Source code for prody.database.pfam

# -*- coding: utf-8 -*-
"""This module defines functions for interfacing Pfam database."""

__author__ = 'Anindita Dutta, Ahmet Bakan, Cihan Kaya'

from prody.dynamics.analysis import calcFracDimension
import re
from numbers import Integral

import numpy as np
from os.path import join, isfile
from io import BytesIO

from prody import LOGGER, PY3K
from prody.utilities import makePath, openURL, gunzip, openFile, dictElement
from prody.utilities import relpath
from prody.proteins import parsePDB

if PY3K:
    import urllib.parse as urllib
    import urllib.request as urllib2
    import urllib
    import urllib2

__all__ = ['searchPfam', 'fetchPfamMSA', 'parsePfamPDBs']

FASTA = 'fasta'
SELEX = 'selex'
STOCKHOLM = 'stockholm'

DOWNLOAD_FORMATS = set(['seed', 'full', 'ncbi', 'metagenomics',
                        'rp15', 'rp35', 'rp55', 'rp75', 'uniprot'])
                  'order': set(['tree', 'alphabetical']),
                  'inserts': set(['lower', 'upper']),
                  'gaps': set(['mixed', 'dots', 'dashes', 'none'])})


prefix = ''

[docs]def searchPfam(query, **kwargs): """Returns Pfam search results in a dictionary. Matching Pfam accession as keys will map to evalue, alignment start and end residue positions. :arg query: UniProt ID, PDB identifier, a protein sequence, or a sequence file. Sequence queries must not contain without gaps and must be at least 16 characters long :type query: str :arg timeout: timeout for blocking connection attempt in seconds, default is 60 :type timeout: int *query* can also be a PDB identifier, e.g. ``'1mkp'`` or ``'1mkpA'`` with chain identifier. UniProt ID of the specified chain, or the first protein chain will be used for searching the Pfam database.""" if isfile(query): from prody.sequence import MSAFile try: seq = next(MSAFile(query)) except: with openFile(query) as inp: seq = ''.join( else: seq = seq[0][1] if not seq.isalpha(): raise ValueError('could not parse a sequence without gaps from ' + query) else: seq = ''.join(query.split()) import xml.etree.cElementTree as ET LOGGER.timeit('_pfam') timeout = int(kwargs.get('timeout', 60)) if len(seq) >= MINSEQLEN: if not seq.isalpha(): raise ValueError(repr(seq) + ' is not a valid sequence') fseq = '>Seq\n' + seq parameters = { 'hmmdb' : 'pfam', 'seq': fseq } enc_params = urllib.urlencode(parameters).encode('utf-8') request = urllib2.Request('', enc_params) results_url = urllib2.urlopen(request).geturl() #res_params = { 'output' : 'xml' } res_params = { 'format' : 'tsv' } enc_res_params = urllib.urlencode(res_params) #modified_res_url = results_url + '?' + enc_res_params modified_res_url = results_url.replace('results','download') + '?' + enc_res_params result_request = urllib2.Request(modified_res_url) # url = ( urllib2.urlopen(request).geturl() + '?output=xml') LOGGER.debug('Submitted Pfam search for sequence "{0}...".' .format(seq[:MINSEQLEN])) try: #xml = urllib2.urlopen(result_request).read() tsv = urllib2.urlopen(result_request).read() # openURL(url, timeout=timeout).read() except: raise ValueError('No matching Pfam domains were found.') # try: # root = ET.XML(xml) # except Exception as err: # raise ValueError('failed to parse results XML, check URL: ' + modified_res_url) matches = {} #for child in root[0]: #if child.tag == 'hits': # accession = child.get('acc') # pfam_id = accession.split('.')[0] # matches[pfam_id]={} # matches[pfam_id]['accession']=accession # matches[pfam_id]['class']='Domain' # matches[pfam_id]['id']=child.get('name') # matches[pfam_id]['locations']={} # matches[pfam_id]['locations']['ali_end']=child[0].get('alisqto') # matches[pfam_id]['locations']['ali_start']=child[0].get('alisqfrom') # matches[pfam_id]['locations']['bitscore']=child[0].get('bitscore') # matches[pfam_id]['locations']['end']=child[0].get('alisqto') # matches[pfam_id]['locations']['evalue']=child.get('evalue') # matches[pfam_id]['locations']['evidence']='hmmer v3.0' # matches[pfam_id]['locations']['hmm_end']=child[0].get('alihmmto') # matches[pfam_id]['locations']['hmm_start']=child[0].get('alihmmfrom') # matches[pfam_id]['locations']['significant']=child[0].get('significant') # matches[pfam_id]['locations']['start']=child[0].get('alisqfrom') # matches[pfam_id]['type']='Pfam-A' # return matches if PY3K: tsv = tsv.decode() lines = tsv.split('\n') keys = lines[0].split('\t') root = {} for i, line in enumerate(lines[1:-1]): root[i] = {} for j, key in enumerate(keys): root[i][key] = line.split('\t')[j] for child in root.values(): accession = child['Family Accession'] pfam_id = accession.split('.')