:40 2022 +0000
+++ b/smudgeplot.xml Thu Jun 30 22:45:21 2022 +0000

[

b'@@ -1,5 +1,5 @@\n-<tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@">\n- <description> - inference of ploidy and heterozygosity structure using whole genome sequencing</description>\n+<tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@" profile="21.05">\n+ <description>inference of ploidy and heterozygosity structure using whole genome sequencing</description>\n \n <macros>\n <token name="@TOOL_VERSION@">0.2.5</token>\n@@ -24,7 +24,7 @@\n ## Jellyfish kmer count\n ## ---------------------------------------------------------------------\n \n- #if $file.input.reads[0].is_of_type("fastq.gz") or $file.input.reads[0].is_of_type("fasta.gz")\n+ #if $file.input.reads[0].is_of_type("fastqsanger.gz") or $file.input.reads[0].is_of_type("fasta.gz")\n gunzip -c\n #for $f in $file.input.reads\n #if $f\n@@ -89,13 +89,13 @@\n help="For more control, create your own Kmer dump using Jellyfish.\n See Smudgeplot on GitHub for more details: https://github.com/KamilSJaron/smudgeplot"\n >\n- <option value="reads" selected="true"> Sequencing reads </option>\n- <option value="dump"> Kmer dump file </option>\n+ <option value="reads" selected="true">Sequencing reads</option>\n+ <option value="dump">Kmer dump file</option>\n </param>\n \n <when value="reads">\n <param\n- name="reads" type="data" format="fastq,fasta"\n+ name="reads" type="data" format="fastqsanger,fastqsanger.gz,fasta.gz,fasta"\n label="Sequencing reads" multiple="true"\n help="Sequencing reads corresponding to your genome.\n Don\'t worry about read pairing as it is not used in Kmer-counting.\n@@ -142,47 +142,88 @@\n </inputs>\n \n <outputs>\n- <data\n- name="smudgeplot" format="png"\n- from_work_dir="my_genome_smudgeplot.png"\n- label="${tool.name} on ${on_string}: Smudgeplot"\n- />\n- <data\n- name="smudgeplot_log" format="png"\n- from_work_dir="my_genome_smudgeplot_log10.png"\n- label="${tool.name} on ${on_string}: Smudgeplot (log10)"\n- />\n- <data\n- name="genome_summary" format="tabular"\n- from_work_dir="my_genome_summary_table.tsv"\n- label="${tool.name} on ${on_string}: Genome summary table"\n- >\n- <filter>table_output</filter>\n- </data>\n- <data\n- name="genome_summary_verbose" format="txt"\n- from_work_dir="my_genome_verbose_summary.txt"\n- label="${tool.name} on ${on_string}: Genome verbose summary"\n- >\n- <filter>verbose_output</filter>\n- </data>\n- <data\n- name="genome_warnings" format="txt"\n- from_work_dir="my_genome_warnings.txt"\n- label="${tool.name} on ${on_string}: Genome warnings"\n- >\n- <filter>warnings_output</filter>\n- </data>\n+ <data\n+ name="smudgeplot" format="png"\n+ from_work_dir="my_genome_smudgeplot.png"\n+ label="${tool.name} on ${on_string}: Smudgeplot"\n+ />\n+ <data\n+ name="smudgeplot_log" format="png"\n+ from_work_dir="my_genome_smudgeplot_log10.png"\n+ label="${tool.name} on ${on_string}: Smudgeplot (log10)"\n+ />\n+ <data\n+ name="genome_summary" format="tabular"\n+ from_work_dir="my_genome_summary_table.tsv"\n+ label="${tool.name} on ${on_string}: Genome summary table"\n+ >\n+ <filter>table_output</filter>\n+ </data>\n+ <data\n+ name="genome_summary_verbose" format="txt"\n+ from_work_dir="my_genome_verbose_summary.txt"\n+ label="${tool.name} on ${on_string}: Genome verbose summary"\n+ >\n+ <filter>verbose_output</filter>\n+ </data>\n+ <data\n+ name="genome_warnings" format="txt"\n+ from'..b'${on_string}: Genome warnings"\n+ >\n+ <filter>warnings_output</filter>\n+ </data>\n </outputs>\n \n <tests>\n- <test>\n- <param name="input_select" value="reads"/>\n- <param name="reads" value="test_reads.fasta" ftype="fasta"/>\n- <param name="lower_cutoff" value="2"/>\n- <param name="upper_cutoff" value="25"/>\n- <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n- </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="input_select" value="reads"/>\n+ <param name="reads" value="test_reads.fasta" ftype="fasta"/>\n+ <param name="lower_cutoff" value="2"/>\n+ <param name="upper_cutoff" value="25"/>\n+ <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n+ </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="input_select" value="reads"/>\n+ <param name="reads" value="test_reads.fasta.gz" ftype="fasta.gz"/>\n+ <param name="lower_cutoff" value="2"/>\n+ <param name="upper_cutoff" value="25"/>\n+ <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n+ </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="input_select" value="reads"/>\n+ <param name="lower_cutoff" value="2"/>\n+ <param name="upper_cutoff" value="80"/>\n+ <param\n+ name="reads"\n+ value="test_reads.fasta,test_reads_2.fasta,test_reads_3.fasta"\n+ ftype="fasta"\n+ />\n+ <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n+ </test>\n+ \n+ <test expect_num_outputs="5">\n+ <param name="input_select" value="reads"/>\n+ <param name="reads" value="test_reads.fasta" ftype="fasta"/>\n+ <param name="lower_cutoff" value="2"/>\n+ <param name="upper_cutoff" value="25"/>\n+ <param name="table_output" value="true"/>\n+ <param name="verbose_output" value="true"/>\n+ <param name="warnings_output" value="true"/>\n+ <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n+ <output name="genome_summary" ftype="tabular" file="my_genome_summary_table.tsv"/>\n+ <output name="genome_summary_verbose" ftype="txt" file="my_genome_verbose_summary.txt"/>\n+ <output name="genome_warnings" ftype="txt" file="my_genome_warnings.txt"/>\n+ </test>\n+ \n+ <test expect_num_outputs="2">\n+ <param name="input_select" value="dump"/>\n+ <param name="dump" value="dump.jf" ftype="txt"/>\n+ <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>\n+ </test>\n </tests>\n \n <help><![CDATA[\n@@ -195,9 +236,9 @@\n \n Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:\n \n-.. image:: https://raw.githubusercontent.com/usegalaxy-au/tools-au/master/tools/smudgeplot/static/img/smudge.png\n+.. image:: $PATH_TO_IMAGES/smudge.png\n :height: 520\n- :alt: Smudge plot image\n+ :alt: Example smudgeplot graph\n \n Every haplotype structure has a unique smudge on the graph and the heat of the smudge indicates how frequently the haplotype structure is represented in the genome compared to the other structures. The image above is an ideal case, where the sequencing coverage is sufficient to beautifully separate all the smudges, providing very strong and clear evidence of triploidy.\n \n@@ -246,6 +287,6 @@\n \n ]]></help>\n <citations>\n- <citation type="doi">https://doi.org/10.1038/s41467-020-14998-3</citation>\n+ <citation type="doi">10.1038/s41467-020-14998-3</citation>\n </citations>\n </tool>\n'

