diff --git a/anvio/docs/__init__.py b/anvio/docs/__init__.py index cb78b1fbc1..1e44c82e6f 100644 --- a/anvio/docs/__init__.py +++ b/anvio/docs/__init__.py @@ -377,11 +377,23 @@ "provided_by_anvio": True, "provided_by_user":True }, + "pfam-accession": { + "name": "PFAM ACCESSION", + "type": "TXT", + "provided_by_anvio": False, + "provided_by_user": True + }, + "hmm-file": { + "name": "HMM MODEL FILE", + "type": "TXT", + "provided_by_anvio": False, + "provided_by_user": True + }, "hmm-source": { "name": "HMM SOURCE", "type": "HMM", "provided_by_anvio": False, - "provided_by_user":True + "provided_by_user": True }, "hmm-hits": { "name": "HMM PROFILE", diff --git a/anvio/docs/artifacts/hmm-file.md b/anvio/docs/artifacts/hmm-file.md new file mode 100644 index 0000000000..f41f88d1c8 --- /dev/null +++ b/anvio/docs/artifacts/hmm-file.md @@ -0,0 +1,3 @@ +A flat text HMM that literally desribes the properties of the model and lists transition probabilities. + +Such files are typically generated by the program `hmmbuild` (which is a part of the [HMMER](http://hmmer.org/) package and installed in every anvi'o environment) from FASTA files of aligned sequnces. diff --git a/anvio/docs/artifacts/pfam-accession.md b/anvio/docs/artifacts/pfam-accession.md new file mode 100644 index 0000000000..370ec9d3d2 --- /dev/null +++ b/anvio/docs/artifacts/pfam-accession.md @@ -0,0 +1,3 @@ +One or more accession numbers that match to valid entries in the [Pfam database](https://www.ebi.ac.uk/interpro/entry/pfam/). + +Such as [PF00001](https://www.ebi.ac.uk/interpro/entry/pfam/PF00001/) or [PF14437](https://www.ebi.ac.uk/interpro/entry/pfam/PF14437/). diff --git a/sandbox/anvi-script-gen-defense-finder-models-to-hmm-directory b/sandbox/anvi-script-gen-defense-finder-models-to-hmm-directory index a2dda908a5..0eba93b16f 100755 --- a/sandbox/anvi-script-gen-defense-finder-models-to-hmm-directory +++ b/sandbox/anvi-script-gen-defense-finder-models-to-hmm-directory @@ -21,7 +21,7 @@ __license__ = "GPL 3.0" __version__ = anvio.__version__ __authors__ = ['ge0rges'] __provides__ = ["hmm-source"] -__requires__ = ["hmm"] +__requires__ = [] __description__ = ("This program generates an anvi'o compatible HMM directory to be used with `anvi-run-hmms` " "from the MDMParis Defense Finder Models.") diff --git a/sandbox/anvi-script-hmm-to-hmm-directory b/sandbox/anvi-script-hmm-to-hmm-directory index 88bed6e926..80cc93b0ef 100755 --- a/sandbox/anvi-script-hmm-to-hmm-directory +++ b/sandbox/anvi-script-hmm-to-hmm-directory @@ -18,8 +18,8 @@ __credits__ = [] __license__ = "GPL 3.0" __version__ = anvio.__version__ __authors__ = ['ge0rges'] +__requires__ = ["hmm-file"] __provides__ = ["hmm-source"] -__requires__ = ["hmm"] __description__ = ("You give this program one or more HMM files from `hmmbuild`, and it generates " "an anvi'o compatible HMM directory to be used with `anvi-run-hmms`") diff --git a/sandbox/anvi-script-pfam-accessions-to-hmms-directory b/sandbox/anvi-script-pfam-accessions-to-hmms-directory index 058da15c62..11b21e6bd3 100755 --- a/sandbox/anvi-script-pfam-accessions-to-hmms-directory +++ b/sandbox/anvi-script-pfam-accessions-to-hmms-directory @@ -17,8 +17,8 @@ __credits__ = [] __license__ = "GPL 3.0" __version__ = anvio.__version__ __authors__ = ['meren'] +__requires__ = ["pfam-accession"] __provides__ = ["hmm-source"] -__requires__ = [] __description__ = ("You give this program one or more PFAM accession ids, and it generates " "an anvi'o compatible HMM directory to be used with `anvi-run-hmms`") @@ -76,7 +76,7 @@ def main(args): except: failed_accession_ids.add(pfam_accession) continue - + try: data_dict[pfam_accession] = {} data_dict[pfam_accession]['ga'] = utils.get_attribute_from_hmm_file(fp, 'GA ') @@ -87,7 +87,7 @@ def main(args): except ValueError: run.warning(f"The PFAM accession {pfam_accession} could not be included due to a missing attribute. " f"Anvi'o will continue without it") - + progress.end() if len(failed_accession_ids): @@ -154,11 +154,11 @@ if __name__ == '__main__': parser = ArgumentParser(description=__description__) parser.add_argument('--pfam-accessions-list', nargs='+', help="One or more PFAM accession IDs " - "(such as PF14437.6). If you have multiple accessions, you can separate them from " + "(such as PF14437). If you have multiple accessions, you can separate them from " "each other with a space. If you have too many, consider using the " "`--pfam-accessions-file` parameter instead.", metavar='PFAM_ACCESSION') parser.add_argument('--pfam-accessions-file', help="A single column text file where each column " - "is a single PFAM accession ID (such as PF14437.6). You may have as many accession " + "is a single PFAM accession ID (such as PF14437). You may have as many accession " "ids as you like in this file.", metavar='FILE') parser.add_argument('-O', '--output-directory', metavar='PATH', help="Output directory for the " "anvi'o-formatted HMMs. Choose the name wisely as this will be the name that will "