Sequence Searches#

pyhmmer.hmmer.phmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)#

Search protein sequences against a sequence database.

Parameters:

  • queries (iterable of DigitalSequence or DigitalMSA) – The query sequences to search for in the sequence database. Passing a single object is supported.

  • sequences (iterable of DigitalSequence) – A database of sequences to query. If you plan on using the same sequences several times, consider storing them into a DigitalSequenceBlock directly. If a SequenceFile is given, profiles will be loaded iteratively from disk rather than prefetched.

  • cpus (int) – The number of threads to run in parallel. Pass 1 to run everything in the main thread, 0 to automatically select a suitable number (using psutil.cpu_count), or any positive number otherwise.

  • callback (callable) – A callback that is called everytime a query is processed with two arguments: the query, and the total number of queries. This can be used to display progress in UI.

  • builder (Builder, optional) – A builder to configure how the queries are converted to HMMs. Passing None will create a default instance.

  • backend (str) – The parallel backend to use for workers to be executed. Supports threading to use thread-based parallelism, or multiprocessing to use process-based parallelism.

Yields:

TopHits – A top hits instance for each query, in the same order the queries were passed in the input.

Raises:

AlphabetMismatch – When any of the query sequence the profile or the optional builder do not share the same alphabet.

Note

Any additional keyword arguments passed to the phmmer function will be passed transparently to the Pipeline to be created in each worker thread.

Added in version 0.2.0.

Changed in version 0.3.0: Allow using DigitalMSA queries.

Changed in version 0.7.0: Queries may now be an iterable of different types, or a single object.

pyhmmer.hmmer.nhmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)#

Search nucleotide sequences against a sequence database.

Parameters:

  • queries (iterable of DigitalSequence, DigitalMSA, HMM) – The query sequences or profiles to search for in the sequence database. Passing a single object is supported.

  • sequences (iterable of DigitalSequence) – A database of sequences to query. If you plan on using the same sequences several times, consider storing them into a DigitalSequenceBlock directly. If a SequenceFile is given, profiles will be loaded iteratively from disk rather than prefetched.

  • cpus (int) – The number of threads to run in parallel. Pass 1 to run everything in the main thread, 0 to automatically select a suitable number (using psutil.cpu_count), or any positive number otherwise.

  • callback (callable) – A callback that is called everytime a query is processed with two arguments: the query, and the total number of queries. This can be used to display progress in UI.

  • builder (Builder, optional) – A builder to configure how the queries are converted to HMMs. Passing None will create a default instance.

  • backend (str) – The parallel backend to use for workers to be executed. Supports threading to use thread-based parallelism, or multiprocessing to use process-based parallelism.

Yields:

TopHits – A top hits instance for each query, in the same order the queries were passed in the input.

Note

Any additional keyword arguments passed to the nhmmer function will be passed to the LongTargetsPipeline created in each worker thread. The strand argument can be used to restrict the search on the direct or reverse strand.

Caution

This function is not just phmmer for nucleotide sequences; it actually uses a LongTargetsPipeline internally instead of processing each target sequence in its entirety when searching for hits. This avoids hitting the maximum target size that can be used (100,000 residues), which may be a problem for some larger genomes.

Added in version 0.3.0.

Changed in version 0.4.9: Allow using Profile and OptimizedProfile queries.

Changed in version 0.7.0: Queries may now be an iterable of different types, or a single object.