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__()
Initialize the class.