| Previous changeset 0:16e44ec438c4 (2017-10-19) Next changeset 2:d3a2072d8745 (2019-05-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit a1535cdf1f6fe06a9b11110c0c9627eef732d398 |
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modified:
maker.xml test-data/annot.gff3 test-data/annot_mapped.gff3 test-data/annot_reuse.gff3 test-data/evidences.gff3 test-data/evidences_reuse.gff3 |
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added:
test-data/annot_repbase.gff3 test-data/fake_repbase.embl |
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| diff -r 16e44ec438c4 -r 73a79dec987b maker.xml --- a/maker.xml Thu Oct 19 15:58:39 2017 -0400 +++ b/maker.xml Sun Jul 01 16:12:18 2018 -0400 |
| [ |
| b'@@ -1,11 +1,19 @@\n <?xml version="1.0"?>\n-<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">\n+<tool id="maker" name="Maker" profile="16.04" version="@VERSION@.1">\n <description>genome annotation pipeline</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <command><![CDATA[\n+ RM_LIB_PATH=\\$(dirname \\$(which RepeatMasker))/../share/RepeatMasker/Libraries &&\n+ mkdir lib &&\n+ export REPEATMASKER_LIB_DIR=\\$(pwd)/lib &&\n+ for file in \\$(ls \\$RM_LIB_PATH) ; do ln -s \\$RM_LIB_PATH/\\$file lib/\\$file ; done &&\n+ #if $repeat_masking.repeat_source.source_type == "repbase":\n+ cp \'${repeat_masking.repeat_source.repbase_file}\' \'lib/${repeat_masking.repeat_source.repbase_file_name}\' &&\n+ #end if\n+\n maker -CTL\n \n &&\n@@ -104,28 +112,41 @@\n #end if\n \n #-----Repeat Masking (leave values blank to skip repeat masking)\n-#if $repeat_masking.repeatmasker.do_rm == \'simple\'\n-model_org=simple # select a model organism for RepBase masking in RepeatMasker\n+#if $repeat_masking.repeat_source.source_type == \'repbase\'\n+\n+#if $repeat_masking.repeat_source.species_source.species_from_list == \'yes\'\n+model_org=${repeat_masking.repeat_source.species_source.species_list}\n+#else\n+model_org=${repeat_masking.repeat_source.species_source.species_name}\n+#end if\n+\n rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker\n-#else if $repeat_masking.repeatmasker.do_rm == \'lib\'\n+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n+\n+#else if $repeat_masking.repeat_source.source_type == \'library\'\n model_org= # select a model organism for RepBase masking in RepeatMasker\n-rmlib=${repeat_masking.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker\n+rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker\n+\n+#if $repeat_masking.repeat_source.repeat_protein\n+repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner\n+#else\n+repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner\n+#end if\n+#if $repeat_masking.repeat_source.rm_gff\n+rm_gff=${repeat_masking.repeat_source.rm_gff} # pre-identified repeat elements from an external GFF3 file\n+#else\n+rm_gff= # pre-identified repeat elements from an external GFF3 file\n+#end if\n+\n+softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n+\n #else\n model_org= # select a model organism for RepBase masking in RepeatMasker\n rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker\n-#end if\n-#if $repeat_masking.repeat_protein\n-repeat_protein=${repeat_masking.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner\n-#else\n-repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner\n+softmask=0 # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n #end if\n-#if $repeat_masking.rm_gff\n-rm_gff=${repeat_masking.rm_gff} # pre-identified repeat elements from an external GFF3 file\n-#else\n-rm_gff= # pre-identified repeat elements from an external GFF3 file\n-#end if\n+\n prok_rm=0 # forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no\n-softmask=${repeat_masking.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)\n \n #-----Gene Prediction\n #if $abinitio_gene_prediction.snaphmm\n@@ -359,32 +380,69 @@\n </section>\n \n <section name="repeat_masking" title="Repeat masking" expanded="True">\n- <conditional name="repeatmasker">\n- <param name="do_rm" type="select" label="Enabl'..b' <output name="output_evidences" file="evidences_proc.gff3" compare="sim_size"/>\n </test>\n@@ -445,6 +505,7 @@\n <param name="reannotation|maker_gff" value="evidences.gff3"/>\n <param name="reannotation|est_pass" value="true"/>\n <param name="est_evidences|est2genome" value="1"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="no"/>\n <output name="output_gff" file="annot_reuse.gff3"/>\n <output name="output_evidences" file="evidences_reuse.gff3" compare="sim_size"/>\n </test>\n@@ -455,6 +516,7 @@\n <param name="abinitio_gene_prediction|aug_prediction|augustus_species" value="human"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="no"/>\n <output name="output_gff" file="annot_human.gff3" compare="sim_size"/>\n <output