o ॵi@sHdZddlZddlZddlZddlmZddlmZGdddeZ dS)z@A Python wrapper for hmmbuild - construct HMM profiles from MSA.N)logging)utilsc@sjeZdZdZdddedefddZ dd ed efd d Zd ed efddZ ddeded efddZ dS)Hmmbuildz&Python wrapper of the hmmbuild binary.F)singlemx binary_pathrcCs||_||_dS)aiInitializes the Python hmmbuild wrapper. Args: binary_path: The path to the hmmbuild executable. singlemx: Whether to use --singlemx flag. If True, it forces HMMBuild to just use a common substitution score matrix. Raises: RuntimeError: If hmmbuild binary not found within the path. N)rr)selfrrr h/home/ubuntu/.local/lib/python3.10/site-packages/modelscope/models/science/unifold/msa/tools/hmmbuild.py__init__s zHmmbuild.__init__faststoreturncCs|j||dS)aBuilds a HHM for the aligned sequences given as an A3M string. Args: sto: A string with the aligned sequences in the Stockholm format. model_construction: Whether to use reference annotation in the msa to determine consensus columns ('hand') or default ('fast'). Returns: A string with the profile in the HMM format. Raises: RuntimeError: If hmmbuild fails. model_construction)_build_profile)rr rr r r build_profile_from_sto*szHmmbuild.build_profile_from_stoa3mcCsPg}|D]}|dstdd|}||dqd|}|j|ddS)a'Builds a HHM for the aligned sequences given as an A3M string. Args: a3m: A string with the aligned sequences in the A3M format. Returns: A string with the profile in the HMM format. Raises: RuntimeError: If hmmbuild fails. >z[a-z]+ r r) splitlines startswithresubappendjoinr)rrlineslinemsar r r build_profile_from_a3m<s   zHmmbuild.build_profile_from_a3mrrc Cs|dvr td|dt}tj|d}tj|d}t|d }||Wdn1s4wY|jg}|dkrI| d ||j rQ| d | d ||gt d |tj|tjtjd }td|\} } |} t d| d| dWdn1swY| rtd| d| dft|dd }|} Wdn1swYWd| SWd| S1swY| S)aBuilds a HMM for the aligned sequences given as an MSA string. Args: msa: A string with the aligned sequences, in A3M or STO format. model_construction: Whether to use reference annotation in the msa to determine consensus columns ('hand') or default ('fast'). Returns: A string with the profile in the HMM format. Raises: RuntimeError: If hmmbuild fails. ValueError: If unspecified arguments are provided. >r handzInvalid model_construction z - onlyhand and fast supported.z query.msaz output.hmmwNr!z--z --singlemxz--aminozLaunching subprocess %s)stdoutstderrzhmmbuild queryz hmmbuild stdout: %s stderr: %s zutf-8z'hmmbuild failed stdout: %s stderr: %s )encoding) ValueErrorrtmpdir_managerospathropenwriterrrextendrinfo subprocessPopenPIPEtiming communicatewaitdecode RuntimeErrorread) rrr query_tmp_dir input_queryoutput_hmm_pathfcmdprocessr#r$retcodehmmr r r rPsb            ) ))zHmmbuild._build_profileN)r ) __name__ __module__ __qualname____doc__strboolr rr rr r r r rs$ r) rBr(rr.abslrrrobjectrr r r r s