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1 # -*- coding: utf-8 -*-
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2
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3 from ftplib import FTP
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4 import optparse
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5 import sys
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6
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7 class GetData:
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8
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9 def __init__(self, gbkid, fnafile, pttfile, rntfile, gfffile):
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10 self.gbkid = gbkid
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11 self.fnafile = fnafile
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12 self.pttfile = pttfile
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13 self.rntfile = rntfile
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14 self.gfffile = gfffile
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15 self.ftpurl = 'ftp.ncbi.nlm.nih.gov'
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16 self.folder = '/genomes/Bacteria/'
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17
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18 def getData(self):
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19 """ """
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20 strainName = self._getStrainName()
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21 print strainName
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22 if not strainName:
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23 sys.exit("Unrecognized RefSeq Genomic Accession ID")
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24 ftp = FTP(self.ftpurl)
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25 ftp.login()
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26 newDir = self.folder + strainName
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27 ftp.cwd(newDir)
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28
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29 directoryFiles = []
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30 ftp.retrlines('NLST', directoryFiles.append)
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31 for fileName in directoryFiles:
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32 try:
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33 if '.fna' in fileName and self.gbkid in fileName:
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34 #print "downloading", fileName
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35 with open(self.fnafile, 'w') as outFile:
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36 ftp.retrbinary("RETR " + fileName, outFile.write)
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37 elif '.ptt' in fileName and self.gbkid in fileName:
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38 #print "downloading", fileName
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39 with open(self.pttfile, 'w') as outFile:
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40 ftp.retrbinary("RETR " + fileName, outFile.write)
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41 elif '.rnt' in fileName and self.gbkid in fileName:
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42 #print "downloading", fileName
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43 with open(self.rntfile, 'w') as outFile:
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44 ftp.retrbinary("RETR " + fileName, outFile.write)
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45 elif '.gff' in fileName and self.gbkid in fileName:
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46 #print "downloading", fileName
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47 with open(self.gfffile, 'w') as outFile:
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48 ftp.retrbinary("RETR " + fileName, outFile.write)
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49 #elif '.gbk' in fileName and self.gbkid in fileName:
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50 # print "downloading", fileName
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51 # with open(fileName, 'w') as outFile:
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52 # ftp.retrbinary("RETR " + fileName, outFile.write)
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53 except:
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54 pass
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55
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56 def _getStrainName(self):
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57 """ """
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58 ftp = FTP(self.ftpurl)
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59 ftp.login()
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60 ftp.cwd(self.folder)
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61
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62 straindirectories = []
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63 ftp.retrlines("NLST " , straindirectories.append)
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64 #print "scanning directories..."
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65 for strainName in straindirectories:
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66 try:
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67 newDir = self.folder + strainName
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68 ftp.cwd(newDir)
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69 strainFiles = []
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70 ftp.retrlines('NLST', strainFiles.append)
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71 for element in strainFiles:
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72 if self.gbkid in element:
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73 return strainName
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74 except:
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75 pass
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76 return None
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77
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78
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79 def __main__():
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80 """ main function """
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81 parser = optparse.OptionParser()
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82 parser.add_option('-i', dest='gbkid', help='RefSeq Genomic Accession ID')
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83 parser.add_option('--fna', dest='fnafile', help='Output FASTA file name')
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84 parser.add_option('--ptt', dest='pttfile', help='Output PTT file name')
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85 parser.add_option('--rnt', dest='rntfile', help='Output RNT file name')
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86 parser.add_option('--gff', dest='gfffile', help='Output GFF file name')
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87 (options, args) = parser.parse_args()
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88 if len(args) > 0:
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89 parser.error('Wrong number of arguments')
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90
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91 S = GetData(options.gbkid, options.fnafile, options.pttfile, options.rntfile, options.gfffile)
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92 S.getData()
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93
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94
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95 if __name__ == "__main__":
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96 __main__()
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