Bio.ExPASy.Prosite module

Parser for the prosite dat file from Prosite at ExPASy.

See https://www.expasy.org/prosite/

Tested with:

  • Release 20.43, 10-Feb-2009

  • Release 2017_03 of 15-Mar-2017.

Functions:

  • read Reads a Prosite file containing one Prosite record

  • parse Iterates over records in a Prosite file.

Classes:

  • Record Holds Prosite data.

Bio.ExPASy.Prosite.parse(handle)

Parse Prosite records.

This function is for parsing Prosite files containing multiple records.

Arguments:

  • handle - handle to the file.

Bio.ExPASy.Prosite.read(handle)

Read one Prosite record.

This function is for parsing Prosite files containing exactly one record.

Arguments:

  • handle - handle to the file.

class Bio.ExPASy.Prosite.Record

Bases: object

Holds information from a Prosite record.

Main attributes:

  • name ID of the record. e.g. ADH_ZINC

  • type Type of entry. e.g. PATTERN, MATRIX, or RULE

  • accession e.g. PS00387

  • created Date the entry was created. (MMM-YYYY for releases before January 2017, DD-MMM-YYYY since January 2017)

  • data_update Date the ‘primary’ data was last updated.

  • info_update Date data other than ‘primary’ data was last updated.

  • pdoc ID of the PROSITE DOCumentation.

  • description Free-format description.

  • pattern The PROSITE pattern. See docs.

  • matrix List of strings that describes a matrix entry.

  • rules List of rule definitions (from RU lines). (strings)

  • prorules List of prorules (from PR lines). (strings)

NUMERICAL RESULTS:

  • nr_sp_release SwissProt release.

  • nr_sp_seqs Number of seqs in that release of Swiss-Prot. (int)

  • nr_total Number of hits in Swiss-Prot. tuple of (hits, seqs)

  • nr_positive True positives. tuple of (hits, seqs)

  • nr_unknown Could be positives. tuple of (hits, seqs)

  • nr_false_pos False positives. tuple of (hits, seqs)

  • nr_false_neg False negatives. (int)

  • nr_partial False negatives, because they are fragments. (int)

COMMENTS:

  • cc_taxo_range Taxonomic range. See docs for format

  • cc_max_repeat Maximum number of repetitions in a protein

  • cc_site Interesting site. list of tuples (pattern pos, desc.)

  • cc_skip_flag Can this entry be ignored?

  • cc_matrix_type

  • cc_scaling_db

  • cc_author

  • cc_ft_key

  • cc_ft_desc

  • cc_version version number (introduced in release 19.0)

The following are all lists if tuples (swiss-prot accession, swiss-prot name).

DATA BANK REFERENCES:

  • dr_positive

  • dr_false_neg

  • dr_false_pos

  • dr_potential Potential hits, but fingerprint region not yet available.

  • dr_unknown Could possibly belong

  • pdb_structs List of PDB entries.

__init__(self)

Initialize the class.