| Previous changeset 10:bfc70c8cc5ca (2020-12-11) Next changeset 12:39b40a9a6296 (2021-08-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker commit c4bf14b461856220df4b4bbdbb4b9bbad1ff8749" |
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modified:
repeatmasker.xml test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.log test-data/small.fasta.stats test-data/small_dfam.fasta.cat test-data/small_dfam.fasta.log test-data/small_dfam.fasta.stats test-data/small_dfam_up.fasta.cat test-data/small_dfam_up.fasta.log test-data/small_dfam_up.fasta.stats |
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added:
macros.xml test-data/small_dfam_rattus.fasta.cat test-data/small_dfam_rattus.fasta.log test-data/small_dfam_rattus.fasta.masked test-data/small_dfam_rattus.fasta.stats |
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| diff -r bfc70c8cc5ca -r 72aade318318 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 20 12:56:42 2021 +0000 |
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| @@ -0,0 +1,33 @@ +<macros> + <token name="@TOOL_VERSION@">4.1.2-p1</token> + <token name="@GALAXY_TOOL_VERSION@">galaxy0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0157</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0237</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">repeatmasker</requirement> + </requirements> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>repeatmasker</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{RepeatMasker, + title = {RepeatMasker Open-4.0}, + howpublished = {\url{http://www.repeatmasker.org}}, + author = {Smit, AFA and Hubley, R and Green, P.}, + year = {2013-2015}} + </citation> + </citations> + </xml> +</macros> |
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| diff -r bfc70c8cc5ca -r 72aade318318 repeatmasker.xml --- a/repeatmasker.xml Fri Dec 11 22:26:02 2020 +0000 +++ b/repeatmasker.xml Thu May 20 12:56:42 2021 +0000 |
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| @@ -1,11 +1,13 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.1.1" profile="17.01"> - <description>screen DNA sequences for interspersed repeats and low complexity regions</description> - - <requirements> - <requirement type="package" version="4.1.1">repeatmasker</requirement> - </requirements> - - <command detect_errors="exit_code"><![CDATA[ +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01"> + <description>screen DNA sequences for interspersed repeats and low complexity regions</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro='edam_ontology' /> + <expand macro='requirements' /> + <version_command>repeatmasker --version</version_command> + <command detect_errors="exit_code"><![CDATA[ RM_PATH=\$(which RepeatMasker) && if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi && @@ -97,12 +99,10 @@ </param> <when value="yes"> <param name="species_list" type="select" label="Species"> - <option value="vertebrate">Vertebrate (other than below)</option> - <option value="mammal">Mammal (other than below)</option> - <option value="human" selected="true">Human</option> - <option value="rodent">Rodent</option> - <option value="mouse">Mouse</option> - <option value="rat">Rat</option> + <option value="human" selected="true">Human (Homo sapiens)</option> + <option value="rodent">Rodent (Order Rodentia)</option> + <option value="mouse">Mouse (Mus musculus)</option> + <option value="rattus">Rat (Rattus sp.)</option> <option value="danio">Danio (zebra fish)</option> <option value="drosophila">Fruit fly (Drosophila melanogaster)</option> <option value="elegans">Caenorhabditis elegans (nematode)</option> @@ -219,6 +219,15 @@ <output name="output_repeat_catalog" file="small_dfam_up.fasta.cat" lines_diff="2" /> <output name="output_log" file="small_dfam_up.fasta.log" lines_diff="2"/> </test> + <test expect_num_outputs="4"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="dfam" /> + <param name="species_list" value="rattus" /> + <output name="output_masked_genome" file="small_dfam_rattus.fasta.masked" /> + <output name="output_table" file="small_dfam_rattus.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small_dfam_rattus.fasta.cat" lines_diff="2" /> + <output name="output_log" file="small_dfam_rattus.fasta.log" lines_diff="2"/> + </test> </tests> <help><![CDATA[ RepeatMasker is a program that screens DNA for interspersed repeats and low @@ -234,13 +243,5 @@ .. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html ]]> </help> - <citations> - <citation type="bibtex"> - @misc{RepeatMasker, - title = {RepeatMasker Open-4.0}, - howpublished = {\url{http://www.repeatmasker.org}}, - author = {Smit, AFA and Hubley, R and Green, P.}, - year = {2013-2015}} - </citation> - </citations> + <expand macro="citations" /> </tool> |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small.fasta.cat --- a/test-data/small.fasta.cat Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small.fasta.cat Thu May 20 12:56:42 2021 +0000 |
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| @@ -98,6 +98,6 @@ ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.1 , default mode +RepeatMasker version 4.1.2-p1 , default mode run with rmblastn version 2.10.0+ RM Library: |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small.fasta.gff --- a/test-data/small.fasta.gff Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small.fasta.gff Thu May 20 12:56:42 2021 +0000 |
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| @@ -1,5 +1,5 @@ ##gff-version 2 -##date 2020-12-11 +##date 2021-05-20 ##sequence-region rm_input.fasta scaffold_1 RepeatMasker similarity 613 632 0.0 + . Target "Motif:(GT)n" 1 20 scaffold_1 RepeatMasker similarity 780 824 18.3 + . Target "Motif:(ATAATA)n" 1 45 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small.fasta.log --- a/test-data/small.fasta.log Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small.fasta.log Thu May 20 12:56:42 2021 +0000 |