diff -r e53b0473d575 -r 24e471d13fe9 static/images/smudge.png

Binary file static/images/smudge.png has changed

diff -r e53b0473d575 -r 24e471d13fe9 test-data/dump.jf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dump.jf Thu Jun 30 22:45:21 2022 +0000

b'@@ -0,0 +1,2575 @@\n+CCCCTCCCAGTAGTTTTGCTA 24\n+ACAATTGGGACGGGGAGTAAA 24\n+AAAGCAAAGTTAATTGCGACG 25\n+GCTGGATTTCTGTAGCTTATA 2\n+ATGTTCAAGATAACGATCCAC 25\n+TACATTCGGTACGTAGAGGGA 25\n+ACGACGGCGGACTCAAACACT 24\n+ACTGGAATATCGGGAGACCCC 25\n+TGTTGACATGTATAGGCAACA 25\n+CATCGCTGGCAAGTGTTGTCG 24\n+GTGAGAAGTTCCCTCTACGTA 25\n+CAGAGAAACACCCTGTCGCAC 25\n+ATGCCCCTGTCCACACGAGAC 25\n+GGGTAACAACCCTCTCAACCA 25\n+AAGAAGCGATCAGTTCGCGAT 23\n+GATACTGTATACGACAATTAC 25\n+ATACGCACCGACGGATGTAAT 23\n+CTCTCTCATATTTAAGCAAAC 25\n+AGTTCCCTCTGCGTACCGAAT 24\n+GTACTTAGATAGTTAGACCTA 25\n+GTGTACTTTGTGGGTTATGCA 25\n+CGAAAGAGACTGTGTGTTGAA 25\n+ACAGTGGAACGGATTGCTCCC 25\n+ATGGTACCTAGTCTGCAAGTG 25\n+GAAAGAGTCTGTGAGTTGAAC 25\n+AAGGAGGAATCGGAAATCGTG 25\n+AAGTGACTATACGGTAGCAGA 25\n+AAGTCAGTCGTCGGTCCCAGA 24\n+GCACATCTTGGTCATGGTACC 25\n+AAGATAACGATCCACCCGCTA 25\n+ATATTGTTGGCTATACATGTC 24\n+AATTAGTGGGATGAATTACAC 25\n+ACTCCTTTTGGTAGGCTCTCC 24\n+CTTGCTACTCTAGTCGGATAA 24\n+CAACTAGGGGTAACCACCCTC 24\n+ACCCTAATACCGTCGCAATTA 25\n+GTATTCACATATACGTCCCAA 25\n+CGTATTCTAGACAGGTGACTC 25\n+AGTGGAACGGAGTGCTCCCCC 25\n+AGAATCTTAGTGCATAACCCA 25\n+CGCATGGTTCAACTCACAGAC 25\n+GGGCTTCAGTTGAGATGAAAC 25\n+AAAAGGAGTTGGCAGCCATAC 24\n+CTTGCTACTCGAGTCGGATAA 25\n+GGTTGGCAGCCATACATTTCA 25\n+ATGTATAGCCAACAATATACC 24\n+AAGAAAACGATCCACCCGCTA 23\n+CCCTAGTCTGCAAGTGATTGC 24\n+CAAGTGTAATTCATCCCACTA 25\n+CGCGCTTGGTATATTGTTGCC 25\n+ACGCATAACAGGGAAGATTCG 25\n+CTGTGTGTTGAACCATGCGGC 25\n+CTCAGTCTCAGGACCCACTAC 24\n+GGGTGGATCGTTATCTTGAAC 25\n+CTGATATCTGTACAAATTTGC 25\n+TCCGACAACACTTGCCAGCGA 24\n+CTCCACGGTCTCATGAACCAC 24\n+GAACGGAGTGCTCCCCCCCCC 25\n+ACGACTGACTCGTATTCTAGA 25\n+ACCGCCAACCTAACTACACAC 25\n+AACAAGAGACCGCGAACTGAT 24\n+AGACTGTGTGTTGAACCATGC 25\n+AGTTTCGAGGTGTGTTCCTAG 25\n+AGACTGCGTAAGAAAATAACC 25\n+CAGTCGTCGGTACCAGAAACA 25\n+AACCGCCAACCTAACTACACA 25\n+ACGTGGCACAGTGGAACGGAT 25\n+GTCGTCTGCGAAGCCCTTTCA 25\n+ATTTTCTTACGAAGTCTGCCG 25\n+ACATATGAAAAGGGTGATGAT 25\n+GTTGGGACGTATATGTGAATA 25\n+AGCCAGAGAGCCTACCAAAAG 25\n+CACTATGGCGACCGCGTTTCC 25\n+CCCTAGTTGAGGAACCGCCAA 25\n+GCACTAGTGGGATGAATGACA 25\n+CTAATATTATCAGCTACAGAA 24\n+ACAAAGTACACGCTCCGGTAA 25\n+AGTCTCGTGTGGACAGGGGCA 25\n+AGAACATTGATGCTACTAAAC 24\n+CATTCGAATCGTCGCAGGGGA 24\n+TAGTGCGGGTACACGTGGTGA 24\n+CCGGTTTTCGCGCGCTGCTAC 25\n+AATAGCGACGGTATTAGGGTG 24\n+ACCTAGTCTGCAAGTGATTGC 25\n+CTCTCAAATTTAAGCAAACCC 25\n+ACCCTGCGACGAATCGAATGG 23\n+CATTCATGTAACAAGAGATCG 25\n+CGAGGGATAACCGCGGCCGCG 25\n+CCCTCTGCGTACCGAATGTAA 24\n+CACGGTCTCATGAACCACCAA 24\n+ACCACATATATATTGTAAACC 25\n+AGACAGGTTTTCGCGCGCTGC 24\n+CCCCCAAAAGAGGGTTCGCGA 25\n+ACCTTGCCATCGCTGGCAAGT 24\n+ATAGGAGCGTCACACTGGAAT 24\n+GGCCCATGTATGCTTCAGAAC 