name="output_evidences" file="evidences_human.gff3" compare="sim_size"/>\n </test>\n@@ -465,6 +527,7 @@\n <param name="abinitio_gene_prediction|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="no"/>\n <output name="output_gff" file="annot_model.gff3" compare="sim_size"/>\n <output name="output_evidences" file="evidences_model.gff3" compare="sim_size"/>\n </test>\n@@ -472,10 +535,21 @@\n <param name="genome" value="genome.fasta"/>\n <param name="est_evidences|est" value="est.fasta"/>\n <param name="est_evidences|est2genome" value="1"/>\n- <param name="repeat_masking|repeatmasker|do_rm" value="no"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="no"/>\n <output name="output_gff" file="annot_norm.gff3"/>\n <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>\n </test>\n+ <test>\n+ <param name="genome" value="genome.fasta"/>\n+ <param name="est_evidences|est" value="est.fasta"/>\n+ <param name="est_evidences|est2genome" value="1"/>\n+ <param name="repeat_masking|repeat_source|source_type" value="repbase"/>\n+ <param name="repeat_masking|repeat_source|repbase_file" value="fake_repbase.embl" />\n+ <param name="repeat_masking|repeat_source|repbase_file_name" value="fake.embl" />\n+ <param name="repeat_masking|repeat_source|species_list" value="anopheles" />\n+ <output name="output_gff" file="annot_repbase.gff3"/>\n+ <output name="output_evidences" file="evidences_norm.gff3" compare="sim_size"/>\n+ </test>\n </tests>\n <help><![CDATA[\n MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER\'s inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.\n' |
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| diff -r 16e44ec438c4 -r 73a79dec987b test-data/annot.gff3 --- a/test-data/annot.gff3 Thu Oct 19 15:58:39 2017 -0400 +++ b/test-data/annot.gff3 Sun Jul 01 16:12:18 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 ### -### HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 ### -### |
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| diff -r 16e44ec438c4 -r 73a79dec987b test-data/annot_mapped.gff3 --- a/test-data/annot_mapped.gff3 Thu Oct 19 15:58:39 2017 -0400 +++ b/test-data/annot_mapped.gff3 Sun Jul 01 16:12:18 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=YES000002-RA:cds;Parent=YES000002-RA; HS08198 maker CDS 1772 1848 . + 2 ID=YES000002-RA:cds;Parent=YES000002-RA; ### -### HS04636 maker gene 1813 6903 . + . ID=YES000001;Name=YES000001;Alias=maker-HS04636-exonerate_est2genome-gene-0.0; HS04636 maker mRNA 1813 6903 8728 + . ID=YES000001-RA;Parent=YES000001;Name=YES000001-RA;Alias=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_QI=49|1|1|1|0|0|9|0|572;_eAED=0.00; HS04636 maker exon 1813 1934 . + . ID=YES000001-RA:exon:0;Parent=YES000001-RA; @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=YES000001-RA:cds;Parent=YES000001-RA; HS04636 maker CDS 6494 6903 . + 2 ID=YES000001-RA:cds;Parent=YES000001-RA; ### -### |
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| diff -r 16e44ec438c4 -r 73a79dec987b test-data/annot_repbase.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annot_repbase.gff3 Sun Jul 01 16:12:18 2018 -0400 |
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| @@ -0,0 +1,43 @@ +##gff-version 3 +HS08198 maker gene 352 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0 +HS08198 maker mRNA 352 1848 2869 + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192 +HS08198 maker exon 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 421 582 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 812 894 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1053 1123 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1208 1315 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1587 1688 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker exon 1772 1848 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 352 397 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker five_prime_UTR 421 444 . + . ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 445 582 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 812 894 . + 0 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1053 1123 . + 1 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1208 1315 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1 +### +### +HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0 +HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 +HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2055 2198 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 2852 2995 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 3426 3607 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4340 4423 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 4543 4789 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5072 5358 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 5860 6007 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker exon 6494 6903 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker five_prime_UTR 1813 1861 . + . ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 1862 1934 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2055 2198 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 2852 2995 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 3426 3607 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4340 4423 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 4543 4789 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5072 5358 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1 +### +### |
