Mercurial > repos > rnateam > rnacommender
view pfam_utils/__init__.py @ 2:55ff4f15adc0 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit b40b4a9d2805f321adced1a6cc3632a24f3ca8dd
author | rnateam |
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date | Tue, 19 Jul 2016 09:24:18 -0400 |
parents | 8918de535391 |
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"""Utils for PFAM.""" import xml.etree.ElementTree as ET from math import ceil from time import sleep from xml.etree.ElementTree import ParseError import requests import pandas as pd import fasta_utils __author__ = "Gianluca Corrado" __copyright__ = "Copyright 2016, Gianluca Corrado" __license__ = "MIT" __maintainer__ = "Gianluca Corrado" __email__ = "gianluca.corrado@unitn.it" __status__ = "Production" def search_header(): """Return the header of a Pfam scan search.""" return "<seq id> <alignment start> <alignment end> \ <envelope start> <envelope end> <hmm acc> <hmm name>\ <type> <hmm start> <hmm end> <hmm length> <bit score>\ <E-value> <significance> <clan>\n" def sequence_search(seq_id, seq): """ Search a sequence against PFAM. Input ----- seq_id : str Name of the protein sequence. seq : str Protein sequence. Output ------ ret : str Formatted string containing the results of the Pfam scan for the given sequence """ def add_spaces(text, mul=8): """Add spaces to a string.""" l = len(text) next_mul = int(ceil(l / mul) + 1) * mul offset = next_mul - l if offset == 0: offset = 8 return text + " " * offset url = "http://pfam.xfam.org/search/sequence" params = {'seq': seq, 'evalue': '1.0', 'output': 'xml'} req = requests.get(url, params=params) xml = req.text try: root = ET.fromstring(xml) # sometimes Pfam returns the HTML code except ParseError: print "resending: %s" % seq_id return "%s" % sequence_search(seq_id, seq) result_url = root[0][1].text # wait for Pfam to compute the results sleep(4) while True: req2 = requests.get(result_url) if req2.status_code == 200: break else: sleep(1) result_xml = req2.text root = ET.fromstring(result_xml) try: matches = root[0][0][0][0][:] # Sometimes raised when the sequence has no matches except IndexError: return "" ret = "" for match in matches: for location in match: ret += add_spaces(seq_id) ret += add_spaces(location.attrib['ali_start']) ret += add_spaces(location.attrib['ali_end']) ret += add_spaces(location.attrib['start']) ret += add_spaces(location.attrib['end']) ret += add_spaces(match.attrib['accession']) ret += add_spaces(match.attrib['id']) ret += add_spaces(match.attrib['class']) ret += add_spaces(location.attrib['hmm_start']) ret += add_spaces(location.attrib['hmm_end']) ret += add_spaces("None") ret += add_spaces(location.attrib['bitscore']) ret += add_spaces(location.attrib['evalue']) ret += add_spaces(location.attrib['significant']) ret += "None\n" return ret def read_pfam_output(pfam_out_file): """Read the output of PFAM scan.""" cols = ["seq_id", "alignment_start", "alignment_end", "envelope_start", "envelope_end", "hmm_acc", "hmm_name", "type", "hmm_start", "hmm_end", "hmm_length", "bit_score", "E-value", "significance", "clan"] try: data = pd.read_table(pfam_out_file, sep="\s*", skip_blank_lines=True, skiprows=1, names=cols, engine='python') except: return None return data def download_seed_seqs(acc): """ Download seed sequences from PFAM. Input ----- acc : str Accession number of a Pfam domain Output ------ fasta : str Seed sequences in fasta format """ url = "http://pfam.xfam.org/family/%s/alignment/seed" % acc req = requests.get(url) stockholm = req.text fasta = fasta_utils.stockholm2fasta(stockholm) return fasta