23\n+AGCATATGGTTTGAATAGATC 23\n+CACACGCCATTGTTGTACTCA 24\n+AGAAGCGATCAGTTCGCGGTC 24\n+AATCTATATATCCGCGGCGGT 24\n+GGGGGGATTCTTGCTACTCGA 25\n+CGCAGTCTGCCGATATTGTCA 25\n+AGGCACAATGGAGACATCACG 25\n+CGCCAACCTAACTACACACGC 25\n+CTAGCCGCGACGTTTCGATAA 25\n+CAGTCCAGCTTTTTAATGGAC 25\n+CACAGACTCTTTCGATGAAAG 25\n+ATGGCGACCGCGTTTCCCCTG 25\n+AATTACACTTGTCTGACATAT 25\n+ATCTTGAACATTCCCAAAGAC 25\n+AGCGGTTCTCCGGCTGAATAA 25\n+TAATCTCGCAAGCCCACAGTA 2\n+ACTTGGACAGAACTTTAGTTA 25\n+ACTATACGGTAGCAGAACTAC 24\n+ATTGATGCTACTAAACGCCGC 24\n+AACCGCCACCCTAACTACACA 25\n+AAGAGATCGCGAACTGATCGC 24\n+CTAGTTGAGGAACCGCCACCC 25\n+ACAGTACGGGCGCCCAAACGT 24\n+GCCGGCTTCGCATTAGTTTCA 24\n+GCGGTGCAACTCGTCGCATAC 25\n+ACATTCATGTAACAAGAGATC 25\n+GACGGTTACTCGTGCTTCGAA 24\n+CGCATAACAGGGAAGATTCGA 25\n+ATATACGCGGCGTTTAGTAGC 24\n+ACTTGTATTCTAGACAGGTGA 24\n+AACTAATGCGAAGCCGGCACT 24\n+ATAGTTAGACTTATTCAGCCG 24\n+ACTGAGTACAATAATGGCGTG 24\n+ACCTCGAATCTTCCCTGTTAT 25\n+CGGAGTGCTCCCCCCCCCCTC 25\n+AAAGAACCACATATATATTGT 25\n+GTATTCAGATATACGTCCCAA 24\n+GATAAGCACATAAGAGCACGC 25\n+CACGTGTTGACATGTATAGGC 25\n+ATGGCTGCCAACCCCTTTTGG 25\n+ATACGACAATTACTTGGACAG 25\n+GTATACGACAATTACTTGGAC 25\n+AAAAAGGGTTCGCGATCAAAC 25\n+TTAAATGGACGCACAGAGTAA 23\n+GTGGTTACCCCTAGTTGAGGA 25\n+TACTCCCCGTCCCAATTGTCA 24\n+ATAGCCAACAATATACCAAGC 25\n+CTCAAAGTACACGCTCCGGTA 25\n+AGATTCGAGGTGTATTCCTAG 25\n+GTCGCAGCTCGCGTCCTAATA 25\n+AGCCCTTTCATCGAAAGAGTC 25\n+CCGGCAGAGAAACACCCTGTC 25\n+CCGGATAAGCATATAAGAGCA 25\n+AAACACTTACCTTGCCATCGC 25\n+AGGTGTGTTCCTAGGGCGATA 25\n+ATAGTGCGGGTACACGTGGTG 24\n+AGTCGTCGGTACCAGAAACAG 25\n+CCT'..b'TTTACCTTGCCATGGCT 25\n+GCAACTCATCGCATACTAGCC 25\n+ATTCTTGCTACTCGAGTCGGA 25\n+AACATTGATGCTACTAAACGC 24\n+ATCGCCGGATAGGAGCGTGAC 24\n+AAGGTAAATGTTTGAGTCCGC 24\n+TGGTATATTGTTGGCTATACA 24\n+ACGACTGACTTGTATTCTAGA 24\n+ACTCATCGCATACTAGCCAGA 25\n+GGGGGGAGCACTCCGTTCCAC 25\n+GCATCAATGTTCTGATACATA 25\n+ACGCAGCTACTGAAACGCACC 24\n+GCAGGGGAAACGCGGTCGCCA 25\n+AGTAAAAGGCGATAAATGCAT 25\n+TTGCTACTCGAGTCGGATAAA 25\n+CCATTAAAAAGCTGGACTGGA 25\n+ACTCGTGCTTCGAATGAGGAC 25\n+ACCCTAATACCGTCGCTATTA 24\n+AGCTACTGATACGCACCGACG 22\n+AGTGCGGGTACACGTGGTGAG 24\n+CCGCGACGTTTTGATAATCGA 24\n+ACGAATCTATATATCCGCGGC 24\n+GGGGGGAGCAATCCGTTCCAC 25\n+GGGAGATCCTCCAAGTCAAAA 24\n+ACTATGGCGACCGCGTTTCCC 25\n+AGAAAACGATCCACCCGCTAC 23\n+AAGCATACATGGGCCGAAAGG 22\n+GTTGACATGTATAGCCAACAA 24\n+TATACGCGGCGTTTAGTAGCA 24\n+CCACTACTTTGGGATTGACCA 25\n+ACTCCCCCAAAAAAGGGTTCG 25\n+AGGAACCGCCAACCTAACTAC 25\n+CATGTATAGCCAACAATATAC 24\n+GGTTTGCTTAAATATGAGAGA 25\n+AAAAGAACTTCTTTGCACTAT 24\n+TCACTTGCAGACTAGGTACCA 25\n+GGAGGCCGTAATACGATACCC 24\n+TAAAAGGCGATAAATGCATAA 25\n+CAAGGTAAGTGTTTGAGTCCG 25\n+AGAATACGAGTCAGTCGTCGG 25\n+CTGTCCACACGATACTGTATA 25\n+TATTGTTGGCTATACATGTCA 24\n+GATGGTTGAGAGGGTGGTTAC 24\n+AGTAGCATCAATGTTCTGAAG 25\n+AGTTGCTGATCGATTATCAAA 25\n+TAGTAGCATCAATGTTCTGAA 25\n+GTCTGTTTCTGGGACCGACGA 24\n+AAAAGGGGTTGGCAGCCATAC 