[0] matches[pfam_id]={} matches[pfam_id]['accession'] = accession matches[pfam_id]['class'] = 'Domain' matches[pfam_id]['id'] = child['Family id'] matches[pfam_id]['locations'] = {} matches[pfam_id]['locations']['ali_end'] = child['Ali. End'] matches[pfam_id]['locations']['ali_start'] = child['Ali. Start'] matches[pfam_id]['locations']['bitscore'] = child['Bit Score'] matches[pfam_id]['locations']['end'] = child['Env. End'] matches[pfam_id]['locations']['cond_evalue'] = child['Cond. E-value'] matches[pfam_id]['locations']['ind_evalue'] = child['Ind. E-value'] matches[pfam_id]['locations']['evidence'] = 'hmmer v3.0' matches[pfam_id]['locations']['hmm_end'] = child['Model End'] matches[pfam_id]['locations']['hmm_start'] = child['Model Start'] #matches[pfam_id]['locations']['significant'] = child['significant'] matches[pfam_id]['locations']['start'] = child['Env. Start'] matches[pfam_id]['type'] = 'Pfam-A' return matches else: if len(seq) <= 5: idcode = None from prody import parsePDBHeader try: polymers = parsePDBHeader(seq[:4], 'polymers') except Exception as err: LOGGER.warn('failed to parse header for {0} ({1})' .format(seq[:4], str(err))) else: chid = seq[4:].upper() for poly in polymers: if chid and poly.chid != chid: continue for dbref in poly.dbrefs: if dbref.database != 'UniProt': continue idcode = dbref.idcode accession = dbref.accession'UniProt ID code {0} for {1} chain ' '{2} will be used.' .format(idcode, seq[:4], poly.chid)) break if idcode is not None: break if idcode is None: LOGGER.warn('A UniProt ID code for PDB {0} could not be ' 'parsed.'.format(repr(seq))) url = prefix + 'protein/' + seq + '?output=xml' else: url = prefix + 'protein/' + idcode + '?output=xml' else: url = prefix + 'protein/' + seq + '?output=xml' LOGGER.debug('Retrieving Pfam search results: ' + url) xml = None while LOGGER.timing('_pfam') < timeout: try: xml = openURL(url, timeout=timeout).read() except Exception: pass else: if xml not in ['PEND','RUN']: break if not xml: raise IOError('Pfam search timed out or failed to parse results ' 'XML, check URL: ' + url) else:'Pfam search completed in %.2fs.', '_pfam') if xml.find(b'There was a system error on your last request.') > 0: LOGGER.warn('No Pfam matches found for: ' + seq) return None elif xml.find(b'No valid UniProt accession or ID') > 0: try: url = prefix + 'protein/' + accession + '?output=xml' LOGGER.debug('Retrieving Pfam search results: ' + url) xml = openURL(url, timeout=timeout).read() except: try: ag = parsePDB(seq, subset='ca') ag_seq = ag.getSequence() return searchPfam(ag_seq) except: raise ValueError('No valid UniProt accession or ID for: ' + seq) if xml.find(b'No valid UniProt accession or ID') > 0: try: url = '' + accession + '.xml' xml = openURL(url, timeout=timeout).read() root = ET.XML(xml) accession = root[0][0].text url = prefix + 'protein/' + accession + '?output=xml' LOGGER.debug('Retrieving Pfam search results: ' + url) xml = openURL(url, timeout=timeout).read() except: raise ValueError('No valid UniProt accession or ID for: ' + seq) try: root = ET.XML(xml) except Exception as err: raise ValueError('failed to parse results XML, check URL: ' + url) if len(seq) >= MINSEQLEN: try: xml_matches = root[0][0][0][0] except IndexError: raise ValueError('failed to parse results XML, check URL: ' + url) else: key = '{' + prefix + '}' results = dictElement(root[0], key) try: xml_matches = results['matches'] except KeyError: raise ValueError('failed to parse results XML, check URL: ' + url) matches = dict() for child in xml_matches: try: accession = child.attrib['accession'][:7] except KeyError: raise ValueError('failed to parse results XML, check URL: ' + url) if not'^P(F|B)[0-9]{5}$', accession): raise ValueError('{0} does not match pfam accession' ' format'.format(accession)) match = matches.setdefault(accession, dict(child.items())) locations = match.setdefault('locations', []) for loc in child: locations.append(dict(loc.items())) if len(seq) < MINSEQLEN: query = 'Query ' + repr(query) else: query = 'Query sequence' if matches: + ' matched {0} Pfam families.'.format(len(matches))) else: + ' did not match any Pfam families.') return matches
