# HG changeset patch # User drosofff # Date 1434911385 14400 # Node ID 0bdc5a73c8d1fb2ab086c7bfecae6693b432ca64 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ diff -r 000000000000 -r 0bdc5a73c8d1 retrieve_fasta_from_NCBI.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/retrieve_fasta_from_NCBI.py Sun Jun 21 14:29:45 2015 -0400 @@ -0,0 +1,279 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" +From a taxonomy ID retrieves all the nucleotide sequences +It returns a multiFASTA nuc/prot file + +Entrez Database UID common name E-utility Database Name +Nucleotide GI number nuccore +Protein GI number protein + +Retrieve strategy: + +esearch to get total number of UIDs (count) +esearch to get UIDs in batches +loop untile end of UIDs list: + epost to put a batch of UIDs in the history server + efetch to retrieve info from previous post + +retmax of efetch is 1/10 of declared value from NCBI + +queries are 1 sec delayed, to satisfy NCBI guidelines (more than what they request) + + +python get_fasta_from_taxon.py -i 1638 -o test.out -d protein +python get_fasta_from_taxon.py -i 327045 -o test.out -d nuccore # 556468 UIDs +""" +import sys +import logging +import optparse +import time +import urllib +import urllib2 +import httplib +import re +class Eutils: + + def __init__(self, options, logger): + self.logger = logger + self.base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/" + self.query_string = options.query_string + self.dbname = options.dbname + if options.outname: + self.outname = options.outname + else: + self.outname = 'NCBI_download' + '.' + self.dbname + '.fasta' + self.ids = [] + self.retmax_esearch = 100000 + self.retmax_efetch = 1000 + self.count = 0 + self.webenv = "" + self.query_key = "" + + def retrieve(self): + """ """ + self.get_count_value() + self.get_uids_list() + self.get_sequences() + + def get_count_value(self): + """ + just to retrieve Count (number of UIDs) + Total number of UIDs from the retrieved set to be shown in the XML + output (default=20). By default, ESearch only includes the first 20 + UIDs retrieved in the XML output. If usehistory is set to 'y', + the remainder of the retrieved set will be stored on the History server; + + http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch + """ + self.logger.info("retrieving data from %s" % self.base) + self.logger.info("for Query: %s and database: %s" % + (self.query_string, self.dbname)) + querylog = self.esearch(self.dbname, self.query_string, '', '', "count") + self.logger.debug("Query response:") + for line in querylog: + self.logger.debug(line.rstrip()) + if '' in line: + self.count = int(line[line.find('')+len('') : line.find('')]) + self.logger.info("Founded %d UIDs" % self.count) + + def get_uids_list(self): + """ + Increasing retmax allows more of the retrieved UIDs to be included in the XML output, + up to a maximum of 100,000 records. + from http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch + """ + retmax = self.retmax_esearch + if (self.count > retmax): + num_batches = (self.count / retmax) + 1 + else: + num_batches = 1 + self.logger.info("Batch size for esearch action: %d UIDs" % retmax) + self.logger.info("Number of batches for esearch action: %d " % num_batches) + for n in range(num_batches): + querylog = self.esearch(self.dbname, self.query_string, n*retmax, retmax, '') + for line in querylog: + if '' in line and '' in line: + uid = (line[line.find('')+len('') : line.find('')]) + self.ids.append(uid) + self.logger.info("Retrieved %d UIDs" % len(self.ids)) + + def esearch(self, db, term, retstart, retmax, rettype): + url = self.base + "esearch.fcgi" + self.logger.debug("url: %s" % url) + values = {'db': db, + 'term': term, + 'rettype': rettype, + 'retstart': retstart, + 'retmax': retmax} + data = urllib.urlencode(values) + self.logger.debug("data: %s" % str(data)) + req = urllib2.Request(url, data) + response = urllib2.urlopen(req) + querylog = response.readlines() + time.sleep(1) + return querylog + + def epost(self, db, ids): + url = self.base + "epost.fcgi" + self.logger.debug("url_epost: %s" % url) + values = {'db': db, + 'id': ids} + data = urllib.urlencode(values) + req = urllib2.Request(url, data) + #self.logger.debug("data: %s" % str(data)) + req = urllib2.Request(url, data) + serverResponse = False + while not serverResponse: + try: + response = urllib2.urlopen(req) + serverResponse = True + except: # catch *all* exceptions + e = sys.exc_info()[0] + self.logger.info( "Catched Error: %s" % e ) + self.logger.info( "Retrying in 10 sec") + time.sleep(10) + querylog = response.readlines() + self.logger.debug("query response:") + for line in querylog: + self.logger.debug(line.rstrip()) + if '' in line: + self.query_key = str(line[line.find('')+len(''):line.find('')]) + if '' in line: + self.webenv = str(line[line.find('')+len(''):line.find('')]) + self.logger.debug("*** epost action ***") + self.logger.debug("query_key: %s" % self.query_key) + self.logger.debug("webenv: %s" % self.webenv) + time.sleep(1) + + def efetch(self, db, query_key, webenv): + url = self.base + "efetch.fcgi" + self.logger.debug("url_efetch: %s" % url) + values = {'db': db, + 'query_key': query_key, + 'webenv': webenv, + 'rettype': "fasta", + 'retmode': "text"} + data = urllib.urlencode(values) + req = urllib2.Request(url, data) + self.logger.debug("data: %s" % str(data)) + req = urllib2.Request(url, data) + serverTransaction = False + counter = 0 + while not serverTransaction: + counter += 1 + self.logger.info("Server Transaction Trial: %s" % ( counter ) ) + try: + response = urllib2.urlopen(req) + fasta = response.read() + if "Resource temporarily unavailable" in fasta: + serverTransaction = False + else: + serverTransaction = True + except urllib2.HTTPError as e: + serverTransaction = False + self.logger.info("urlopen error:%s, %s" % (e.code, e.read() ) ) + except httplib.IncompleteRead as e: + serverTransaction = False + self.logger.info("IncompleteRead error: %s" % ( e.partial ) ) + if self.dbname != "pubmed": + assert fasta.startswith(">"), fasta + fasta = self.sanitiser(self.dbname, fasta) # + time.sleep(1) + return fasta + + def sanitiser(self, db, fastaseq): + if db not in "nuccore protein" : return fastaseq + regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}") + sane_seqlist = [] + seqlist = fastaseq.split("\n\n") + for seq in seqlist[:-1]: + fastalines = seq.split("\n") + if len(fastalines) < 2: + self.logger.info("Empty sequence for %s" % ("|".join(fastalines[0].split("|")[:4]) ) ) + self.logger.info("%s download is skipped" % ("|".join(fastalines[0].split("|")[:4]) ) ) + continue + if db == "nuccore": + badnuc = 0 + for nucleotide in fastalines[1]: + if nucleotide not in "ATGC": + badnuc += 1 + if float(badnuc)/len(fastalines[1]) > 0.4: + self.logger.info("%s ambiguous nucleotides in %s or download interrupted at this offset | %s" % ( float(badnuc)/len(fastalines[1]), "|".join(fastalines[0].split("|")[:4]), fastalines[1]) ) + self.logger.info("%s download is skipped" % (fastalines[0].split("|")[:4]) ) + continue + fastalines[0] = fastalines[0].replace(" ","_")[:100] # remove spaces and trim the header to 100 chars + cleanseq = "\n".join(fastalines) + sane_seqlist.append(cleanseq) + elif db == "protein": + fastalines[0] = fastalines[0][0:100] + fastalines[0] = fastalines[0].replace(" ", "_") + fastalines[0] = fastalines[0].replace("[", "_") + fastalines[0] = fastalines[0].replace("]", "_") + fastalines[0] = fastalines[0].replace("=", "_") + fastalines[0] = fastalines[0].rstrip("_") # because blast makedb doesn't like it + fastalines[0] = re.sub(regex, "_", fastalines[0]) + cleanseq = "\n".join(fastalines) + sane_seqlist.append(cleanseq) + self.logger.info("clean