25\n+GTGACTATACGGTAGCAGAAC 25\n+ACAAGAGATCGCGAACTGATC 24\n+GTTCGCCCATCTCCATAAAAA 24\n+GGTACCGAGTCACAATGGAGA 25\n+CGACGTTTTGATAATCGATCA 24\n+ATGTTCAAGAAAACGATCCAC 22\n+TATGAAAAGGGTGATGATCCA 25\n+TTCGATTCGTCGCAGGGTAAA 23\n+ACATATGAAAAGGGTGAGGAT 22\n+CTGTCGCAGCTCGCGTCCTTA 25\n+GATATCCCTCGTGTCGTCCAA 25\n+GTGTACTTTGAGGGTTATGCA 25\n+ATTCACATATACGTCCCAACG 25\n+AAGGGCTTCGCAGACGACTCT 25\n+GTATACAGTATCGTGTGGACA 25\n+ATCCGTCGGTGCGTATCAGTA 23\n+ATATTGTAAACCATGCATAAG 23\n+AGTGGACCGGAGCAAGCGCTG 25\n+AACCACATATATATTGTAAAC 25\n+CATTGTTGTACTCAGTGTGCA 24\n+AAACTAGTGGGTCCTGAGACT 25\n+TATGCTTATCCGGTTATATGA 25\n+AGTTCCCTCTACGTACCGAAT 25\n+CGCGATCTCTTGTTACATGAA 24\n+TAGCATCAATGTTCTGATACA 25\n+TATCGGCAGACTGCGTAAGAA 25\n+GTTGAGATGAAACTAATGCGA 25\n+AATCTGCGCTTGCTCCGGTCC 25\n+ACCCACCAGGTTGGTGGTTCA 24\n+ATAGTTAGACCTATTCAGCCG 25\n+TACGTACCGAATGTAACGTCA 25\n+TCGTCGCATACTAGCCGGAGA 25\n+ACATTCGGTACGTAGAGGGAA 25\n+TTGCTACTCTAGTCGGATAAA 24\n+CGACTAGAGTAGCAAGAATCC 24\n+ATTGGGACGGGGAGTAAAGAA 24\n+CTTTCAGTGTACTGGATCCTC 24\n+CCCTCTACGTACCGAATGTAA 25\n+CCCCCCCCCTCCCAGTAGTTC 24\n+TGTTGACATGTATAGCCAACA 24\n+AATCAGCGCTTGCTCCGGTCC 25\n+TATATTGTAAACCATGCATAA 23\n+CACGCCGCGTACTTAGTGCGA 24\n+CAGAACTACTGGGAGGGGGGG 24\n+CAGAGAAACACCCTGACGCAC 25\n+GCTCGCGTCCTTATATTATCA 24\n+CAATGTTCTGAAGCATACATG 25\n+CGACAGGGTGTTTCTCTGCCG 25\n+CTTGCCAGCGATGGCAAGGTA 24\n+ATATATATTGTAAACCATGCA 23\n+GAACCCTCTTTTGGGGGAGTC 25\n+CATATAAGAGCACGCTGAAGA 25\n+AGATCGCGAACTGATCGCTTC 23\n+CCCTGATCAATTCAAACCATA 25\n+AATTGTCGTATACAGTATCGT 25\n+AAAATCTGCGCTTGCTCCGGT 25\n+CTAGTGCAGGTCGAATTGAAA 25\n+GGCTCTCCGGCTAGTATGCGA 25\n+CCTAGGAATACACCTCGAATC 25\n+TAGAGGGAACTTCTCACGAGA 25\n+AATCTCTCTCATATTTAAGCA 25\n+GAATACACCTCGAATCTTCCC 25\n+TATAACCGGATAAGCATATAA 25\n+GGGATATCCGCGGCCGCGTAA 24\n+TACGACAATTACTTGGACAGA 25\n+ATGGCAAGGTAAATGTTTGAG 25\n+GTATACGACAATTACTTTGAC 25\n+AACTTCCCTGTTATGCATTTA 25\n+GAAAAGGGTGATGATCCAGTA 25\n+CAATTAACTTTGCTTTCAGTG 25\n+CGCTGGCAAGTGTTGTCGGAA 24\n+AAGAGACCGCGAACTGATCGC 24\n+AATTTGAGAGAGATTCCTTTA 24\n+AGCATATGGTTTGAATTGATC 25\n+CGCGAAAACCGGTCTCACCAC 25\n+GTATACAGTCTCGTGTGGACA 25\n+ATCCCAAAGTAGTGGGTCCTG 25\n+ATGGCTGGCAAGTGTTGTCGG 25\n+AGTCTCTTTCGATGAAAGGAC 25\n+AATATTATCAGCTACAGAAAT 24\n+AAAGTTCTGTCCAAGTAATTG 25\n+CGTAGCGGGTGGATCGTTATC 25\n+CAACACTTGCCAGCCATGGCA 25\n+ATCAATGTTCTGAAGCATACA 25\n+GGTACCGAGGCACAATGGAGA 25\n+AGGTGTATTCCTAGGGCGATA 24\n+CGAAGCCCTTTCATCGAAAGA 25\n+ATACTAGCCAGAGAGCCTACC 25\n+GCAGCTACTGAAACGCACCGA 24\n+AACTAGTGGGTCCTGAGACTG 25\n+GGTTCTTTACTCCCCGTCCCA 24\n+GATATCTGTACAAATTTGCCC 25\n+CTAGAATACAAGTCAGTCGTC 24\n+ATTCATGTAACAAGAGACCGC 25\n+TCGATGAAAGGGCTTCGCAGA 25\n+AGGAATACACCTCGAATCTTC 25\n+ACCTTGCCATGGCTGGCAAGT 25\n+AACTGGAAAATTTTATGGAGA 25\n+AGTTCGGTCTCACCTCTCACG 24\n+GTCAAAGGAACTTCTTTGCAC 25\n+CACGCGGTGGGTATTCACATA 24\n+ACGCCATTGTTGTACTCAGTG 24\n+ATAGGAGCGTGACACTGGAAT 25\n+GGAAGATTCGAGGTGTATTCC 25\n+CCCTACGCAGCTACTGAAACG 25\n+ACGCGGCCGCGGATATCCCTC 24\n'