[docs]def fetchPfamMSA(acc, alignment='full', compressed=False, **kwargs): """Returns a path to the downloaded Pfam MSA file. :arg acc: Pfam ID or Accession Code :type acc: str :arg alignment: alignment type, one of ``'full'`` (default), ``'seed'``, ``'ncbi'``, ``'metagenomics'``, ``'rp15'``, ``'rp35'``, ``'rp55'``, ``'rp75'`` or ``'uniprot'`` where rp stands for representative proteomes :arg compressed: gzip the downloaded MSA file, default is **False** *Alignment Options* :arg format: a Pfam supported MSA file format, one of ``'selex'``, (default), ``'stockholm'`` or ``'fasta'`` :arg order: ordering of sequences, ``'tree'`` (default) or ``'alphabetical'`` :arg inserts: letter case for inserts, ``'upper'`` (default) or ``'lower'`` :arg gaps: gap character, one of ``'dashes'`` (default), ``'dots'``, ``'mixed'`` or **None** for unaligned *Other Options* :arg timeout: timeout for blocking connection attempt in seconds, default is 60 :arg outname: out filename, default is input ``'acc_alignment.format'`` :arg folder: output folder, default is ``'.'``""" url = prefix + 'family/acc?id=' + acc handle = openURL(url, timeout=int(kwargs.get('timeout', 60))) orig_acc = acc acc = handle.readline().strip() if PY3K: acc = acc.decode() url_flag = False if not'(?<=PF)[0-9]{5}$', acc): raise ValueError('{0} is not a valid Pfam ID or Accession Code' .format(repr(orig_acc))) if alignment not in DOWNLOAD_FORMATS: raise ValueError('alignment must be one of full, seed, ncbi or' ' metagenomics') if alignment == 'ncbi' or alignment == 'metagenomics' or alignment == 'uniprot': url = (prefix + 'family/' + acc + '/alignment/' + alignment + '/gzipped') url_flag = True extension = '.sth' else: if not kwargs: url = (prefix + 'family/' + acc + '/alignment/' + alignment + '/gzipped') url_flag = True extension = '.sth' else: align_format = kwargs.get('format', 'selex').lower() if align_format not in FORMAT_OPTIONS['format']: raise ValueError('alignment format must be of type selex' ' stockholm or fasta. MSF not supported') if align_format == SELEX: align_format, extension = 'pfam', '.slx' elif align_format == FASTA: extension = '.fasta' else: extension = '.sth' gaps = str(kwargs.get('gaps', 'dashes')).lower() if gaps not in FORMAT_OPTIONS['gaps']: raise ValueError('gaps must be of type mixed, dots, dashes, ' 'or None') inserts = kwargs.get('inserts', 'upper').lower() if(inserts not in FORMAT_OPTIONS['inserts']): raise ValueError('inserts must be of type lower or upper') order = kwargs.get('order', 'tree').lower() if order not in FORMAT_OPTIONS['order']: raise ValueError('order must be of type tree or alphabetical') url = (prefix + 'family/' + acc + '/alignment/' + alignment + '/format?format=' + align_format + '&alnType=' + alignment + '&order=' + order[0] + '&case=' + inserts[0] + '&gaps=' + gaps + '&download=1') response = openURL(url, timeout=int(kwargs.get('timeout', 60))) outname = kwargs.get('outname', None) if not outname: outname = orig_acc folder = str(kwargs.get('folder', '.')) filepath = join(makePath(folder), outname + '_' + alignment + extension) if compressed: filepath = filepath + '.gz' if url_flag: f_out = open(filepath, 'wb') else: f_out = openFile(filepath, 'wb') f_out.write( f_out.close() else: if url_flag: gunzip(, filepath) else: with open(filepath, 'wb') as f_out: f_out.write( filepath = relpath(filepath)'Pfam MSA for {0} is written as {1}.' .format(orig_acc, filepath)) return filepath
[docs]def parsePfamPDBs(query, data=[], **kwargs): """Returns a list of :class:`.AtomGroup` objects containing sections of chains that correspond to a particular PFAM domain family. These are defined by alignment start and end residue numbers. :arg query: UniProt ID or PDB ID If a PDB ID is provided the corresponding UniProt ID is used. If this returns multiple matches then start or end must also be provided. This query is also used for label refinement of the Pfam domain MSA. :type query: str :arg data: If given the data list from the Pfam mapping table will be output through this argument. :type data: list :keyword start: Residue number for defining the start of the domain. The PFAM domain