sequences appended: %d" % (len(sane_seqlist) ) ) + return "\n".join(sane_seqlist) + + def get_sequences(self): + """ + Total number of records from the input set to be retrieved, up to a maximum + of 10,000. Optionally, for a large set the value of retstart can be iterated + while holding retmax constant, thereby downloading the entire set in batches + of size retmax. + + http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch + + """ + batch_size = self.retmax_efetch + count = self.count + uids_list = self.ids + self.logger.info("Batch size for efetch action: %d" % batch_size) + self.logger.info("Number of batches for efetch action: %d" % ((count / batch_size) + 1)) + with open(self.outname, 'w') as out: + for start in range(0, count, batch_size): + end = min(count, start+batch_size) + batch = uids_list[start:end] + self.epost(self.dbname, ",".join(batch)) + mfasta = '' + while not mfasta: + self.logger.info("retrieving batch %d" % ((start / batch_size) + 1)) + mfasta = self.efetch(self.dbname, self.query_key, self.webenv) + out.write(mfasta + '\n') + + +LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s' +LOG_DATEFMT = '%Y-%m-%d %H:%M:%S' +LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] + + +def __main__(): + """ main function """ + parser = optparse.OptionParser(description='Retrieve data from NCBI') + parser.add_option('-i', dest='query_string', help='NCBI Query String') + parser.add_option('-o', dest='outname', help='output file name') + parser.add_option('-l', '--logfile', help='log file (default=stderr)') + parser.add_option('--loglevel', choices=LOG_LEVELS, default='INFO', help='logging level (default: INFO)') + parser.add_option('-d', dest='dbname', help='database type') + (options, args) = parser.parse_args() + if len(args) > 0: + parser.error('Wrong number of arguments') + + log_level = getattr(logging, options.loglevel) + kwargs = {'format': LOG_FORMAT, + 'datefmt': LOG_DATEFMT, + 'level': log_level} + if options.logfile: + kwargs['filename'] = options.logfile + logging.basicConfig(**kwargs) + logger = logging.getLogger('data_from_NCBI') + + E = Eutils(options, logger) + E.retrieve() + + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 0bdc5a73c8d1 retrieve_fasta_from_NCBI.