├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── data ├── Blast_db │ ├── isfinder_is.fasta │ ├── isfinder_is.nhr │ ├── isfinder_is.nin │ ├── isfinder_is.nog │ ├── isfinder_is.nsd │ ├── isfinder_is.nsi │ ├── isfinder_is.nsq │ ├── isfinder_orf.fasta │ ├── isfinder_orf.phr │ ├── isfinder_orf.pin │ ├── isfinder_orf.pog │ ├── isfinder_orf.psd │ ├── isfinder_orf.psi │ ├── isfinder_orf.psq │ ├── isfinder_orf_all.phr │ ├── isfinder_orf_all.pin │ ├── isfinder_orf_all.pog │ ├── isfinder_orf_all.psd │ ├── isfinder_orf_all.psi │ └── isfinder_orf_all.psq ├── models │ ├── fasta │ │ └── outliers.fasta │ ├── hmm │ │ ├── hmm_all_fams.hmm │ │ ├── hmm_all_subfams.hmm │ │ └── thresholds.txt │ └── msa │ │ ├── IS1 │ │ ├── IS1.sto │ │ └── IS1_cut.sto │ │ ├── IS110 │ │ ├── IS110.sto │ │ └── IS110_cut.sto │ │ ├── IS1182 │ │ ├── IS1182.sto │ │ └── IS1182_cut.sto │ │ ├── IS1380 │ │ ├── IS1380.sto │ │ └── IS1380_cut.sto │ │ ├── IS1595 │ │ ├── IS1595.sto │ │ └── IS1595_cut.sto │ │ ├── IS1634 │ │ ├── IS1634.sto │ │ └── IS1634_cut.sto │ │ ├── IS200_IS605 │ │ ├── IS200_IS605.sto │ │ └── IS200_IS605_cut.sto │ │ ├── IS21 │ │ ├── IS21.sto │ │ └── IS21_cut.sto │ │ ├── IS256 │ │ ├── IS256.sto │ │ └── IS256_cut.sto │ │ ├── IS3 │ │ ├── IS3.sto │ │ └── IS3_cut.sto │ │ ├── IS30 │ │ ├── IS30.sto │ │ └── IS30_cut.sto │ │ ├── IS3_IS150 │ │ ├── IS3_IS150.sto │ │ └── IS3_IS150_cut.sto │ │ ├── IS3_IS2 │ │ ├── IS3_IS2.sto │ │ └── IS3_IS2_cut.sto │ │ ├── IS3_IS3 │ │ ├── IS3_IS3.sto │ │ └── IS3_IS3_cut.sto │ │ ├── IS3_IS407 │ │ ├── IS3_IS407.sto │ │ └── IS3_IS407_cut.sto │ │ ├── IS3_IS51 │ │ ├── IS3_IS51.sto │ │ └── IS3_IS51_cut.sto │ │ ├── IS4 │ │ ├── IS4.sto │ │ └── IS4_cut.sto │ │ ├── IS481 │ │ ├── IS481.sto │ │ └── IS481_cut.sto │ │ ├── IS4_IS10 │ │ ├── IS4_IS10.sto │ │ └── IS4_IS10_cut.sto │ │ ├── IS4_IS231 │ │ ├── IS4_IS231.sto │ │ └── IS4_IS231_cut.sto │ │ ├── IS4_IS4 │ │ ├── IS4_IS4.sto │ │ └── IS4_IS4_cut.sto │ │ ├── IS4_IS4Sa │ │ ├── IS4_IS4Sa.sto │ │ └── IS4_IS4Sa_cut.sto │ │ ├── IS4_IS50 │ │ ├── IS4_IS50.sto │ │ └── IS4_IS50_cut.sto │ │ ├── IS4_ISH8 │ │ ├── IS4_ISH8.sto │ │ └── IS4_ISH8_cut.sto │ │ ├── IS4_ISPepr1 │ │ ├── IS4_ISPepr1.sto │ │ └── IS4_ISPepr1_cut.sto │ │ ├── IS5_IS1031 │ │ ├── IS5_IS1031.sto │ │ └── IS5_IS1031_cut.sto │ │ ├── IS5_IS427 │ │ ├── IS5_IS427.sto │ │ └── IS5_IS427_cut.sto │ │ ├── IS5_IS5 │ │ ├── IS5_IS5.sto │ │ ├── IS5_IS5_cut.sto │ │ ├── IS5_IS5_delete.sto │ │ ├── IS5_IS5_delete_cut.sto │ │ ├── IS5_IS5_full.sto │ │ ├── IS5_IS5_full_cut.sto │ │ ├── IS5_IS5_mode3.sto │ │ ├── IS5_IS5_model1.sto │ │ ├── IS5_IS5_model1_cut.sto │ │ ├── IS5_IS5_model2.sto │ │ ├── IS5_IS5_model2_cut.sto │ │ └── IS5_IS5_model3_cut.sto │ │ ├── IS5_IS903 │ │ ├── IS5_IS903.sto │ │ └── IS5_IS903_cut.sto │ │ ├── IS5_ISH1 │ │ ├── IS5_ISH1.sto │ │ └── IS5_ISH1_cut.sto │ │ ├── IS5_ISL2 │ │ ├── IS5_ISL2.sto │ │ └── IS5_ISL2_cut.sto │ │ ├── IS5_None │ │ ├── IS5_None.sto │ │ ├── IS5_None_m1_cut.sto │ │ ├── IS5_None_m2_cut.sto │ │ ├── IS5_None_m3_cut.sto │ │ ├── IS5_None_model1.sto │ │ ├── IS5_None_model1_cut.sto │ │ ├── IS5_None_model1_final.sto │ │ ├── IS5_None_model2.sto │ │ ├── IS5_None_model2_cut.sto │ │ ├── IS5_None_model2_final.sto │ │ ├── IS5_None_model3.sto │ │ ├── IS5_None_model3_cut.sto │ │ ├── IS5_None_zvysok.sto │ │ └── IS5_None_zvysok_zo_zvysku.sto │ │ ├── IS6 │ │ ├── IS6.sto │ │ └── IS6_cut.sto │ │ ├── IS607 │ │ ├── IS607.sto │ │ └── IS607_cut.sto │ │ ├── IS630 │ │ ├── IS630.sto │ │ └── IS630_cut.sto │ │ ├── IS66 │ │ ├── IS66.sto │ │ └── IS66_cut.sto │ │ ├── IS701 │ │ ├── IS701.sto │ │ └── IS701_cut.sto │ │ ├── IS91 │ │ ├── IS91.sto │ │ └── IS91_cut.sto │ │ ├── IS982 │ │ ├── IS982.sto │ │ └── IS982_cut.sto │ │ ├── ISAs1 │ │ ├── ISAs1.sto │ │ └── ISAs1_cut.sto │ │ ├── ISAzo13 │ │ ├── ISAzo13.sto │ │ └── ISAzo13_cut.sto │ │ ├── ISH3 │ │ ├── ISH3.sto │ │ └── ISH3_cut.sto │ │ ├── ISH6 │ │ ├── ISH6.sto │ │ └── ISH6_cut.sto │ │ ├── ISKra4 │ │ ├── ISKra4.sto │ │ └── ISKra4_cut.sto │ │ ├── ISL3 │ │ ├── ISL3.sto │ │ └── ISL3_cut.sto │ │ ├── ISLre2 │ │ ├── ISLre2.sto │ │ └── ISLre2_cut.sto │ │ ├── ISNCY_IS1202 │ │ ├── ISNCY_IS1202.sto │ │ └── ISNCY_IS1202_cut.sto │ │ ├── ISNCY_IS892 │ │ └── ISNCY_IS892.sto │ │ ├── ISNCY_ISA1214 │ │ ├── ISNCY_ISA1214.sto │ │ └── ISNCY_ISA1214_cut.sto │ │ ├── ISNCY_ISC1217 │ │ ├── ISNCY_ISC1217.sto │ │ └── ISNCY_ISC1217_cut.sto │ │ ├── ISNCY_ISDol1 │ │ ├── ISNCY_ISDol1.sto │ │ └── ISNCY_ISDol1_cut.sto │ │ ├── ISNCY_ISLbi1 │ │ ├── ISNCY_ISLbi1.sto │ │ └── ISNCY_ISLbi1_cut.sto │ │ ├── ISNCY_ISM1 │ │ ├── ISNCY_ISM1.sto │ │ └── ISNCY_ISM1_cut.sto │ │ ├── ISNCY_ISMae2 │ │ ├── ISNCY_ISMae2.sto │ │ └── ISNCY_ISMae2_cut.sto │ │ ├── ISNCY_ISPlu15 │ │ └── ISNCY_ISPlu15.sto │ │ ├── ISNCY_None │ │ └── ISNCY_None.sto │ │ └── Tn3 │ │ ├── Tn3.sto │ │ └── Tn3_cut.sto └── test_data │ ├── NC_002608.fasta │ └── NC_002608.gb ├── definitions.py ├── digIS_search.py ├── digis_docker_wrapper.sh ├── evaluation ├── archaea_complete_genomic_files.txt └── bacteria_complete_genomic_files.txt ├── requirements.txt └── src ├── blast ├── Blast.py ├── BlastDB.py ├── BlastHit.py ├── BlastHsp.py ├── BlastHspFlat.py ├── BlastN.py ├── BlastP.py ├── BlastQuery.py └── BlastX.py ├── common ├── Classifier.py ├── RangesHits.py ├── classification.py ├── csv_utils.py ├── genbank.py ├── genome.py ├── gff_utils.py ├── grange.py ├── misc.py ├── ranges.py └── sequence.py ├── genbank └── RecordGenbank.py ├── hmmer ├── Hmmer.py ├── HmmerHit.py ├── HmmerHsp.py └── HmmerHspFlat.py └── search_tool ├── RecordDigIS.py ├── RecordDigISAttrib.py ├── digIS.py ├── digISConfiguration.py └── digISMultifasta.py /.gitignore: -------------------------------------------------------------------------------- 1 | __pycache__/ 2 | 3 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/janka2012/digIS/HEAD/Dockerfile -------------------------------------------------------------------------------- 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