| Next changeset 1:19f42b3ea391 (2022-09-01) |
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Commit message:
planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379 |
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added:
isescan.xml macro.xml test-data/NC_012624.fna test-data/TEST_1/test_1.fna.gff test-data/TEST_1/test_1.fna.is.fna test-data/TEST_1/test_1.fna.orf.faa test-data/TEST_1/test_1.fna.orf.fna test-data/TEST_1/test_1.fna.sum test-data/TEST_1/test_1.fna.tsv test-data/TEST_1/test_1.log test-data/test_2.fna.gff test-data/test_2.fna.is.fna test-data/test_2.fna.orf.faa test-data/test_2.fna.orf.fna test-data/test_2.fna.sum test-data/test_2.fna.tsv test-data/test_2.log |
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| diff -r 000000000000 -r debe9c750cdd isescan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isescan.xml Thu Sep 01 09:29:56 2022 +0000 |
| [ |
| @@ -0,0 +1,87 @@ +<tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description> Insertion Sequence Elements detection in prokaryotic genomes </description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro='xrefs'/> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_file' input && + isescan.py + --seqfile input + --output 'results' + $remove_short_is + --nthread \${GALAXY_SLOTS:-7} + #if '$log_activate' + | tee '$logfile' + #end if + ]]> + </command> + <inputs> + <param name="input_file" type="data" format="fasta" label="Genome fasta input" help="Fasta sequence to analyse for IS"/> + <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue="" + label="Remove incomplete IS elements" + help="Remove partial IS elements which include IS element with length > 400 or single copy IS element without perfect TIR"/> + <param name="log_activate" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Keep the log file"/> + </inputs> + <outputs> + <data format="txt" name="logfile" from_work_dir="results"> + <filter> log_activate == True </filter> + </data> + <data format="tabular" name="summary" from_work_dir="results/input.sum"/> + <data format="tabular" name="all_results" from_work_dir="results/input.tsv"/> + <data format="gff" name="annotation" from_work_dir="results/input.gff"/> + <data format="fasta" name="is_fasta" from_work_dir="results/input.is.fna"/> + <data format="fasta" name="orf_fna" from_work_dir="results/input.orf.fna"/> + <data format="fasta" name="orf_faa" from_work_dir="results/input.orf.faa"/> + </outputs> + <tests> + <test expect_num_outputs="7"> <!-- TEST_1 default parameters --> + <param name="input_file" value="NC_012624.fna"/> + <output name="logfile" value="TEST_1/test_1.log" lines_diff="70"/> + <output name="summary" value="TEST_1/test_1.fna.sum" lines_diff="2"/> + <output name="all_results" value="TEST_1/test_1.fna.tsv" lines_diff="1"/> + <output name="annotation" value="TEST_1/test_1.fna.gff" lines_diff="1"/> + <output name="is_fasta" value="TEST_1/test_1.fna.is.fna" lines_diff="1"/> + <output name="orf_fna" value="TEST_1/test_1.fna.orf.fna" lines_diff="1"/> + <output name="orf_faa" value="TEST_1/test_1.fna.orf.faa" lines_diff="1"/> + </test> + <test expect_num_outputs="7"> <!-- TEST_1 remove short is --> + <param name="input_file" value="NC_012624.fna"/> + <param name="remove_short_is" value="true"/> + <output name="logfile" value="test_2.log" lines_diff="50"/> + <output name="summary" value="test_2.fna.sum" lines_diff="1"/> + <output name="all_results" value="test_2.fna.tsv" lines_diff="1"/> + <output name="annotation" value="test_2.fna.gff" lines_diff="1"/> + <output name="is_fasta" value="test_2.fna.is.fna" lines_diff="1"/> + <output name="orf_fna" value="test_2.fna.orf.fna" lines_diff="1"/> + <output name="orf_faa" value="test_2.fna.orf.faa" lines_diff="1"/> + </test> + <test expect_num_outputs="6"> <!