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/retrieve_fasta_from_NCBI.xml Sun Jun 21 14:29:45 2015 -0400 @@ -0,0 +1,64 @@ + + + retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query. + +The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose + +See `Entrez help`_ for explanation of query formats + +Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields. + +Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset) + +**Acknowledgments** + +This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_. + +It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. + +.. _Entrez help: http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options +.. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon +.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en +.. _MIT license: http://opensource.org/licenses/MIT + + + + 10.1186/1471-2105-14-73 + + diff -r 000000000000 -r 0bdc5a73c8d1 test-data/output.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fa Sun Jun 21 14:29:45 2015 -0400 @@ -0,0 +1,134 @@ +>gi|9629650|ref|NC_001834.1|_Drosophila_C_virus,_complete_genome +TTTATATCGTGTGTACATATAAATATGTACACACGGCTTTTAGGTAGAATATTGTTTTCAATGTTGATTT +TAAAGGTAACTTTGGTTATTATGCTTTACGGTTTTCATTGTTGATGGTATTTGTGGCCTGCGGTCCCTAA +TTGTTGAATTATTTATTCTGATACGTTGTTTTCATTGTTGATGGTAAGGATTCTTATTTTGAAGTGGTTT +TTCAGAAGATAACTCTAAATATGAATTATGCCTTATTGTTTTCAATGTTGATGGCCTTCGTTTAAATACT +CTTTGTTAATGACGGTAATCAAAGATTACATCTCAAACTTAGATTAATATTTTTAAGTAGGGTATACTGA +GTTAGTCCTCTCTCTTTACTGATTTTGATATCTGGTAATTGACTTCGAAGAAAGATGCGTCTTTTGGATT +TGTAATGACTGGGCCTTAAGTTCATAGGTGTTATTACATGGAGGAACACATTACTTTGGTTGATGATGAT +GTTTTGATGATGACTTTCAATGTATGTGCTTATGTTAAGCCTGACATAAGAACTTACTAGTTTGCATAAT +GCAAAGGGTTAGTATATGATTTTTAGTATGTGGATTTTGACACTGCCTTTGATTAGGATGTGTGAATGAT +TTTGAAACATATTAAGATGTTTATACGAGCGTGTTGTTTACTATTTTCAGGATATGTGGAAGCGGTTGTG +TATGATCTATACGCACATTTAGTTCCCAGAGGGCGTTGTCGTCTCCCCCTAAGCAAGGGAGAAACACGTG +GCACATGATCTTGCGCTTAACGATAAAAATGGAATCTGATAAAAGTATGGCCTGTTTAAATAGAATTTTG +ATGAATAAGATGATGTTTGTGGAAGATAAGATCTCTACCCTTAAGATGGTTGCTGATTATTATCAAAAAG +AAGTAAAGTATGATTTTGATGCAGTTGAATCTCCCCGTGAGGCACCTGTATTTAGATGTACTTGTCGATT +CCTTGGTTATACCATTATGACTCAAGGCATCGGTAAGAAGAATCCGAAACAGGAAGCTGCACGTCAGATG +TTGCTCTTGTTATCAGGAGATGTTGAGACTAACCCTGGACCCGTTCAATCGCGCCCCGTGTATTATCGTT +ACAACGACCCTAGATATACACGGTTGGAAAAAGCTATTGAACGTCGAGACGATAAAATTAAAACATTAAT +TAAAGAGTTGCGTCGACAAATCAAAAATAGGAAAATTTATTCCCAAGGAATGTTTGATAAATTAACTAAA +CAAATTTCTGATGGGATAAAAGATGGTGTTGGCTCTGAACAGATGAATGGAAATTTGACTCGTATTTGTG +ATTTCCTAGAGAACACTCTTCCTGGGTTACAAGCAAATATTCAAGCCACTGTGATTGATACAACAGACAA +ATATGTTTCTTTAAAAGAGGATATTATGAAGATTGTTTTAGTGATATTGCTTGTTCGTCTTTTAATGGTT +TGGAAGAAGTATCGTGCTTCTCTGTGTGTTATTTTAATCTTTATTTTTAAATTTTATGGATTCGATCAAA +AGTTGATTGATTTAATTATGGATTTGAAGAATAAAATATTTTCACAGGGTGCATTGGAAGATACAGTTGA +GGAGGTTGTATATCATCCTTGGTTCCATACGTGTGGAAAAATCATCTTTGCGGTTATGGCTTTCTTAACA +ATTAAGAAAATTCCTGGTAAACAGGATTGGGATAGTTACATAACACGTTTAGATCGTATCCCAAAATCTA +TTGAGGGAGCTAAAAAGATCACTGATTACTGTTCAGAATATTTTAATATTGCTAATGATCAGATCAAGAT +GATGGTTCTTGGAAAGACTAAAGAAGAATTGCAACGTGCTAATGGACTATATGGAGAAATTCAAGCTTGG +GCTCAAGAGGTTCGCCAGTATTTGGAATTGGATCAACGGAATAAAATTGATCTAGATACTGAAACCGCAA +ATCGTGTTGAACAACTTTGGATAAAGGGCTTGAAATTCAAGAGTGAACCCCTTTTGAGTAAGGAAATGTC +AGCTTTAGTTCATACAACTCTTTTACCAGCTAAGCAATTGTACGAGTATGTATCGTGTTCTCCTGTTAAA +GGGGGAGGACCACGTATGCGTCCAATTTGTTTATGGTTGGTAGGTGAATCAGGAGTTGGTAAGACTGAAA +TGGTATATCCATTGTGCATTGATGTTCTTCGGGAAATGGGGATGATTAAGAAAGATGATTTTCATCATCA +AGTTTATGGTCGTCAAGTTGAAACTGAATTCTGGGATGGTTATAAAGGACAGAAAATTGTCATTTATGAT +GATGCATTTCAGAAGAAAGATGACAAAACAGCAGCTAACCCAGAAATTTTTGAGGTTATTCGCTCTTGCA +ACACTTTTCCTCAGCATTTACATATGGCAGCTCTTCATGATAAAAATACTTTTTCTGCTGCTGAATTACT +CTTATATACCACTAATGATTATAATGTTAAGCTGGAATCTATTACTTTTCCCGATGCTTTCTTTAATCGT +ATGGGCGATATGGCTTATAAAGTTAGTCCTAAGAAAGAGTATGGTATTGAAACCGAGAAAGGGAATTCAG +GTAAAACTTATTTAAAATTGGATAAGAGTAAATTGGACAAAACAAAAGCTATTGACCTTTCAGTGTATGA +ATTCCAAAAAATTGTACGTGACGAGAAAAGTGATGCAGGTTGGATTGATTCTGGATCACCCTTGGACTAT +GAAGATTTTGCTAAATTAGTGTGTTCAAAATGGAAAGAAGCGAAACAATCTTCAATGAATAAATTGAAAT +TTTTGGAAGAATATGCTATTCGTGCTCAGGTTGGATCAGAAGAAAATTCTGAATATGGTGATTGTATAGA +TTTTGTCGATGATATTGCCAAACGCTTACAAAAAGGTGAAACTCTTGAAGAAATAGAGTTTGATTATGCC +TCAGATCCAGAGATGTTTACTCAATACTATCATTTTAAATCTACAATTAAACCGGCATCGCGTTGGCAGA +AGTATAAGGATCGGATGGACATTTGTTTGAGCGACTGTAAGACTTATTTAGCAAAGAAATACGAAGAAAT +TAAGAAAATTCTTGCCGAACATCCTATCTTGACGATTTTAGGAATGATAGGGGTTGCCTTATCTGCTCTG +GCAATGTACTATTGGTTTTCTAAATCGTTGGATCCTGTAGAAGCCGAGGTTGCTCCTTCTGGTGACGCTA +AAACAGTGCGCTTACCAAGGAAACTCGTTGAGATTGGTGCTTCTGGAGATGTTAAAACACAGAAGATTGT +GAAACCCGTTGTAGAGACCGAATGGCATCGTAACAATAAAGGAGAGATTGAAATTTCTTGTGATGAATGT +GGTATGCATAGGATGTCTGCATTTAACAATATGACAGATGAAGAATTTGATAACTGTACATATGAAGATT +TGAATAAGGACCAGAAACGTGAACTTGCCCAGTGGTCTACTAAAGATTCTTGGTTAGGTCGATTCTTTTT +GAGTCGAGATCGCAAGAATAAGGTTGGAATTTGGGCCGAAGTGGGACAATCAGGTGATGTTAAAACAAAT +AAAGCTCAGATTAAACGTGTTGAAGCTGGAGCCGAAGAATTAGTTACTGTTGCTTTAACTCAAGGTTGTT +CTGATGATGCTGCACACAATTTGATGATTGACGTTTTCCAAAAAAATACATATAGAATGTCATACTTCCG +TGGAGACAAGCGTTATCAACTTGGAAATTGTACATTTGTTCGTGGTTGGTCTTTTATTATGCCATATCAT +TTTGTACAGGCTGTGTTTGCGCGAAGATTGCCACCTAACACGATTATTTCTTTGTCCCAACAGATGTCTG +AAGATTTAATGCAAATTCCATTATCACACTTCTTTTCTGCTGGTGTTGACAATTTTTATTTAACAGATAA +TTGTGTGCGCTTGCCATTTAAAAATGGAGATTTTCGCGATTGTGTTATGGTTAATTTACATTCACGAATG +TGCACGCCACATCGTGATTTGGTTCGGCATTTTATTTTAACTTCTGATCAAGGTAAATTGAAGGGATCTT +TTAGTGGTGCAATGGCAACTTTCCATGTTAACAATATGGGTTTATATCGTGTTTATAATTGGCTAAATGC +AGTTCGTCCTTGCGATAAAAAGATAGAAATTTTCCACCCTGAAGATGGTTTTGAGTATCCCGAAGAATCA +TATATTCAACGTGACTGTTATGAATATAATGCACCGACTCGTACTGGGGATTGTGGATCTATTATTGGAT +TGTATAATAAATATTTAGAAAGGAAAATCATCGGTATGCACATTGCTGGAAATGATGCAGAAGAGCATGG +TTATGCGTGCCCTTTGACACAAGAGTGTCTTGAGACTGCTTTTTCTGCTTTAGTAAATAAAAATAAGAAG +AATATTTCCTCACAATTTTATTATGAAATACCCAATATGGTTGATCCACTCGGTGATAGTAGTGTTCCTG +AAGGTAAGTTTTACGCTTTAGGAAAGTCATCTATTCGTGTGGGACAGGCAGTTAATTCGTCCATAATTCC +TTCTCGAATTTATGGGAAGTTGTCTGTTCCTACAATGAAACCAGCACTACTCAAGCCAACGATTCTGAAT +AACAAAGTACATAATCCTTTATTGTCGGGACTTAAGAAATGTGGTGTAGACACTGCGGTCTTGAGTGATG +ATGAAGTTTTGAGTGCTTCACAAGATGTTTGTCGTGTTATGTTGAACCAATATAATAAAAATTTGAATAA +AACAAAGTATCAACGCATTTTAACATATGAGGAAGCTATTCGTGGAACCCAAGATGATGAATTTATGTGT +GCTATTAATCGTACAACGTCACCAGGATTTCCTTATGCACAAATGAAAAGAAATGCTCCAGGTAAACAGC +AATGGATGGGTTTTGGTGAAGAATTTGATTTTACAAGTAATTATGCACTAGCTTTGCGGAAAGATGTTGA +ACAACTCATTGAAGATTGTGCTAGCGGAAAAATATCTAATGTCATTTTTGTAGATACATTGAAAGATGAG +CGACGCGATATAGCTAAAGTAAATGTAGGTAAAACGCGTGTATTTTCTGCAGGTCCTCAACATTTTGTAG +TTGCATTTCGCCAATATTTCCTACCTTTTGCTGCTTGGTTGATGCATAATCGCATTTCGAACGAAGTAGC +AGTTGGCACTAATGTTTATTCATCTGATTGGGAACGTATTGCAAAACGTCTTAAAACAAAAGGTAGTCAC +GTCATTGCGGGGGACTTTGGAAATTTCGATGGATCTTTAGTAGCACAAATTTTGTGGGCCATATTTTGGG +AAATTTTTGTTGTATGGCTTAAGCAATTTATTGATATAGAGAATTCAGAAGGAAAACGTATTTTATGTAT +CTGTCTTGGTTTGTGGTCACATTTAGTTCACTCTGTTCATATTTATGAAGATAATGTATATATGTGGACT +CATTCTCAACCTTCTGGCAATCCTTTCACTGTTATTATTAATTGCTTGTATAATTCGATTATTATGCGAC +TGTCATGGATTCGTGTGATGGAGAAATTTCAACCTAGACTTAAGTCCATGAAGTGGTTCAACGAATATGT +CGCCTTGATAACATATGGTGACGACAATGTTTTAAACATTGATGCAAAGGTTGTGGAATGGTTTAATCAG +ATTAACATTAGTGAGGTTATGACTGAAATGCGACATGAATATACGGACGAAGCTAAAACTGGTGATATTG +TTAAATCTCGTAAATTAGAAGATATTTTCTTTTTGAAGAGAAAATTTCGTTTTAGCCCAGAATTACAACG +CCATGTTGCTCCATTGAAGATCGAAGTTATTTATGAAATGTTGAATTGGTCTCGCCGCTCTATAGATCCA +GATGAAATCTTGATGTCGAACATTGAAACGGCTTTTCGTGAAGTAGTTTACCACGGAAAAGAAGAATACG +ATAAACTAAGGTCAGCGGTATTGGCGTTGAAGGTACCCCAGGAACTTCCTGAAAACCCTCAGATTTTGAC +GTACAACCAATATTTGCACGATATTGAATATCTTGCGGACCCTTTGTACGACTTTTAGTTAAGATGTGAT +CTTGCTTCCTTATACAATTTTGAGAGGTTAATAAGAAGGAAGTAGTGCTATCTTAATAATTAGGTTAACT +ATTTAGTTTTACTGTTCAGGATGCCTATTGGCAGCCCCATAATATCCAGGACACCCTCTCTGCTTCTTAT +ATGATTAGGTTGTCATTTAGAATAAGAAAATAACCTGCTAACTTTCAAACAAATAATAATAACATTGAAA +ATGAAGATCGGAAAATTACTTCCGAGCAAAAAGAGATTGTACACTTTTCTAGTGAAGGAGTTACCCCTAG +TACCACTGCGGTGCCTGATATCGTTAGTCTTTCAACAGATTATTTGTCTATGACTACTCGTGAAGATCGT +ATCCACACGATTAAAGATTTTCTTTCTCGTCCAATTATAATTCAAACTGGTCTTTGGTCTTCCGCTACAA +CTGCCGAAACTCAATTGTATACTGCTAATTTCCCTGAAGTGTTCATTTCTAATACTATGTATCAAGAAAA +GTTGCGTGGGTTCGTGGGTTTGCGAGCAACTTTAGTCATTAAAGTGCAAGTGAATTCCCAACCTTTCCAG +CAAGGACGATTGATGCTACAGTATTATCCGTATGCACAGTATATGCCTAACCGTGTTTCTTTGGTGAATT +CCACTCTCCAAGGACGCTCTGGTTGTCCTCGAACAGATTTGGATTTGAGCGTTGGTACGGAAGTTGAAAT +GCGAATTCCTTATGTGTCCCCTCATGTATATTACAATCTTATTACTGGACAAGGATCATTTGGCGCTATA +TATTTGGTTGTATATAGCCAACTAAGAGATCAAGTTACAGGAACAGGTTCTGTTGAATATACTGTTTGGG +CTCATTTGGAAGATGTAGATGTGCAATACCCGACCGGTGCAAACATTTTCACGGGTAGCTCTCCAAATTT +TGCCTCTTTGGGTCAGAAAATGAGTGATGGAAAATTCACTGAAAAAGACTTGAGAGATATTTGGACTTCA +AAAGCGTACAATAAACAACCAGACAAAATTTTCGCACAAGTGGCTTCTGAAATAACACAACTCAAAGAAT +CAGGAACAATTAGTTCTGGAATTGGACAAGTTTCTGAAGGTCTTTCTACCATGTCTAAAATCCCTATACT +CGGAAATATGTTTACAAAACCCGCCTGGATTTCAGCTCAAGTATCTAATATCTTCAAGATGCTTGGTTTT +TCAAAACCCACTGTTCAAGGTCTTCCTTGTGAATCGAAACTGCGTGGTCAAGTTCGAATGGCGAATTTTG +ATGGCGCTGATACATCACATAAATTGGCTTTGTCTGCCCAAAACGAAATTGAAACAAAATCTGGACTTTC +TGGAACTTCTCCTGATGAAATGGATTTATCACACGTCCTTTCCATACCAAATTTTTGGGATCGTTTTACT +TGGAACACAACCGATGCCACTAGTTCTATTTTATGGGATAATTATGTTACACCAATGAAAATTAAACCAT +ATTCCTCTACAATATTAGATAGATTTAGATGCACTCATATGGGTTTTGTAGCCAACACACACGGTTATTG +GTGTGGATCAATAGTTTATACTTTTAAATTTGTTAAGACTCAATTTCATTCTGGACGTTTACGCATTAGT +TTTATTCCATTTTATTATAATACGACTATATCTGCAGGAGTTCCCGATGTTTCTCGTACCCAAAAAGTAA +TCGTTGATCTGCGCACCTCTACAGAAGTCTCTTTCACTATTCCGTATGTGTCTTCACGACCTTGGATGTA +CTGTATTCGTCCTGAAGCTTCGTGGCTTGGAACCGATAATGCTTTGATGTACAACGCCGTTACGGGTATA +GTGAGAGTTGAGGTTCTTAACCAGTTGGTTGCCGCTAACAACGTGTTTCAATCTATAGACACTATTGTTG +AAGTTAGTGGTGGTCCTGATTTAACTTTTGCAGCACCAATGGCTCCCTCTTATGTTCCTTATTCTGGAGG +TTTTACTTTAGCAGATGATGCGGCAGCAAAGAAACAGCGTGAGGAGGAGTATGACAACAACATACCTCAA +ACTATTTCTAATCGTGGAAAACGTGAGGTTGAAGATGCTCGTATTGTTGCGCAAGTAATGGGTGAAGATT +TAGCTATTCAAAGAAACGATGCTCAACATGGTGTTCATCCAATGACTATAGACACTCATAAGATCGACTC +AAATTGGTCTCCGGAAGCGCATTGTATTGGTGAAAAGATTATGTCTATTCGCCAATTGATTAAGCGTTTT +GGCATGGCTTTGAACTCCTTGAATTTGATAAGTGATGCACCAAACACCTTGATAGCACCATTTTCAGTTC +AGCACCCAACTCCTGTTGTTGCCCCTGCTGAACCCATGTCCCTTTTTGAATATTATTATTTCATTTATGG +ATTTTGGAGAGGTGGCATGAGATTTAAACTTCAGGCAGTACGTACAAACTCAGCAGAAACATCAGTTAAA +ACCGACACAACTTGGACTGTAAATTTGTGGAATTCTGTACAAGATTCTTTTAATTCTCTAATTAATGTAT +TTAGTACTACTGATTACCCTATAAAATCCACAGGAGCACTTCCAGCCGGAACAAGCGGTTTTGGCAATTC +GATGACGTATATAGATCCTGAGGTTGAAGGTTTTATGGAATTTGAGATTCCATATTATAATATCTCCCAT +ATTTCTCCAGCTACAACCTATGTTCGTGGTACTGAATCTCCTATTACAATTAATAGTGTCTTGCGTGGAC +ATTTGCCACCACAAATTGTGGCTGTTGCACCACAGGGCACTATTGCCACTACAGATGTAGTGAACGCTCA +ATTTGCTCGTGCTCCTTCTGACGACTTTTCATTTATGTATCTCGTTGGTGTTCCACCACTTACCAACGTC +GCTCGTCCCTAACTCCCTTACTATTCTGGATCCTTTAAAATTTATTAGGATAGACAAAAATTAACTCTAT +ATTAGATAGTATTAGATTAAGTTTCTTTTTGGTTTTGGGTTTTATTCAGTAACTATCTGCCCTGCTTACA +CGGGTATTATTTTTAATTCTTGTCCCTTCTGGACTCTTTTATTTTGTATTTTCAAAATTTTTACTAATTT +TTAGTCAGAGTCCTTAGGGGCTACCAGGTTTTTCGCAATTTTCCTGCTTACTGACAGTAATTGCAATTTC +GAATTAAAATAATAGTTGTTTTCT