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| @@ -1,4 +1,4 @@ -SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID +SW scoret% div.t% del.t% ins.tquery sequencetpos in query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID 18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small.fasta.stats --- a/test-data/small.fasta.stats Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small.fasta.stats Thu May 20 12:56:42 2021 +0000 |
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| @@ -53,8 +53,8 @@ Runs of >=20 X/Ns in query were excluded in % calcs -RepeatMasker version 4.1.1 , default mode - +RepeatMasker version 4.1.2-p1 , default mode + run with rmblastn version 2.10.0+ -The query was compared to unclassified sequences in ".../dataset_a9c6a294-8dbb-4a71-ad9c-e36735923fbf.dat" - +The query was compared to unclassified sequences in ".../dataset_a3b3078d-de09-4651-9e83-62019a3d45ba.dat" +FamDB: |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam.fasta.cat --- a/test-data/small_dfam.fasta.cat Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam.fasta.cat Thu May 20 12:56:42 2021 +0000 |
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| @@ -113,6 +113,6 @@ ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.1 , default mode +RepeatMasker version 4.1.2-p1 , default mode run with rmblastn version 2.10.0+ -RM Library: CONS-Dfam_3.2 +RM Library: CONS-Dfam_3.3 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam.fasta.log --- a/test-data/small_dfam.fasta.log Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam.fasta.log Thu May 20 12:56:42 2021 +0000 |
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| @@ -1,4 +1,4 @@ -SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID +SW scoret% div.t% del.t% ins.tquery sequencetpos in query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID 18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam.fasta.stats --- a/test-data/small_dfam.fasta.stats Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam.fasta.stats Thu May 20 12:56:42 2021 +0000 |
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| @@ -45,7 +45,7 @@ The query species was assumed to be human -RepeatMasker version 4.1.1 , default mode - +RepeatMasker version 4.1.2-p1 , default mode + run with rmblastn version 2.10.0+ - +FamDB: CONS-Dfam_3.3 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_rattus.fasta.cat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_rattus.fasta.cat Thu May 20 12:56:42 2021 +0000 |
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| @@ -0,0 +1,103 @@ +18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 + + scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632 + + (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 + +Matrix = Unknown +Transitions / transversions = 1.00 (0/0) +Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) + +16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 + + scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824 + v - v - i v vv i + (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45 + +Matrix = Unknown +Transitions / transversions = 0.40 (2/5) +Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) + +12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 + + scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274 + - i v v iv -i vv v + (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46 + +Matrix = Unknown +Transitions / transversions = 0.50 (3/6) +Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) + +15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 + + scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898 + v i i - vv vv i - - - + (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 + + scaffold_1 4899 -CTC 4901 + - + (TC)n#Simple_ 51 TCTC 54 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) + +13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 + + scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278 + v i - v -i - i v - v v + (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47 + + scaffold_1 6279 AAATAA 6284 + - + (TAATTAA)n#Si 48 -AATAA 52 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) + +15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 + + scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597 + v i i viv i vi v -v i - + (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48 + + scaffold_1 6598 GACAGAGAG 6606 + v + (GACA)n#Simpl 49 GACAGACAG 57 + +Matrix = Unknown +Transitions / transversions = 0.86 (6/7) +Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) + +67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 + + scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 + i i - + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 + + scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050 + + (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 + +Matrix = Unknown +Transitions / transversions = 1.00 (2/0) +Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) + +19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 + + scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113 + v v i - i v + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 + +Matrix = Unknown +Transitions / transversions = 0.67 (2/3) +Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) + +## Total Sequences: 1 +## Total Length: 14220 +## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 +## Total NonSub ( excluding all non ACGT bases ):14220 +RepeatMasker version 4.1.2-p1 , default mode +run with rmblastn version 2.10.0+ +RM Library: CONS-Dfam_3.3 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_rattus.fasta.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_rattus.fasta.log Thu May 20 12:56:42 2021 +0000 |
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| @@ -0,0 +1,10 @@ +SW scoret% div.t% del.t% ins.tquery sequencetpos in query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID + +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 +16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 +12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 +15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 +13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 +15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 7 |
