{"id":25977615,"url":"https://github.com/nylander/hmmer-parser","last_synced_at":"2026-04-20T15:02:15.107Z","repository":{"id":195810704,"uuid":"185570946","full_name":"nylander/HMMer-parser","owner":"nylander","description":null,"archived":false,"fork":false,"pushed_at":"2023-09-19T14:28:29.000Z","size":47,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2023-09-19T17:59:20.874Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nylander.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-05-08T09:06:18.000Z","updated_at":"2023-09-19T17:59:22.754Z","dependencies_parsed_at":"2023-09-19T17:59:22.615Z","dependency_job_id":"b905a9a5-d424-467d-a79f-b4fee2e00d3b","html_url":"https://github.com/nylander/HMMer-parser","commit_stats":null,"previous_names":["nylander/hmmer-parser"],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FHMMer-parser","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FHMMer-parser/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FHMMer-parser/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FHMMer-parser/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nylander","download_url":"https://codeload.github.com/nylander/HMMer-parser/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241966988,"owners_count":20050324,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-05T04:38:43.811Z","updated_at":"2026-04-20T15:02:10.084Z","avatar_url":"https://github.com/nylander.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# hmmer-parser.pl\n\n## USAGE\n\n    ./hmmer-parser.pl [options] -i output-file-from-hmmsearch-or-nhmmer\n\n## DESCRIPTION\n\nParses output from [hmmer](http://hmmer.org/) searches (hmmsearch or nhmmer).\n\nPrints hits in fasta format with descriptions added to the fasta header (tab separated).\n\nWill print to stdout or to file.\n\nPrints hits in fasta format with descriptions added to the fasta header (tab separated).\n\nExample output fasta header:\n\n    \u003eTRINITY_DN52935_c2_g1_i1        Query:COI       Identity:83.35  E-value:1.2e-277        Score:926.9     Result:PRESENT\n\nA label \"PRESENT\" will be there if identity requirements are fulfilled:\n\n    if ( (percent identity in HSP \u003e= PERCENTAGE) and (percent coverage of HSP to query \u003e= COVERAGE) )\n\nIf not \"PRESENT\", then the tag can be labeled as \"ABSENT\" or \"TRUNCATED\" depending on the\nvalues of percent identity in HSP and the percent coverage of HSP to query.\n\nThe values of PERCENTAGE and COVERAGE can be set by options -p and -c and will only affect\nthe tag \"Result\" in the output fasta headers.\n\n## OPTIONS\n\n    -i \u003cinfile\u003e  Infile. Mandatory.\n    -m, -n=\u003cnr\u003e  Maximum number of hits to show.\n                 Default is \"1\".\n    -s=\u003cstring\u003e  Sort output sequences on either \"E-value\", \"Score\", or \"Identity\".\n                 \"Score\" is default.\n    -p=\u003cinteger\u003e Minimum percentage for residual identity in alignment.\n                 Default is \"80\".\n    -c=\u003cinteger\u003e Minimum coverage ((length of query in alignment pair/original length of query)*100).\n                 Default is \"80\".\n    -o \u003coufile\u003e  Outfile.\n    -v           Be verbose (or --noverbose).\n\n## REQUIREMENTS\n\nBioPerl, Bio::SearchIO::hmmer.\n\nExample installation on Ubuntu 22.04:\n\n    $ sudo apt install \\\n          libbio-perl-perl \\\n          libbio-perl-run-perl \\\n          libbio-searchio-hmmer-perl\n\n## WORKED EXAMPLES\n\n### hmmsearch (HMMER 3.3.2); one coi sequence against 24 coi sequences\n\n    $ scripts/fas2sto.pl data/ref-coi.fas \u003e data/ref-coi.sto\n    $ hmmbuild --cpu 4 data/ref-coi.hmm data/ref-coi.sto\n    $ hmmsearch --cpu 4 data/ref-coi.hmm \\\n        data/coi.fas \u003e data/coi-vs-ref-coi.hmmsearch.out\n\nParse\n\n    $ ./hmmer-parser.pl \\\n        -i data/coi-vs-ref-coi.hmmsearch.out \\\n        -o data/coi-vs-ref-coi.hmmsearch.hmm-parser.fas\n\n### nhmmer (HMMER 3.3.2); coi HMM-profile (calculated from a coi multiple sequence alignment) against one genome (nt)\n\n    $ wget -O - \\\n       \"https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/335/GCF_000002335.3_Tcas5.2/GCF_000002335.3_Tcas5.2_genomic.fna.gz\" | \\\n       gunzip -c \u003e data/GCF_000002335.3.fna\n    $ scripts/fas2sto.pl data/ref-coi.fas \u003e data/ref-coi.sto\n    $ hmmbuild --cpu 4 data/ref-coi.hmm data/ref-coi.sto\n    $ nhmmer --cpu 4 \\\n        -o data/GCF_000002335.ref-coi-vs-GCF_000002335.3.nhmmer.out \\\n        data/ref-coi.hmm \\\n        data/GCF_000002335.3.fna\n\nParse\n\n    $ ./hmmer-parser.pl \\\n        -i data/GCF_000002335.ref-coi-vs-GCF_000002335.3.nhmmer.out \\\n        -o data/GCF_000002335.ref-coi-vs-GCF_000002335.3.nhmmer.hmm-parser.fas\n\n## NOTES\n\nTested on output from hmmsearch and nhmmer from HMMer v.3.1b2 and v.3.3.2.\nBeware of change in output format between HMMer versions.\n\n## AUTHOR\n\nJohan Nylander\n\n## COMPANY\n\nNRM\n\n## LICENSE\n\nMIT. See [LICENSE file](LICENSE)\n\n## DOWNLOAD\n\n\u003chttps://github.com/nylander/HMMer-parser\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fhmmer-parser","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnylander%2Fhmmer-parser","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fhmmer-parser/lists"}