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| diff -r 16e44ec438c4 -r 73a79dec987b test-data/annot_reuse.gff3 --- a/test-data/annot_reuse.gff3 Thu Oct 19 15:58:39 2017 -0400 +++ b/test-data/annot_reuse.gff3 Sun Jul 01 16:12:18 2018 -0400 |
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| @@ -17,7 +17,6 @@ HS08198 maker CDS 1587 1688 . + 2 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 HS08198 maker CDS 1772 1848 . + 2 ID=maker-HS08198-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-est2genome-gene-0.0-mRNA-1 ### -### HS04636 maker gene 1813 6903 . + . ID=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0;score=8728 HS04636 maker mRNA 1813 6903 8728 + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-est2genome-gene-0.0;Name=maker-HS04636-est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572 HS04636 maker exon 1813 1934 . + . ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 @@ -40,4 +39,3 @@ HS04636 maker CDS 5860 6007 . + 0 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 HS04636 maker CDS 6494 6903 . + 2 ID=maker-HS04636-est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-est2genome-gene-0.0-mRNA-1 ### -### |
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| diff -r 16e44ec438c4 -r 73a79dec987b test-data/evidences.gff3 --- a/test-data/evidences.gff3 Thu Oct 19 15:58:39 2017 -0400 +++ b/test-data/evidences.gff3 Sun Jul 01 16:12:18 2018 -0400 |
| b |
| b'@@ -1,62 +1,42 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n ###\n-HS08198\trepeatmasker\tmatch\t578\t651\t13\t+\t.\tID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +\n-HS08198\trepeatmasker\tmatch_part\t578\t651\t13\t+\t.\tID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +\n-###\n-HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:11:3.2.0.0;Name=HS08198.g2\n-HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:28:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n-HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:29:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n-HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:30:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n-HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:31:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:32:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n-HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:33:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n-HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:34:3.2.0.0;Parent=HS08198:hit:11:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n-HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:12:3.2.0.0;Name=HS08198.g2\n-HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:35:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15\n-HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:36:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 53 217 +;Gap=M4 I2 M3 I3 M5 D1 M9 D1 M139\n-HS08198\test2genome\tmatch_part\t812\t894\t2869\t+\t.\tID=HS08198:hsp:37:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:38:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:39:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:40:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:41:3.2.0.0;Parent=HS08198:hit:12:3.2.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:2:3.2.0.0;Name=HS08198.g2\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:19:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:20:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:21:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:22:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n+HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:23:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n+HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:24:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n+HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:25:3.2.0.0;Parent=HS08198:hit:2:3.2.