-- TEST_1 remove short is and no logfile --> + <param name="input_file" value="NC_012624.fna"/> + <param name="remove_short_is" value="true"/> + <param name="log_activate" value="False"/> + <output name="summary" value="test_2.fna.sum" lines_diff="1"/> + <output name="all_results" value="test_2.fna.tsv" lines_diff="1"/> + <output name="annotation" value="test_2.fna.gff" lines_diff="1"/> + <output name="is_fasta" value="test_2.fna.is.fna" lines_diff="1"/> + <output name="orf_fna" value="test_2.fna.orf.fna" lines_diff="1"/> + <output name="orf_faa" value="test_2.fna.orf.faa" lines_diff="1"/> + </test> + </tests> + <help><![CDATA[ + **What it does** + ISEScan is a python pipeline to identify Insertion Sequence elements (both complete and incomplete IS elements) in genome. + If you want isescan to report only complete IS elements, you need to set command removeShortIS. + + **Input data** + ISEScan accept fasta file format as input + + **Parameters** + You can remove the short partial IS elements which include IS element with length < 400 or single copy IS element without perfect TIR/> + + ]]> + </help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r debe9c750cdd macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Thu Sep 01 09:29:56 2022 +0000 |
| [ |
| @@ -0,0 +1,23 @@ +<macros> + <token name="@TOOL_VERSION@">1.7.2.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="version_command"> + <version_command><![CDATA[isescan.py --version]]> </version_command> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>ISEScan</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">isescan</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btx433</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r debe9c750cdd test-data/NC_012624.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012624.fna Thu Sep 01 09:29:56 2022 +0000 |
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| b'@@ -0,0 +1,605 @@\n+>gi|228288719|ref|NC_012624.1| Sulfolobus islandicus Y.N.15.51 plasmid pYN01, complete sequence\n+TTTTTAAAAACCCTGCATAGTGATGATCTCCAAAAAAGAGTTTTTACCTATTCTTGCATACTCTATTCCA\n+ACATATGTACTAGTGTATCCATCATTTTTTGTTAACACTCTAGCAAGGGAATTCCCATACTGGGAGGCAT\n+TCCTACTACTCTCCCTACCCTTTCTAGGGAGAGTAGTAGGATCCCTAATTTACCAATTCTTCAAATCCTA\n+CATCATACCGCTCCTAACCCTTAGCATACTCACGCTCCTACAAATCGATTTAAACATAATATTTCCCGTC\n+AGATTCTTGATCGGCATAATCTTCGGACTAATGACCAGCTACGCAGTTGACAATGCTGTTAAAACGAACA\n+ACTTAGTGTTAGGTTTAACCACAGCGGGCTGGAGTATAGGATGGATACTATCATATATAGCATATACAAC\n+AATCCATAATTGGAATCAAATATGCATAATCAGCAGCATAATAATAGTATCCATAGCACTCCTAGACAGA\n+AGAGTAAGCCTAGATAAAATCAAAATCAATATAAGCTTACCAAAAACGTCATCCATAATAGTCTACTTCT\n+CAGCGTTAACCCCGGCATTCACACTACAAATAATTCCGAGCATATTCGAAAAAGCACACACAACATGGCT\n+AATACTCCCTTCGTATCTACTTTCCATAGCTGCGTATACTATACTACCAATAATAGCAAGCAAAATAGGA\n+CTAAAGAGATGCATCATAATAACAACCCTAGGAATACTAATTAGTGGAATAACAACATTCCTAATAACAC\n+CCTACACCCTATTACCATATACCTCACTAGGACTAGGAATACTTTCACTAATACCGAAATACTTAACAAC\n+GAAAAACGAAAAAGCCAACACTCTGGGAATAGCCCTAAATATAGGATCAATAGGAGGACTAATAATACCA\n+ACGCTATACACAATAATACCGACAAGCCCAGAATCAATACTCATAATAACTTCAATAATATTGTTAACAA\n+TCTAAAAAATTGTAATGAGGGTTTTTAAAAACCCCAAAAGTGAAGGTGGTGAAATGATTTCGCCTGACTT\n+AGCAATAAAAATTCTTCTATTAGTTCCTTCAGTAATATTCTTCTTCTACAGTGCAGTATATTTAATGTTA\n+TTTGAGCTAAATGTACAACCTAAACTGAGCAAATTCTACAGAAATACTAGTCTAGTTTTAGCTGGAGGTG\n+GTATACTATTATTGACAATTTATTTAATGATTTAGATAGCATAGATGATATAATTTTAATAATATTGGCA\n+AATGCTAACGGAACTGTTAAAGAAATGGCAGAGAAAACGGGAATAAAAGAAGAAGCTGTATATCATCTTT\n+TAGAATTTCTAACAATAGCTGGGATTGTGAAGAAAGAGAATGATAGATATTCTATAGATAAAACAATGAG\n+AACTATAGCTCAACTTTTGATAGATTTTAAAGACGGAGATGACGTGAATTGAAGAAAATAGTAATAAAAA\n+CAGAACTTCCTTATAATTATAGAAAGCTTAAGGGATTTTTCATTTCACCTGGGGTGCTCAGATTATTTTA\n+TGACGTAAAGAGTGTAGAAGTTGCAGGGAATTTATCATATATTATTAACAACAAGTACAATGCAATAATG\n+TATTTCAGTAATGTTGATATTGTATGGGAGATTTATAATGGTAGATTAAAGGATAAGATCTCAGTATGGT\n+TATATCCAATTGGTGATAATACAGGATTACACTTGAAATTCGAAACTAATAGAATACTCCCGCTAAAGAA\n+ACCTCTAGAAAATGAAGTCAAAGCAGGAGTAGAATTGCTAAAAAGTTTGTTAGATGCTTTGAGGAGGTTC\n+TGATGAAGTTAAGAACCCATTACATCTTCTCAACCGGTTTATTGACGCTTCTGGACTCTGTACTCTTTCA\n+TGAATATTTTTACTACGCTTTAATCTTGAGCGGAATAGTTTCGGTAATAGGTAATTCCTTGATTGATAGG\n+ATTGGCCATAAGGAGATTGCCACTAGGTATGGGTATATCCCGGTAAGGACACCTTTAACCCATACAATTC\n+CTAGAAGTGTAGTTTGGGGTATTGTCTCCGTAGTCCCGGTCTTTATTCTCTTATTGATTTATTATTATGG\n+GTTTAGCTATCACGAGTACTATTTCTCCCTTAGCAATAAGGTGGTGTTGTTAATATTGTTAAATGGTGTA\n+GTTGTTGGGCCCTCTCATTTGTTCCTGGACGTATTTACGGAAAGGGGAATATATCATAAAGTAAATGGTA\n+AGTGGAGGAGATTCGCATTGGCACACTTCTCCTATGATAACCCCTTAGTAAATGGATTAGCAATCTTACT\n+AGGAATTATAATGCTGCTAGCAGCACTTTATCTACATAACTACCATTATTACAACTATTATTTCTAACGA\n+GATAATAATAGTATAAAGATAAAAACAAAAAAGTTTTTAAATCTGTTTTTACAGAAGTAGAAATGGGGGA\n+TGAGGGGATGATGAGTAGGGTCAGAATTGACCTATGATAGGACACTCGGCAGCTGACCTGACCCCCTCAT\n+CCCTAATTTATTCTTACCTTATCTAACTATTAAGCTTTTCTTCTCATTGAATTTTGAAAAATTGAGCAAA\n+GAATGAGGTTGGATCCTAACGTTAAATTTACGACGTGAGAAAAATTCAATAAACTCCCCAGTTTGCTAAG\n+AAAAATTCTTTCTTCTAATTTCTTAATCTCATCTAATTTTGTATTATTAGCTAATAATGTACAATAAATG\n+CAGCTGAGGAGTGATATGATGCAACATAGATACGCTAAACATTCTCTATAATAAACTGAAATATGATAAT\n+GTATTCGAATTGAATTAAGCATCTTTATAATTAGGCAAATTTGTATAACACAAATATAAGTGTGCGTAAT\n+TATTGCAGAAATAGTTATCAAGACACTTGTTAAAATAAAAGAAATGATGAGAAGAGTTTTATTTCTCATA\n+ATATTATAAATTTTATTTAAAAAGCTCAGTTGAATTAACTCCAGTTTACTCTACAAAAATTCAAAGTAGT\n+TAATCCTGCACGGATCTCAAATTTTTTAGTTAAAAGAGCAAGGTAATGCGATAATGACCATAAATACTAC\n+ACTTTGTTAACCCTACTATTCCCAGTTTGGGAACTCATTTTCAGCCCCCTTCTAAGGAGGTAACACTTTG\n+TTAACCCTAGTTAAGGTTTATTAAGGGAAATTTCTCAATACAATTTTATGGAAGTTAAGATAGAGAAACA\n+TAAGTCAAGGTTTACCATTACACAATTAATTTTAATGGCTATGGCTAAAGCTCCTGGGAGCTGCTGTAGT\n+TTGGAATATTTACATGAGAAAACTGGTGTTGATAAGAAGGAGCTGCTAGTATATCTAACAAGGTTAGCCA\n+AAAGAGGAATAATAGAAAGGAAATGGCATAAAAGTAGGGCAGGGAAAGAGAGAATGTATTGTCTGAAGTA\n+TAAGGAGGATATACTATGAGCCCGCCAAATGATAAATTTTTAGAATACGCTAAAGCGCTTTTAGAAACTG\n+CAGAATCTGATTTAGATGCAAGTAAATTTCTTTGGGATTGTAATTATCAAGCTCAGTCAGTGTTTTATCT\n+TCAGCAATCAACCGAGAAGATATTTAAAGCGTTTAGGAGCATGTATCAGTACCTCTTTGTAGAATTTCCC\n+GAATTTATTACAGAGGAACTGATAGCTTCAAGTAATAGTAGAGTTACTAACTTGATGCCCTATCTTACAC\n+TGTTAAATTTAAGGTTAAAAGAGAGAAAACTGAATATTAAAGGCCTGGAAGATTTACTGAAAAAGGA'..b'G\n+ATAGACTGAGAAAAGCTCACGACGATGTTTACGTAATAGTCATAGACCCTATGAGTAACTATAACAGATT\n+CTTTGAAAATGAAGCAGATCTTAACATCGTTTTCGGAGATAATGATTATTTAGGATTGGATCCTGTTAGT\n+TTAGCTAACGAAGGAGTAGTAAGCTCTGGTGACATTGCTGATTTCTTAATAGAATCATATGGAATTCCAG\n+CTGAGCTTCGAGGCATTTTAGTAAGCCAGCTCGAGCAAAATAAATCGTTAAAAGAGCTCATGGACAATTT\n+AGAAGACTTAGCAAGCAAGAAATTTGCTACTGAATACAGAAAATTAGAGAACTTCCTATTGAATATGACA\n+ACGGGTTCTGATAAGTATGTCTTTCAAGGATCTCCGCCTAGTCTAAAGAATAAGAAATTCGTCATTTTGG\n+GATTGAAAACTGAGGACACTAGGAAGAAGCGTTTGGCAGCAACTATGCTAATGCTTTATGCATATTCACT\n+AATTAATAAACTCCCCAAGGATGTCGAGAAATTAATCCTCATCGACGAAGCCCACTTCCTCTTCGAGTAT\n+CAGTCAGTAGCTAAGATCATTGCGATCATTTACCGAACAGCCAGGGCTTTACGGACTTCAATGATCACTA\n+TGACACAACTGATACAACATTATAATATGAACAACTATAGTAGAGAAGCCTGGCAATTGGCTAACAACAA\n+ACTAATATTAAAACAAGAGAAGGAGGCAAAAGACGACCTAGTTAATTTAGCTCATCTTTCTGAAGAAGAG\n+ATTGACTATATCCTGAAATCTTCACGTGGAAGGGGAATTCTGAGGACTGGCGCAATTACTACACACATTC\n+AAATCCAACTCACTGACGAAGAAAAAGAACATTGGAGGACTGAGTGAAATGAGCTTAGTTCAGCTCATTG\n+AAAAAGCTGCGAAGAAATATAATATCAAAATAAATTCTCTCCCTAATGGTGTGATAATTCTTGTAAAAAA\n+TGACATAGGCTATGTGCAAATAGCTGCAGTTAGAAATGTTTACTATGTCAGATACTTAACGAAAAATGAA\n+GCGTATATTATACGTAACTTAAACGAAAAGATCATAGAGCTTATACTGGAAGAAAAGTTAGAAGAAACTG\n+AAGCTATCAAAATCCCTGATGTTTAATAAAAGTAAAGTTCTTTCAATTTCTTTCATTCTCTCTTCTTCAA\n+ATAATTTTTCTTTCAATTTCTGGTCAGATAAATACTTTAGTAATATCTTCTTTCTCGTCTCAGCTTTTCC\n+ATACATAATCCCTTTCTTTTTCAACAACTCATATATTCTCAATGCCTCTTCCTTGTCACCACTATATTCA\n+TATATATAATGTATAATAGGATCCTCCCTAACCACGTGCCTCAGAAGTTTCTTCTTCTGCCTAATCGCGT\n+GTCTGCCTAGTCCTTTCATTTTTAAGAATTTGATATAGTCTCTGGTTACCACTTTTCCTTCTCTTTCTAG\n+AATATATTCGTAAATCGCTAAGTAAAAAGACGCGTCCAATTTTTTCTCATCAATCTTTTGCAAAATTTTA\n+TAGAACATCTCTTTCTCTTTTTCTGTCATAACGCTCTGAAGATAATTCAGTACTATTTTCTTCATATCTT\n+TGATTTCTTTCTCAGTTTCTCTCTTTTGAGAACTTGCTCTTTCGTAATACTCTAGATTTGAATAATCTTG\n+ATATGTATAATTATCAAAGTCTACTACTTCTCCCGTACACGAGTCCACCAGAAACCCTTCGCTGTTCCTT\n+ACTTTGTAGCACTCTTGCATCAGAAAATAGAAGTATTTTAAAAGCCTGTAAGGATTTTGATGGGGAAATC\n+AGTATTACCAGTAAACTCCCCAGTTTACTAAGAAAAAAGACTTAACTTACCCAAACTGTCCCGTTCCAGA\n+TCGCTATTATTTCTGTTTTGACTGCTGCAGTGTATTGAAATGTAGCATAGAATATGTTAGGTATGTAATT\n+CGCTGACGTGAAGCATAGAGTTTCATGTAAATATGGAATATGTTGTCCAGTAGTATTAAGATAGAAGTAA\n+GTCGTCTCATTGTTAAGTGGATTAAAATAGTAGTATATGTTGCCAAACGGGACTTTATTGAACCCACTGT\n+AATATAATGCATTGTAAATATCGACAAGATATATTTCATAATTTCCAGTGATATTCATAAATATTGTATT\n+ATTGTAAATCTGTGGGATTCTGCTTATGTTAAAGAACATTATCTGATAGTTGAAATATTGCAATTTAGGC\n+CATGCAGACAAATTTAGGATATTAGCAGTTACTAAGCTCCAGTTCTCGTAGAAAGATTCAAGCTCTAGAA\n+GATTAGTAAAAACAGAAGATGTAGTATTGAAAGTATACATAACAAATTGTGATGCGAGAACGAAATACTC\n+AAACTTCCAATATTGAAAGTCTGTTTTATTAATTGTTTTCATGATATAATTATACAATGTGTGTGCTAAC\n+GTAGCGTTTTGCTCTAAATAGAACCACGAAATCGCTGCAGACTTGCTATAAATCATTTTTTGAGAGATCC\n+AGTAAGGAGGCTGTACTGTATTATCCTGAACGTTGAAAGTAAGATAGTAGTTTATTGTGTTCCAGTCTTG\n+TTGTGTGTTTAATAGTGGAATAATTTCTATATTACCAGCGTGCCAAATTCTTTCAATAGTATAATTTGCT\n+ATCTGTATGTGATCGTAAGTAACTATCGTAGTACTATTCGCAATCGGATCTGAGCTCCACGTAGTATACG\n+TAAAGTAAGCTGTAATATTTCTAGAATTGTAGATTTTATTATTAATAAGTGTCTGTGGATCTGAACCGTT\n+GTAGACTATTACCATTATTGGTAATGTCACGTTATACTCATACCAGTTGAAATTATAACTTGTAGTAGAT\n+AAATAAGGCCCTGTAGGGTAGTATATATAATAAATATATGTTGTATTATTAACAGTACGTTGATAATGTT\n+TATATCCAGCTCCAGCACTTATACTATAGCTTCCATAAACTTCTTGTGTACTTTCTGGAGGTACTGTAAT\n+CGTTCCATAGATGTAATTAGGCCCATATTCCCCTCCATACCAATAGAAAGTTGTCGCGAAACTCTGAGAA\n+TTTATCAGCTGATTATTTGCATACAGATAGGCTGTACCCCAAACTTTCATCGCGTAATACTCATAAACAT\n+AAGTAACGTTACCTTGATTGTGCGTATATTTATTATATAAATATGTATATTCGTTATATTGAACGTTTAC\n+GCTAGTTTTTACAGAAGTTTCATTAATTATTTTGTAAACTGGGGGGTTTACTGAAATTAGATCTGACGGA\n+GGATAGCTCCAGCCAGACTGAAATCCATTAGGCGCCTCGAGTGTTTTCCCATATTTTACTATTATATCCC\n+ATTTTGAATAGTTTTCTGTATCATTTTCATTTAATGGGAACGGCTGGAGTGAAGTATTCTTATAATTGGT\n+AATATTGACATAGGCACTGCTAGCTATAGATAATAGAGCACCGTATGGCCCTGGAGCAATTTCACTTGCG\n+TTTCTAGCCAATGCATCAAATAAGAGATTTAACATATTGTTGTCAGGCTTTGAGAAGTTGAATAAGATAT\n+ATGCTTCTGGAGAAATATTGTAATAAGGTGCTGGTAGATTACTGTAGCTTCCCCTAACATATTGTAGATC\n+TTGTAACGAAGGGCTTAATGTTACTGTTTTATTATAAATGTACTTAGGCCCTGGGACGCTGTAAGACCCA\n+GAACTTCCTCCTCCACTTCCTATTTGTATTGAAGAATTCTGTTGAGGTACTTTTAGATTTGCAAAACTCG\n+CTATAAATGCCAGAATTATTATTATTGCTATAAATAAAACAGAGAATCTTCTAATATCCATTCCGAATAT\n+ATTATCTCCCATTTTCACTTCCCTACCTTTAGGGG\n' |
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| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.gff Thu Sep 01 09:29:56 2022 +0000 |
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| @@ -0,0 +1,7 @@ +##gff-version 3 +gi|228288719|ref|NC_012624.1| ISEScan insertion_sequence 30355 31343 . + . ID=gi|228288719|ref|NC_012624.1|_IS_1;family=IS5;cluster=IS5_222 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 30355 30382 . + . ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 31316 31343 . + . ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1 +gi|228288719|ref|NC_012624.1| ISEScan insertion_sequence 32413 33650 . - . ID=gi|228288719|ref|NC_012624.1|_IS_2;family=ISH3;cluster=ISH3_198|ISH3||gi|15898236|ref|NP_342841 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 32413 32456 . - . ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 33607 33650 . - . ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2 |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.is.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.is.fna Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,40 @@ +>gi|228288719|ref|NC_012624.1|_30355_31343_+ IS5_222 +AGAATTATACAAAAATTTATAAATAATTATACCGAGTATTACTCATGGGAAAGAGTAAGT +ACAAGAGGGATTGGAGCAAGTACGACGAGAACGTTATAACTAGATACGAGCTAATGTTCC +CCTTCTACGTCTTCCAACACTGGTGGGAATTACTAGCAGAAGAGAATAGGAATGCCAAGA +AAACCTACAAGGCGCCAAAGGAGTTCAACGACTTCCTAGCGTTCCTGCACTTGTTCCTAC +CTTATAGGGCCATAGAAGGAGTATTGAGAGCATTAGAAAGACTGAAAATCATCCCAACAA +GCCTAGACTACTCAACAATATGGGAAAGAGTAAGAAACATGAACATAAAATTCCCAGAGG +CAAATGACCAACTTGAAGTAATAGCAGACGCAACGGGAATAAGCACAAACAAGGGAGGAC +AATACATTATAGCAAAATGGGGAAAAACCAAGGACTCAAAATTCCTCAAGATCGAAATAG +TAATGGATAAGGACCAATTCAACGTAATAAACGCTGAAGTAACCAGCAACGAGGTTCAGA +CTGCAGTTAAGACGGTTAAGGATTTACAAGATAAGGGAAAGAAGGTCAAGAAGTTTTATG +GAGATAAAGCTTATGATGCTAATGAGGTTTACAAGACTGGGGTTGAGGTTGTTGTTCCAC +CTAGGGAGAACGCCTCCACTAGACGCGGTCATCCTGCTAGGAGAAAGGCTGTAAGGGAGT +TCAAGAGGTTGGGTTATAATCGTTGGAGGGAGGAGAGGGGTTACGGTGTTAGGTGGAGGA +TTGAGTCCTTATTCTCTGCTGTGAAGCGTACTTTTGGGGAATCTGTTAGGGCTACAAGTT +TTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTATGCATGGATGGTCCACT +TGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGAGCTTGCGAATAACGTT +GAAATAAATATTAATTACTGAAAAATTCT +>gi|228288719|ref|NC_012624.1|_32413_33650_- ISH3_198|ISH3||gi|15898236|ref|NP_342841 +CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCTGACAGAATAATATCGA +TTCATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAG +CTGAGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCA +CCAAAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAA +GAAAGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGA +AAGCAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCA +AGGGATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACT +GAAGGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAG +ACCGGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGAC +GACAAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGAC +TAAGGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAG +GTTGATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTT +TAAGTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGA +TTACGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGT +GTACAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTAC +TAATCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCAT +AGAGACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGT +TTTCCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAA +GGGGGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGATGATTT +ATTCTATCTAAAAGATTTTCTATTTAAATCAATAGAACCGCTTATTAATAATATAGATTT +ATTTTCAAGGAGGTGATTTTGGGTCTACCGAATAAGGG |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.orf.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.orf.faa Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,13 @@ +>gi|228288719|ref|NC_012624.1|_30399_31298_+ +MGKSKYKRDWSKYDENVITRYELMFPFYVFQHWWELLAEENRNAKKTYKAPKEFNDFLAF +LHLFLPYRAIEGVLRALERLKIIPTSLDYSTIWERVRNMNIKFPEANDQLEVIADATGIS +TNKGGQYIIAKWGKTKDSKFLKIEIVMDKDQFNVINAEVTSNEVQTAVKTVKDLQDKGKK +VKKFYGDKAYDANEVYKTGVEVVVPPRENASTRRGHPARRKAVREFKRLGYNRWREERGY +GVRWRIESLFSAVKRTFGESVRATSFLGQVVEAKLKFWAYAWMVHLANSLVGRAPGIRV +>gi|228288719|ref|NC_012624.1|_32517_33587_- +MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK +GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK +GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK +EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY +ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE +TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.orf.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.orf.fna Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,35 @@ +>gi|228288719|ref|NC_012624.1|_30399_31298_+ +ATGGGAAAGAGTAAGTACAAGAGGGATTGGAGCAAGTACGACGAGAACGTTATAACTAGA +TACGAGCTAATGTTCCCCTTCTACGTCTTCCAACACTGGTGGGAATTACTAGCAGAAGAG +AATAGGAATGCCAAGAAAACCTACAAGGCGCCAAAGGAGTTCAACGACTTCCTAGCGTTC +CTGCACTTGTTCCTACCTTATAGGGCCATAGAAGGAGTATTGAGAGCATTAGAAAGACTG +AAAATCATCCCAACAAGCCTAGACTACTCAACAATATGGGAAAGAGTAAGAAACATGAAC +ATAAAATTCCCAGAGGCAAATGACCAACTTGAAGTAATAGCAGACGCAACGGGAATAAGC +ACAAACAAGGGAGGACAATACATTATAGCAAAATGGGGAAAAACCAAGGACTCAAAATTC +CTCAAGATCGAAATAGTAATGGATAAGGACCAATTCAACGTAATAAACGCTGAAGTAACC +AGCAACGAGGTTCAGACTGCAGTTAAGACGGTTAAGGATTTACAAGATAAGGGAAAGAAG +GTCAAGAAGTTTTATGGAGATAAAGCTTATGATGCTAATGAGGTTTACAAGACTGGGGTT +GAGGTTGTTGTTCCACCTAGGGAGAACGCCTCCACTAGACGCGGTCATCCTGCTAGGAGA +AAGGCTGTAAGGGAGTTCAAGAGGTTGGGTTATAATCGTTGGAGGGAGGAGAGGGGTTAC +GGTGTTAGGTGGAGGATTGAGTCCTTATTCTCTGCTGTGAAGCGTACTTTTGGGGAATCT +GTTAGGGCTACAAGTTTTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTAT +GCATGGATGGTCCACTTGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGA +>gi|228288719|ref|NC_012624.1|_32517_33587_- +ATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAGCTG +AGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCACCA +AAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAAGAA +AGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGAAAG +CAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCAAGG +GATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACTGAA +GGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAGACC +GGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGACGAC +AAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGACTAA +GGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAGGTT +GATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTTTAA +GTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGATTA +CGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGTGTA +CAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTACTAA +TCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCATAGA +GACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGTTTT +CCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAAGGG +GGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGA |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.sum --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.sum Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +# seqid family nIS %Genome bps4IS dnaLen +gi|228288719|ref|NC_012624.1| IS5 1 2.34 989 42245 +gi|228288719|ref|NC_012624.1| ISH3 1 2.93 1238 42245 +input total 2 5.27 2227 42245 |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.fna.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.fna.tsv Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +seqID family cluster isBegin isEnd isLen ncopy4is start1 end1 start2 end2 score irId irLen nGaps orfBegin orfEnd strand orfLen E-value E-value4copy type ov tir +gi|228288719|ref|NC_012624.1| IS5 IS5_222 30355 31343 989 1 30355 30382 31316 31343 24 20 28 0 30399 31298 + 900 1.7e-37 1.7e-37 p 1 AGAATTATACAAAAATTTATAAATAATT:AGAATTTTTCAGTAATTAATATTTATTT +gi|228288719|ref|NC_012624.1| ISH3 ISH3_198|ISH3||gi|15898236|ref|NP_342841 32413 33650 1238 1 32413 32456 33607 33650 48 34 44 0 32517 33587 - 1071 2.3e-147 2.3e-147 c 1 CCCTTATTCGGTAGACCCAAAATCACCTCCTTGAAAATAAATCT:CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCT |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/TEST_1/test_1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TEST_1/test_1.log Thu Sep 01 09:29:56 2022 +0000 |
| [ |
| @@ -0,0 +1,43 @@ +/usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1 +Using 1 threads. +no. of seqs: 1 +Clock time used (by 1 threads) = 0.00 mins +prepare gff file.. +Time elapsed: 0 hours 0 minutes and 0 seconds. +ISEScan starts at Wed Aug 31 15:18:46 2022 +predict and translate genes from genome sequence into protein database using FragGeneScan program + +Begin to translate genome into proteome. +Translating genome into proteome for input , return 0 + +Finish translating genome into proteome. Wed Aug 31 15:18:46 2022 + +Begin to phmmer search against proteome database. Wed Aug 31 15:18:46 2022 +Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa + +Finish phmmer searching against proteome database. Wed Aug 31 15:19:05 2022 + +Begin to profile HMM search against proteome database. Wed Aug 31 15:19:05 2022 +Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa + +Finish profile HMM searching against proteome database. Wed Aug 31 15:19:17 2022 +pred begins at Wed Aug 31 15:19:17 2022 +Begin addNonORFcopy at Wed Aug 31 15:19:18 2022 +Finish addNonORFcopy at Wed Aug 31 15:19:18 2022 +Begin addNonORFcopy1 at Wed Aug 31 15:19:18 2022 +Finish addNonORFcopy1 at Wed Aug 31 15:19:18 2022 +getFullIS() begins at Wed Aug 31 15:19:18 2022 +Start typing IS elements +The single-copy partial IS element with evalue > 1e-50: isLen=989 IS5 bd=[30355, 31343] orf('gi|228288719|ref|NC_012624.1|', 30399, 31298, '+') evalue=1.7e-37 +Finish typing partial