diff -r e53b0473d575 -r 24e471d13fe9 test-data/my_genome_summary_table.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/my_genome_summary_table.tsv Thu Jun 30 22:45:21 2022 +0000

[

@@ -0,0 +1,2 @@
+peak kmers [#] kmers [proportion] summit B / (A + B) summit A + B
+AB 973 1 0.49 47.57

diff -r e53b0473d575 -r 24e471d13fe9 test-data/my_genome_verbose_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/my_genome_verbose_summary.txt Thu Jun 30 22:45:21 2022 +0000

[

@@ -0,0 +1,15 @@
+1n coverage estimates (Coverage of every haplotype; Don't confuse with genome coverage which is (ploidy * 1n coverage).)
+* User defined 1n coverage:
+* Subset 1n coverage estimate: 24.6
+* Highest peak 1n coverage estimate: 25
+1n coverage used in smudgeplot (one of the three above): 25
+* Proposed ploidy: 2
+* Minimal number of heterozygous loci: 47
+Note: This number is NOT an estimate of the total number heterozygous loci, it's merly setting the lower boundary if the inference of heterozygosity peaks is correct.
+* Proportion of heterozygosity carried by pairs in different genome copies (table)
+  genome_copies propotion_of_heterozygosity
+1             2                           1
+* Proportion of heterozygosity carried by paralogs: 0
+* Summary of all detected peaks (table)
+  peak kmers [#] kmers [proportion] summit B / (A + B) summit A + B
+1   AB       973                  1               0.49        47.57

diff -r e53b0473d575 -r 24e471d13fe9 test-data/my_genome_warnings.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/my_genome_warnings.txt Thu Jun 30 22:45:21 2022 +0000

@@ -0,0 +1,20 @@
+
+######################
+## INPUT PROCESSING ##
+######################
+
+#############
+## SUMMARY ##
+#############
+detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 35
+detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 30
+detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 25
+detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 20
+!! Warning, your coverage filter on the lower end (L = 23 ) is higher than half of the 1n coverage estimate ( 1n / 2 = 12.5
+If the real 1n coverage is half of your estimate you would not picked it up due to the filtering.
+If you have sufficient coverage, consider reruning the analysis with lower L (something like (1n / 2) - 5)
+One good way for verificaiton would be to compare it to GenomeScope estimate of haploid coverage
+
+##########
+## PLOT ##
+##########

diff -r e53b0473d575 -r 24e471d13fe9 test-data/test_reads.fasta.gz

Binary file test-data/test_reads.fasta.gz has changed

diff -r e53b0473d575 -r 24e471d13fe9 test-data/test_reads_2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_reads_2.fasta Thu Jun 30 22:45:21 2022 +0000