that starts closest to this will be selected. Default is **1** :type start: int :keyword end: Residue number for defining the end of the domain. The PFAM domain that ends closest to this will be selected. :type end: int """ start = kwargs.pop('start', 1) end = kwargs.pop('end', None) if len(query) > 4 and query.startswith('PF'): pfam_acc = query else: pfam_matches = searchPfam(query) keys = list(pfam_matches.keys()) if isinstance(start, Integral): start_diff = [] for i, key in enumerate(pfam_matches): start_diff.append(int(pfam_matches[key]['locations'][0]['start']) - start) start_diff = np.array(start_diff) pfam_acc = keys[np.where(abs(start_diff) == min(abs(start_diff)))[0][0]] elif isinstance(end, Integral): end_diff = [] for i, key in enumerate(pfam_matches): end_diff.append(int(pfam_matches[key]['locations'][0]['end']) - end) end_diff = np.array(end_diff) pfam_acc = keys[np.where(abs(end_diff) == min(abs(end_diff)))[0][0]] else: raise ValueError('Please provide an integer for start or end ' 'when using a UniProt ID or PDB ID.') from ftplib import FTP from .uniprot import queryUniprot data_stream = BytesIO() ftp_host = '' ftp = FTP(ftp_host) ftp.login() ftp.cwd('pub/databases/Pfam/current_release') ftp.retrbinary('RETR pdbmap.gz', data_stream.write) ftp.quit() zip_data = data_stream.getvalue() data_stream.close() rawdata = gunzip(zip_data) if PY3K: rawdata = rawdata.decode() fields = ['PDB_ID', 'chain', 'nothing', 'PFAM_Name', 'PFAM_ACC', 'UniprotAcc', 'UniprotResnumRange'] data_dicts = [] for line in rawdata.split('\n'): if line.find(pfam_acc) != -1: data_dicts.append({}) for j, entry in enumerate(line.strip().split('\t')): data_dicts[-1][fields[j]] = entry.strip(';') pdb_ids = [data_dict['PDB_ID'] for data_dict in data_dicts] chains = [data_dict['chain'] for data_dict in data_dicts] header = kwargs.pop('header', False) model = kwargs.get('model', None) results = parsePDB(*pdb_ids, chain=chains, header=True, **kwargs) ags, headers = results ags, headers = list(ags), list(headers) if model == 0:'only header is requested and returned') return results if header: results = (ags, headers) else: results = ags LOGGER.progress('Extracting Pfam domains...', len(ags)) comma_splitter = re.compile(r'\s*,\s*').split no_info = [] for i, ag in enumerate(ags): LOGGER.update(i) data_dict = data_dicts[i] pfamRange = data_dict['UniprotResnumRange'].split('-') uniprotAcc = data_dict['UniprotAcc'] try: uniData = queryUniprot(uniprotAcc) except: LOGGER.warn('No Uniprot record found for {0}'.format(data_dict['PBD_ID'])) continue resrange = None found = False for key, value in uniData.items(): if not key.startswith('dbReference'): continue try: pdbid = value['PDB'] except: continue if pdbid != data_dict['PDB_ID']: continue pdbchains = value['chains'] # example chain strings: "A=27-139, B=140-150" or "A/B=27-150" pdbchains = comma_splitter(pdbchains) for chain in pdbchains: chids, resrange = chain.split('=') chids = [chid.strip() for chid in chids.split('/')] if data_dict['chain'] in chids: resrange = resrange.split('-') found = True break if found: break if found: header = headers[i] chain_accessions = [dbref.accession for dbref in header[data_dict['chain']].dbrefs] try: if len(chain_accessions) > 0: right_part = np.where(np.array(chain_accessions) == data_dict['UniprotAcc'])[0][0] else: raise ValueError('There is no accession for a chain in the Header') except: LOGGER.warn('Could not map domains in {0}' .format(data_dict['PDB_ID'] + data_dict['chain'])) no_info.append(i) continue right_dbref = header[data_dict['chain']].dbrefs[right_part] chainStart ='chain {0}'.format(data_dict['chain']) ).getResnums()[0] missing = chainStart - right_dbref.first[0] partStart = ag.getResindices()[np.where(ag.getResnums() == right_dbref.first[0] + missing)][0] pfStart, pfEnd = int(pfamRange[0]), int(pfamRange[1]) uniStart, uniEnd = int(resrange[0]), int(resrange[1]) resiStart = pfStart - uniStart + partStart - missing resiEnd = pfEnd - uniStart + partStart - missing ags[i] ='resindex {0} to {1}'.format( resiStart, resiEnd)) else: no_info.append(i) LOGGER.finish() for i in reversed(no_info): ags.pop(i) if header: headers.pop(i) if isinstance(data, list): data.extend(data_dicts) else: LOGGER.warn('data should be a list in order to get output') return results