IS elements +Begin removeOverlappedHits at Wed Aug 31 15:19:18 2022 +gi|228288719|ref|NC_012624.1|: no intersected hits found +Finish removeOverlappedHits at Wed Aug 31 15:19:18 2022 +Begin reading protein database at Wed Aug 31 15:19:18 2022 +Finish reading protein database at Wed Aug 31 15:19:18 2022 +Write IS elements from all sequences in input into one result file under results +Write 2 IS copies to results/input.csv and results/input.tsv and results/input.raw +Write summarized result to results/input.sum +End in pred Wed Aug 31 15:19:18 2022 +Both complete and partial IS elements are reported. +ISEScan ends at Wed Aug 31 15:19:18 2022 |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.gff Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +##gff-version 3 +gi|228288719|ref|NC_012624.1| ISEScan insertion_sequence 32413 33650 . - . ID=gi|228288719|ref|NC_012624.1|_IS_1;family=ISH3;cluster=ISH3_198|ISH3||gi|15898236|ref|NP_342841 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 32413 32456 . - . ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1 +gi|228288719|ref|NC_012624.1| ISEScan terminal_inverted_repeat 33607 33650 . - . ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1 |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.is.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.is.fna Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,22 @@ +>gi|228288719|ref|NC_012624.1|_32413_33650_- ISH3_198|ISH3||gi|15898236|ref|NP_342841 +CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCTGACAGAATAATATCGA +TTCATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAG +CTGAGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCA +CCAAAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAA +GAAAGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGA +AAGCAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCA +AGGGATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACT +GAAGGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAG +ACCGGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGAC +GACAAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGAC +TAAGGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAG +GTTGATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTT +TAAGTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGA +TTACGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGT +GTACAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTAC +TAATCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCAT +AGAGACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGT +TTTCCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAA +GGGGGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGATGATTT +ATTCTATCTAAAAGATTTTCTATTTAAATCAATAGAACCGCTTATTAATAATATAGATTT +ATTTTCAAGGAGGTGATTTTGGGTCTACCGAATAAGGG |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.orf.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.orf.faa Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,7 @@ +>gi|228288719|ref|NC_012624.1|_32517_33587_- +MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK +GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK +GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK +EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY +ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE +TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.orf.