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| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_rattus.fasta.masked --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_rattus.fasta.masked Thu May 20 12:56:42 2021 +0000 |
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| b'@@ -0,0 +1,286 @@\n+>scaffold_1\n+TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC\n+CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC\n+ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA\n+CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC\n+AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA\n+CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT\n+AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC\n+CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA\n+ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC\n+GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG\n+GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC\n+AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC\n+TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC\n+ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT\n+CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC\n+CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA\n+CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT\n+TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA\n+AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG\n+ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA\n+GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT\n+CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT\n+GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT\n+ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG\n+TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT\n+CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG\n+TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC\n+CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA\n+GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA\n+AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC\n+AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT\n+CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG\n+TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC\n+TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC\n+ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG\n+TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA\n+TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT\n+TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC\n+TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC\n+TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG\n+TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT\n+GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC\n+CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT\n+TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA\n+GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG\n+GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA\n+AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT\n+TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA\n+AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC\n+TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT\n+CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG\n+AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG\n+AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA\n+CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT\n+CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG\n+CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG\n+TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG\n+CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT\n+GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA\n+GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC\n+TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG\n+GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT\n+CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA\n+AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT\n+CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA\n+GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA\n+TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC\n+AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA\n+GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG\n+CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA\n+TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT\n+GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG\n+TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA\n+TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA\n+AACCTAAATCAGATC'..b'TGTCCTTGTGTGACACAGGCTCTA\n+AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC\n+AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG\n+AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC\n+ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT\n+AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA\n+AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT\n+ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT\n+TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT\n+ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA\n+TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA\n+TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT\n+GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA\n+ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA\n+TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG\n+GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT\n+TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT\n+ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA\n+TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG\n+AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA\n+AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC\n+GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT\n+TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG\n+ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG\n+ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA\n+CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA\n+CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT\n+TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG\n+GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG\n+GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC\n+CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA\n+AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC\n+TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG\n+TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC\n+AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC\n+AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT\n+TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA\n+TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC\n+ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA\n+GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG\n+GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT\n+GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC\n+AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA\n+ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC\n+TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT\n+AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT\n+CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC\n+TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT\n+TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT\n+TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA\n+GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG\n+AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG\n+ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT\n+TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA\n+CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA\n+AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG\n+CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA\n+AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA\n+CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG\n+AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC\n+TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC\n+CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC\n+TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT\n+TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC\n+TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA\n+GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT\n+AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA\n+TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT\n+ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG\n+CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA\n+TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC\n+TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC\n+CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT\n+TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC\n+AAGCACCCATGCCTAAATCA\n' |
| b |
| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_rattus.fasta.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_dfam_rattus.fasta.stats Thu May 20 12:56:42 2021 +0000 |
| b |
| @@ -0,0 +1,53 @@ +================================================== +file name: rm_input.fasta +sequences: 1 +total length: 14220 bp (14220 bp excl N/X-runs) +GC level: 39.94 % +bases masked: 378 bp ( 2.66 %) +================================================== + number of length percentage + elements* occupied of sequence +-------------------------------------------------- +SINEs: 0 0 bp 0.00 % + Alu/B1 0 0 bp 0.00 % + B2-B4 0 0 bp 0.00 % + IDs 0 0 bp 0.00 % + MIRs 0 0 bp 0.00 % + +LINEs: 0 0 bp 0.00 % + LINE1 0 0 bp 0.00 % + LINE2 0 0 bp 0.00 % + L3/CR1 0 0 bp 0.00 % + +LTR elements: 0 0 bp 0.00 % + ERVL 0 0 bp 0.00 % + ERVL-MaLRs 0 0 bp 0.00 % + ERV_classI 0 0 bp 0.00 % + ERV_classII 0 0 bp 0.00 % + +DNA elements: 0 0bp 0.00 % + hAT-Charlie 0 0 bp 0.00 % + TcMar-Tigger 0 0 bp 0.00 % + +Unclassified: 0 0 bp 0.00 % + +Total interspersed repeats: 0 bp 0.00 % + + +Small RNA: 0 0 bp 0.00 % + +Satellites: 0 0 bp 0.00 % +Simple repeats: 7 378 bp 2.66 % +Low complexity: 0 0 bp 0.00 % +================================================== + +* most repeats fragmented by insertions or deletions + have been counted as one element + Runs of >=20 X/Ns in query were excluded in % calcs + + +The query species was assumed to be rattus +RepeatMasker version 4.1.2-p1 , default mode + +run with rmblastn version 2.10.0+ +FamDB: CONS-Dfam_3.3 |
| b |
| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_up.fasta.cat --- a/test-data/small_dfam_up.fasta.cat Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam_up.fasta.cat Thu May 20 12:56:42 2021 +0000 |
| b |
| @@ -98,6 +98,6 @@ ## Total Length: 14220 ## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 ## Total NonSub ( excluding all non ACGT bases ):14220 -RepeatMasker version 4.1.1 , default mode +RepeatMasker version 4.1.2-p1 , default mode run with rmblastn version 2.10.0+ RM Library: CONS-_ |
| b |
| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_up.fasta.log --- a/test-data/small_dfam_up.fasta.log Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam_up.fasta.log Thu May 20 12:56:42 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID +SW scoret% div.t% del.t% ins.tquery sequencetpos in query: begintendt(left)trepeattclass/familytpos in repeat: begintendt(left)tID 18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 |
| b |
| diff -r bfc70c8cc5ca -r 72aade318318 test-data/small_dfam_up.fasta.stats --- a/test-data/small_dfam_up.fasta.stats Fri Dec 11 22:26:02 2020 +0000 +++ b/test-data/small_dfam_up.fasta.stats Thu May 20 12:56:42 2021 +0000 |
| b |
| @@ -47,7 +47,7 @@ The query species was assumed to be rodent -RepeatMasker version 4.1.1 , default mode - +RepeatMasker version 4.1.2-p1 , default mode + run with rmblastn version 2.10.0+ - +FamDB: CONS-_ |