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n+HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:3:3.2.0.0;Name=HS08198.g2\n+HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:26:3.2.0.0;Parent=HS08198:hit:3:3.2.0.0;Target=HS08198.g2 3 52 +;Gap=M18 D1 M2 I4 M10 I1 M15\n+HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:27:3.2.0.0;Pa'..b'p=M122\n-HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:19:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:20:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n-HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:21:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n-HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:22:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n-HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:23:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n-HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:24:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n-HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:25:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n-HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:26:3.2.0.0;Parent=HS04636:hit:9:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n+HS04636\tblastn\texpressed_sequence_match\t1815\t6903\t120\t+\t.\tID=HS04636:hit:0:3.2.0.0;Name=HS04636.g1\n+HS04636\tblastn\tmatch_part\t1815\t1934\t120\t+\t.\tID=HS04636:hsp:0:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 129 248 +;Gap=M120\n+HS04636\tblastn\tmatch_part\t1815\t1845\t31\t+\t.\tID=HS04636:hsp:1:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 50 80 +;Gap=M31\n+HS04636\tblastn\tmatch_part\t2055\t2198\t144\t+\t.\tID=HS04636:hsp:2:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\tblastn\tmatch_part\t2852\t2997\t146\t+\t.\tID=HS04636:hsp:3:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 393 538 +;Gap=M146\n+HS04636\tblastn\tmatch_part\t3424\t3609\t186\t+\t.\tID=HS04636:hsp:4:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 535 720 +;Gap=M186\n+HS04636\tblastn\tmatch_part\t4339\t4423\t85\t+\t.\tID=HS04636:hsp:5:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 718 802 +;Gap=M85\n+HS04636\tblastn\tmatch_part\t4542\t4790\t249\t+\t.\tID=HS04636:hsp:6:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 802 1050 +;Gap=M249\n+HS04636\tblastn\tmatch_part\t5068\t5360\t293\t+\t.\tID=HS04636:hsp:7:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1046 1338 +;Gap=M293\n+HS04636\tblastn\tmatch_part\t5859\t6008\t150\t+\t.\tID=HS04636:hsp:8:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1336 1485 +;Gap=M150\n+HS04636\tblastn\tmatch_part\t6490\t6903\t414\t+\t.\tID=HS04636:hsp:9:3.2.0.0;Parent=HS04636:hit:0:3.2.0.0;Target=HS04636.g1 1481 1894 +;Gap=M414\n+HS04636\test2genome\texpressed_sequence_match\t1813\t6903\t8728\t+\t.\tID=HS04636:hit:1:3.2.0.0;Name=HS04636.g1\n+HS04636\test2genome\tmatch_part\t1813\t1934\t8728\t+\t.\tID=HS04636:hsp:10:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 127 248 +;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:11:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:12:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:13:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:14:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:15:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:16:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:17:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:18:3.2.0.0;Parent=HS04636:hit:1:3.2.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n' |
| b |
| diff -r 16e44ec438c4 -r 73a79dec987b test-data/evidences_reuse.gff3 --- a/test-data/evidences_reuse.gff3 Thu Oct 19 15:58:39 2017 -0400 +++ b/test-data/evidences_reuse.gff3 Sun Jul 01 16:12:18 2018 -0400 |
| b |
| b'@@ -1,62 +1,42 @@\n ##gff-version 3\n HS08198\t.\tcontig\t1\t2344\t.\t.\t.\tID=HS08198;Name=HS08198\n ###\n-HS08198\trepeatmasker\tmatch\t578\t651\t13\t+\t.\tID=HS08198:hit:10:1.3.0.0;Name=species:%28AGAAGGT%29n|genus:Simple_repeat;Target=species:%28AGAAGGT%29n|genus:Simple_repeat 1 75 +\n-HS08198\trepeatmasker\tmatch_part\t578\t651\t13\t+\t.\tID=HS08198:hsp:27:1.3.0.0;Parent=HS08198:hit:10:1.3.0.0;Target=species:%2528AGAAGGT%2529n|genus:Simple_repeat 1 75 +\n-###\n-HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:11:3.12.0.0;Name=HS08198.g2;score=140\n-HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:28:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n-HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:29:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n-HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:30:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n-HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:31:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\tblastn\tmatch_part\t1206\t1315\t110\t+\t.\tID=HS08198:hsp:32:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 370 479 +;Gap=M110\n-HS08198\tblastn\tmatch_part\t1586\t1689\t104\t+\t.