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.orf.fna Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,19 @@ +>gi|228288719|ref|NC_012624.1|_32517_33587_- +ATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAGCTG +AGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCACCA +AAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAAGAA +AGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGAAAG +CAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCAAGG +GATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACTGAA +GGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAGACC +GGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGACGAC +AAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGACTAA +GGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAGGTT +GATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTTTAA +GTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGATTA +CGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGTGTA +CAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTACTAA +TCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCATAGA +GACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGTTTT +CCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAAGGG +GGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGA |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.sum --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.sum Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,3 @@ +# seqid family nIS %Genome bps4IS dnaLen +gi|228288719|ref|NC_012624.1| ISH3 1 2.93 1238 42245 +input total 1 2.93 1238 42245 |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.fna.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.fna.tsv Thu Sep 01 09:29:56 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +seqID family cluster isBegin isEnd isLen ncopy4is start1 end1 start2 end2 score irId irLen nGaps orfBegin orfEnd strand orfLen E-value E-value4copy type ov tir +gi|228288719|ref|NC_012624.1| ISH3 ISH3_198|ISH3||gi|15898236|ref|NP_342841 32413 33650 1238 1 32413 32456 33607 33650 48 34 44 0 32517 33587 - 1071 2.3e-147 2.3e-147 c 1 CCCTTATTCGGTAGACCCAAAATCACCTCCTTGAAAATAAATCT:CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCT |
| b |
| diff -r 000000000000 -r debe9c750cdd test-data/test_2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.log Thu Sep 01 09:29:56 2022 +0000 |
| [ |
| @@ -0,0 +1,43 @@ +/usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1 +Using 1 threads. +no. of seqs: 1 +Clock time used (by 1 threads) = 0.00 mins +prepare gff file.. +Time elapsed: 0 hours 0 minutes and 0 seconds. +ISEScan starts at Wed Aug 31 15:19:29 2022 +predict and translate genes from genome sequence into protein database using FragGeneScan program + +Begin to translate genome into proteome. +Translating genome into proteome for input , return 0 + +Finish translating genome into proteome. Wed Aug 31 15:19:29 2022 + +Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022 +Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa + +Finish phmmer searching against proteome database. Wed Aug 31 15:19:48 2022 + +Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022 +Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa + +Finish profile HMM searching against proteome database. Wed Aug 31 15:20:01 2022 +pred begins at Wed Aug 31 15:20:01 2022 +Begin addNonORFcopy at Wed Aug 31 15:20:01 2022 +Finish addNonORFcopy at Wed Aug 31 15:20:01 2022 +Begin addNonORFcopy1 at Wed Aug 31 15:20:01 2022 +Finish addNonORFcopy1 at Wed Aug 31 15:20:01 2022 +getFullIS() begins at Wed Aug 31 15:20:01 2022 +Start removing partial IS elements +Remove single-copy partial IS element with evalue > 1e-50: isLen=989 IS5 bd=[30355, 31343] orf('gi|228288719|ref|NC_012624.1|', 30399, 31298, '+') evalue=1.7e-37 +Finish removing partial IS elements +Begin removeOverlappedHits at Wed Aug 31 15:20:01 2022 +gi|228288719|ref|NC_012624.1|: no intersected hits found +Finish removeOverlappedHits at Wed Aug 31 15:20:01 2022 +Begin reading protein database at Wed Aug 31 15:20:01 2022 +Finish reading protein database at Wed Aug 31 15:20:01 2022 +Write IS elements from all sequences in input into one result file under results +Write 1 IS copies to results/input.csv and results/input.tsv and results/input.raw +Write summarized result to results/input.sum +End in pred Wed Aug 31 15:20:01 2022 +Only complete IS elements are reported. +ISEScan ends at Wed Aug 31 15:20:01 2022 |