b'@@ -0,0 +1,4 @@\n+>maternal_hapl_sequences\n+TTGTACGGACTATTGCCTTGCAGCAGGTCTTAGCCAAATAGCTTCGCTTATCGTTTGAAATCTTAATCGGCCACCACACTATAATCTGTGGTGCTTCTATAGGCGCCTGGCTCGATCATCAGGTCAGCGTCTAGTAGGTTTCTAGCCGCGACGTTTTGATAATCGATCAGCAACTTAAAACTCGCGGGTAGGCCCATAATTTTGCAGTTCGCACCACCACAGTCTGCCATGGTCAACATTCGTTCGTTTGTATCAACCCCGGTGGGCCTCGTTGGAGATTCGCACCTACATAGTGTAACGGAACGATACAAGGCGACCCTGCAAGGAACAGCGTCGGTAATCGCTAGAAGCGATTCATGCGTCATCCGCAGCGGAGCAGGGCTTACGCGGCCGCGGATATCCCTCGTGTCGTCCAAGAGATACAGACAAGCAACATAAAGCAGTGTACTGTAACCCGAGAATAGACTAGTCTTAACGTTGGGAAATTTCACGGACCGAGATAAAGCCTTCTCCTAGGCCCTACGGCACTAATTTCGAGCAGCACTCCGAGACTTGAAGCGGCGACATGAATTTCAGCGATCATTCCCCCTAGTCCAGTCCAGCTTTTAAATGGACGCACAGAGTAACCTTTCATAGGAGTAAAAGGCGATAAACGCATAACAGGGAAGATTCGAGGTGTATTCCTAGGGCGATAACGAGAAAGTTCGATTGAGGCCGATAGTACTGCGCCGTATGTTATCGCGCGTTTTGGCGGATTTACCACTACCTTGGGACTTTTCGACAGTGCCCGGCGTTTGGCACTTCGACGCAGTTCCGTTACAGTGGGAAGAGCGTAGCAGCGCGCGAAAACCTGTCTCACCGCGTGTACCCGCACTATGGCCGTTTAGGCTGAAACAGCCTGTACTCCAAGTCGCTTATCGGAAATGGCGAAGGCACTTTCACGCACGCCGCGTACTTAGTGCGACAGGGTGTTTCTCTGCCGGTTGGCTATTGGTAGGCGACCTAGCATGGTACAGGCAAGTCCAACGTTGGACGTTCGGAACTCAACATCCCTTATATATGGGAGATACGAATCTATATATCCGCGGCGGTTAGTAGCATCAATGTTCTGAAGCATACATGGGCCGAAAGGAGGTTGTGGCACTAACGTCGTTCATCGTCACGGTAGCCTCACAGTGTGCCAATTACGGCGGCAGGACCAATGAAGCGTCAACGATGATATCACGGCACCAAGAACTGGCGTAATTTAGCCACTTACCGATTTAACTTTATGCATTTTATGGTATCAAAGTCTACCAATCAGCCGTGGGCATAGTTTACGGGAGATCCTCCAAGTCAAAGGAACTTCTTTGCACTATGGCGACCGCGTTTACCCTGCGACGAATCGAATGGCCGGCCCCTTAACCATGGGGGGATTCTTGCTACTCTAGTCGGATAAATCAAGGTGACGAAGTGACGGTCGGGAAGCCTGTCGTATGGAAATTATTTGCATGAGAATTATGACCTGTCTGGCAGCCCGCGCCGACCACCCTGTAGTACACTAAGCTCCATCGTGGGACATAGGCGCTTTCTAAATGTCAGCGGAACTTGGACGGTCGTATGTACGTGGACCCCACCTGGCCTACGCAACACTACGACCAATCGCAGTAGTCATTCCTATCTCCGAGCAAATAGTTTCGGGGGCCACAATTAGCCGCGGCGAGAAGACTACCGCGGGACGTTATGCTTTGGGCAATTCAGGAATTTGCTAGCAAACGCTCGGACGCAGCTAGGTGGTACCTTTACCGTACTGTGTACTTAGATAGTTAGACCTATTCAGCCGGAGAACCGCTGCTGCTACGATTCTGCCCGTCGTAGCGTCTAGCCGTACTGGTCATACAAGACATTACATGTGCCACGAGTGGATATCTCGGAAGAGAGCGACTATAAGGGTGGAATTAACCGGGGTATTACTGCAACCGCACTTGCAAAAAAAGACCGTAAGTTCCGGCTGGCGCGTACCGGATGTAGATCTTCACTGTGATTTCCACCGTAGACACACAAATATGGCGGAGGCCGTCTTACCTATCGCGTATTGACATCGAAGGCAGTGGACCGGAGCAAGCGCTGATTTTCTGACACGACCGAATGTACCTATAATACAGACTGTTGGGGCGTAACAATAGTCTTGCACATCGATGAGCTTGAGCTGTGAAGGTAATTAGTTCGGTCTCACCTCTCTCGTTTGGGCGCCCGTACTGTGCAACATGAGTGGCTTAGCCTTGCAAATACTAATACACGTGACGCGTTCCTGAAACAAGCGATGGATATCAGCGCCTAAGCTTGATATACTGCGTATATCCGTTGACCTCATATCGTGGTTCGGGGGTCACAGTAATGCCTGAATGCTTGGATGACGCCGAGCAACGGTAGCATCGATTCCGCCACGGGGGTAGTGCCCCGCGCGGGTCTGTTTCTGGTACCGACGACTGACTCGTATTCTAGACAGGTGACTCAAACTATGACAAGGGATTCCCCGGGCTCAACCCAATACACATTTAGTCACGTTGGGGCACTGCCTGTATCTTTTTGTTCCGACAACAGTTGCCAGCGATGGCAAGGTAAGTGTTTGAGTCCGCCGTCGTTTACCATGACCTAGGGTTACCCAGTCAAGATTATCACCTGACACCTCCAGCTATCGCCCGACTCCCTAAAAGATTTCTCGGAGACCTCAACTGTGGAAGCTTGCTGGATTTCTGTAGCTGATAATATAAGGACGCGAGCTGCGACAGCCACCAGACTTGAAACCTGTCGGGGGCTACCCACGGTGAGCTAGCGCTTGTAACCATCTGGCCCAACATAAGAAGTCTTAAGGGAGTGACTGCATCGTGTGGAAAAAACCAAGGCGTCATGAAAGATCGGTACCCTCGCATAGCATGTTCAAAGTTGCTCTGCGGTCCCGTCTAAGCTACTACTCAGTGATGGACCTCTTAACTTTAAGGCGTTTAGATTTCGGCCTTGCCATAATTCCGCTCGAGAGCCTATGATGCACCATAGCTTTAAGCTGTGGGTTTAGAAGATTGTCCATTAGAAAGTGCATAAAGAGCGAAGAAGCGATCAGTTCGCGGTCTCTTGTTACATGAATGTGCCGCTCTTCGTTTCGTGTTCGCCCATCTCCATAAAATTTTCCAGTTTGCGGTCGCCCCATTAGTGGGATAGAAAGTAGCCGGCCTCAAGCTCTTAGCGGTGCAACTCATCGCATACTAGCCAGAGAGCCTACCAAAAGGGGTTGGCAGCCATACATTTCAGCTAAGATCGGGCCTCCTAGAGAAGAGTACCACTTAACTCGCTAAAGAGGAATATGGTAGAGCGCGTTGGAAGGAAACCCCCAGCGAATTACCCCCGAGCATACATGCACATGTTGAAATTGTCTCGTTATCGGGAACTCTACGTTGACGTTACATTCGGTACGCAGAGGGAACTTCTCACGAGATACTTGGCAAACCCTGATCTATTCAAACCATATGCTTGAAAATGTCCTTTAGGAGCTGGGGGCCGAAGTACGCAAATTTATTCGTTGTATATCCTGCGACTTAGATCGACTTGCCGGATTCCTTTGCTGCCCAGCCAAACGTGGCACAGTGGAACGGAGTGCTCCCCCCCCCCTCCCAGTAGTTTTGCTACCGTATAGTCACTTGGGCCTTGGACCCGACTTAATGACCACCCTAGAGCTCCGGGGGGTATCAAACAGCGGCGTGGGGTGCCCCCCAACTGTAAGTAAGAGGACGTGCTACTTCAGACGGTGCACCCGTGTGTTCAGAGTCGCTGCTGGGAAGAACGGTTAAGGGTTCTCTCCATTACCGGAGCGTGTACTTTGTGGGTTATGCACTAAGATTCTGCAATGGTCCTGATATCTGTACAAATTTGCCCAAAGCACACCACTGCAAGGACTCCACGGCCTCATCAACCACCAACCT'..b'TCATGTACCACCAGATTAAAGAGTACTCCAAAAACTACCTGTCTATACGCATTCCCGTAAAAATCGACACCGCCAATTTGGCTAGGACAGACCCATAAAGGAATCTCTCTCAAATTTAAGCAAACCCCGCTCGGGTATCGTCTATCGTTCTTCGAACGGGTTAGAGACGTAAAGGGGGTCCCTGGGAAATCGGCCGGAAAATTCGGATATTGCCGGAGCCTGGTTGGCAATATGTCAGACAAGTGTCATTCATCCCACTAGTGCAGGTCGAATTGAAAAGGACTTCTGGGGAAAAGTGATTTAGCTGACCCGTGCAAAGGTGTCCTTTTATAAACCCTCGTACTGCGGGCCCGGGTATCGCGGCTATTCGAGTTCTCCTGCTGGAGTCTCCCCCTCTCCCTGAAGGAACTATGAGATATCTTACATTAAAAGTCTACTTCTAAGCATTAAGCACACTTGGGTTTGACCGGTGACGTAACTTATTTAGGCTTGGAGGCGGCCGGATCTCAAGTCCAGATCTCAGGGCCATCTGAGCGGGAATACGACCAATATAAAAAAAGAGTCACACTCGTGGCGGTCCACATTCATTTCCCTCCCACGATTTCCGATTCATCCTTACCCTAAGTAGTGTCTTGCCTGCGTGGGATTACGCGGAAATCGCGCCGGTCGCGTCCCAAGACTACCAAGTGAGAACTACTCACGCAGTTAAGTCCAGTGGAATAATTCACTGCTCGTTGAGGGCGTATAAGATCCCGCATAAGACCCGATGTTGTAAATCGAGGCGAGGTCTAGTAAAAAGGCGTTCCTATCTTCCACAAGGAATACAGATCTCGAGTCATTGCGCTTAACTGTTCAACCCGACACGGGCATCGCACCTGAGTGTACTTCGGGACAACCTCGGTCCTACAGACGCTGTTCGTGCCCTCTGCAAGTATACATAACGTTGCGTGAGAGTCTTCAGCGTGCTCTTATATGCTTATCCGGTTATATGATCCGAGGAGAGAAGGGCAGCTTGGAGCCGAATCGAACGATGGCTCGCTCCCAAAAAGTGCCCCGCATGCGTATGGTTGCGCAATGGAGCTTATATGTGAACAGTGAATGCACAAATGCGCTAGTCCTATGCGCACCAATTTGTATTGTTCCACGGGGCTATGGTGACCCCTTACAAAAGACATATCACGGCCGAAGATATTCTTTGCCTAATTGCCTCCCAGCTGGCCGTTCCTGTCAGGCTATGTAATCAACAGTACTGCCTTAATATGTCTTTGGGAATGTTCAAGATAACGATCCACCCGCTACGCCAAATTACGAGCACGCGGTGGGTATTCAGATATACGTCCCAACGGCCCGTGGTAGTGTCCCAGGGAATCTAAGCGGTAGCTCCTATTGGCAAACTCAGTATTAGTCTAGACAGGTCGTCAGGAAACCCCACGAACTTAGCACATACATTTTACCCGTACAGCGTTGCTTTCGCCTTTCAGCTTTATTAGCCAGCGCCTGGACTAGCTTAAGGTTGCAACCTCTGTGTATCCAAATACAAACAGCTAGCACAGACTGAATATGATACGGGACCAAGATGACAATATCGGCAGACTTCGTAAGAAAATAACCGCACGTGTTGACATGTATAGCCAACAATATACCAAGCGCGAGCTCCTCAACCGTACGGACACAGGTTACGCAATCCCCTACGCAGCTACTGAAACGCACCGACGGATGTAATATCTCGCGGAGCTCTCCATTACATCAGCTTTCTTATAAGTATGAGCGCCTAGCGGGTCATAAGTGTTGGGTGGCCAGTGATCATAACTAAAGTTCTGTCAAAGTAATTGTCGTATACAGTCTCGTGTGGACAGGGGCATAACGTACGCGGCTTGGTTGATGGTTGAGAGGGTGGTTACCCCTAGTTGAGGAACCGCCAACCTAACTACACACGCCATTATTGTACTCAGTGTGCAATCACTTGCAGACTAGGTACCATGACCAAGATGTGCCAGTAGCGGTGTCTTAGGTCTGAGGAAGATGTATACATCGTCTCGCGGTACTATGCGTTTATAATCAGCCGGTATTCGCCACTCAGGAATTTGTTATGCAAAGGAGGTGGCACACTACATCGCTTTATAGGACTCACACAAAAGAGCCAGTAGATCGCCGGATAGGAGCGTGACACTGGAATATCGGGAGACCCCGTCCGTCCAATACGACCGACGCTCGCCGTGGGGAGTAGTCGGATAAATTAAATTGATATAGGAGAGTCTGCTAGTGGTTAGTACGGTTGCCAAACAATGTGCCGGTCGTCTTCGAACTAGTAGGTACCTAATAGTCAGTTAGTAAATCCGGTCGCTCGATTTGAATCGCCCCACTATGCACAATAGTCCCACCCTAATACCGTCGCTATTAACTTTGCTTTCAGTGTACTGGATCATCACCCTTTTCATATGTGTGAATCATCAAATTTACTACCGTTTACGTTTATTTGCCGGAGGAAATGAGACTAAATACCTGTCGGCGTCGCGATGGTAAAAGTTGTCCATAAGGCATGTGAGCTCCTGAATAAAGAGTCGTCTGCGAAGTCCTTTCATCGAAAGAGACTGTGTGTTGAACCATGCGGCTGGTACCGAGTCACAATGGAGACATCACGTGGCCCCGCCCTTCCAGAATTCCAGGACGTGGCCCATACCTGAAGTGGCTGAATCGACTCCCCTCAGTCTCAGGACCCACTAGTTTGGGATTGACCAGCCGCCATAGCCGGGGCGGGCTTGAACATGCGACCAGGCCTTTACGGACAAGCTCCTAGCCTCCATGCATAGGCTCAAAGCATTTGCGCGGGGCGCCATCGTCAAGTCCTGCGGAACTGCGGCATCAGAAGCTTGACGTCCCGGGTCTCGTCTCCGAAGCGTGTGCAAAGCGACCCTGAGTTCAAAGCCCCGATCGACATAGTGACATCTGCTCCCTGGGTGAGCATTGGCACCGCTAACCTCGCAAGCCCACAGTATAGATCCCCCCCCCTAACCTGTAATTCTAAGCACTATGTTATTCCGTTTAGGGGGGAATGCGGAGGACCCTGCTCGTGACAATTGTGACGGGGAGTAAAGAACCACATATATATTATAAACCATGCATAAGACTTCAGGGGCTACTGGCGGACCTCTCGAGCGTTACGAACCACTCTCCCTAATGAGTGCCGGCTTCGCATTAGTTTCATCTCAACTGAAGCCCTATTTATGAGTTTATTACTGCTATCTCGTGACAGAGTACTCGGGGGTTGCGCTGCAGCGGCCCCCTTGAGAACGTCATTTAACTTCAGGTTCCGACCGTCAAAGCACATCATAATCACCTCGCTTCAAGATAGGGTCCTCATTCGAAGCACGAGTAACCGTCATGGAGGCCGTAATACGATACTCAATCACCTGATCCTTGTAAACTCAGCCGGCACTCAGCTTTTGGCGCTCCCTGGGTGAGCATTAGCACCGCTAACCTCGCAAGCCCACAGTATAGATCCCACCCCCTAACCTGTAATTATAAGCACTATGTTATTCCGTTTAGGGGGGAATGCGGAGGACCCTGCTCGAGACAACGGGGACGGGGAGTAAAGAACCACATATATATTGTAAACCATGCATAAGACTTCAGGGCCAACTGGCGGACCTCTCGAGCGTTACGAACCACTCTCCCTAATGAGTGCGGGCTTCGCATTATTTTCATCTCAACTGAAGCCCTATTTATGAGTTTATTACTGCTAACTCGTGACAGAGTACTCGGGGGTTGCGCTGCAGCGGCCACCTTGAGAACCTCATTTAACTTCAGGTTCCGACCGTCAAAGCACATCATAATCACCTCGCTTCAAGATAGGGTCCTCATTCGAATCACGAGTAACCGTCATCGAGGCAGTAATACGATACCCAATCACCTGATCCTTGTAAACTCAGCCGGCACTCAGCTTTTGGCGCTCCCTGGGTGAGCATTAGCACCGCTAACCTCGCAAGCCCACAGTATAG\n'

diff -r e53b0473d575 -r 24e471d13fe9 test-data/test_reads_3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_reads_3.fasta Thu Jun 30 22:45:21 2022 +0000