\tID=HS08198:hsp:33:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 479 582 +;Gap=M104\n-HS08198\tblastn\tmatch_part\t1771\t1848\t78\t+\t.\tID=HS08198:hsp:34:3.12.0.0;Parent=HS08198:hit:11:3.12.0.0;Target=HS08198.g2 581 658 +;Gap=M78\n-HS08198\test2genome\texpressed_sequence_match\t352\t1848\t2869\t+\t.\tID=HS08198:hit:12:3.12.0.0;Name=HS08198.g2;score=2869\n-HS08198\test2genome\tmatch_part\t352\t397\t2869\t+\t.\tID=HS08198:hsp:35:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 3 52 +;Gap=M46\n-HS08198\test2genome\tmatch_part\t421\t582\t2869\t+\t.\tID=HS08198:hsp:36:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 53 217 +;Gap=M162\n-HS08198\test2genome\tmatch_part\t812\t894\t2869\t+\t.\tID=HS08198:hsp:37:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 218 300 +;Gap=M83\n-HS08198\test2genome\tmatch_part\t1053\t1123\t2869\t+\t.\tID=HS08198:hsp:38:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 301 371 +;Gap=M71\n-HS08198\test2genome\tmatch_part\t1208\t1315\t2869\t+\t.\tID=HS08198:hsp:39:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 372 479 +;Gap=M108\n-HS08198\test2genome\tmatch_part\t1587\t1688\t2869\t+\t.\tID=HS08198:hsp:40:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 480 581 +;Gap=M102\n-HS08198\test2genome\tmatch_part\t1772\t1848\t2869\t+\t.\tID=HS08198:hsp:41:3.12.0.0;Parent=HS08198:hit:12:3.12.0.0;Target=HS08198.g2 582 658 +;Gap=M77\n+HS08198\tblastn\texpressed_sequence_match\t444\t1848\t140\t+\t.\tID=HS08198:hit:2:3.12.0.0;Name=HS08198.g2;score=140\n+HS08198\tblastn\tmatch_part\t444\t583\t140\t+\t.\tID=HS08198:hsp:19:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 79 218 +;Gap=M140\n+HS08198\tblastn\tmatch_part\t445\t523\t79\t+\t.\tID=HS08198:hsp:20:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 1 79 +;Gap=M79\n+HS08198\tblastn\tmatch_part\t808\t895\t88\t+\t.\tID=HS08198:hsp:21:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 214 301 +;Gap=M88\n+HS08198\tblastn\tmatch_part\t1053\t1123\t71\t+\t.\tID=HS08198:hsp:22:3.12.0.0;Parent=HS08198:hit:2:3.12.0.0;Target=HS08198.g2 301 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+;Gap=M122\n+HS04636\test2genome\tmatch_part\t2055\t2198\t8728\t+\t.\tID=HS04636:hsp:11:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 249 392 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t2852\t2995\t8728\t+\t.\tID=HS04636:hsp:12:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 393 536 +;Gap=M144\n+HS04636\test2genome\tmatch_part\t3426\t3607\t8728\t+\t.\tID=HS04636:hsp:13:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 537 718 +;Gap=M182\n+HS04636\test2genome\tmatch_part\t4340\t4423\t8728\t+\t.\tID=HS04636:hsp:14:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 719 802 +;Gap=M84\n+HS04636\test2genome\tmatch_part\t4543\t4789\t8728\t+\t.\tID=HS04636:hsp:15:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 803 1049 +;Gap=M247\n+HS04636\test2genome\tmatch_part\t5072\t5358\t8728\t+\t.\tID=HS04636:hsp:16:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1050 1336 +;Gap=M287\n+HS04636\test2genome\tmatch_part\t5860\t6007\t8728\t+\t.\tID=HS04636:hsp:17:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1337 1484 +;Gap=M148\n+HS04636\test2genome\tmatch_part\t6494\t6903\t8728\t+\t.\tID=HS04636:hsp:18:3.12.0.0;Parent=HS04636:hit:1:3.12.0.0;Target=HS04636.g1 1485 1894 +;Gap=M410\n' |
| b |
| diff -r 16e44ec438c4 -r 73a79dec987b test-data/fake_repbase.embl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_repbase.embl Sun Jul 01 16:12:18 2018 -0400 |
| b |
| @@ -0,0 +1,21 @@ +CC Fake repbase-like embl file, using data from DfamConsensus.embl* +CC **************************************************************** +XX +ID ACROBAT1 repeatmasker; DNA; ???; 768 BP. +CC consensus - See RepBase for additional annotations. +XX +SQ Sequence 768 BP; 178 A; 194 C; 215 G; 181 T; 0 other; + ggtgatgctg ccaacttact gatttagtgt atgatggtgt ttttgaggtg ctccagtggc 60 + ttctgtttct atcagctgtc cctcctgttc agctactgac ggggtggtgc gtaacggcaa 120 + aagcaccgcc ggacatcagc gctatctctg ctctcactgc cgtaaaacat ggcaactgca 180 + gttcacttac accgcttctc aacccggtac gcaccagaaa atcattgata tggccatgaa 240 + tggcgttgga tgccgggcaa cagcccgcat tatgggcgtt ggcctcaaca cgattttacg 300 + tcacttaaaa aactcaggcc gcagtcggta acctcgcgca tacagccggg cagtgacgtc 360 + atcgtctgcg cggaaatgga cgaacagtgg ggctatgtcg gggctaaatc gcgccagcgc 420 + tggctgtttt acgcgtatga cagtctccgg aagacggttg ttgcgcacgt attcggtgaa 480 + cgcactatgg cgacgctggg gcgtcttatg agcctgctgt caccctttga cgtggtgata 540 + tggatgacgg atggctggcc gctgtatgaa tcccgcctga agggaaagct gcacgtaatc 600 + agcaagcgat atacgcagcg aattgagcgg cataacctga atctgaggca gcacctggca 660 + cggctgggac ggaagtcgct gtcgttctca aaatcggtgg agctgcatga caaagtcatc 720 + gggcattatc tgaacataaa acactatcaa taagttggag tcattacc 768 +// |