Mercurial > repos > crs4 > edge_pro
diff get_edge_data.py @ 1:f77ce4f92b46 draft
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
| author | crs4 |
|---|---|
| date | Fri, 31 Jan 2014 05:44:03 -0500 |
| parents | 7af33315bc5e |
| children | 407b894abb08 |
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--- a/get_edge_data.py Mon Sep 09 06:11:47 2013 -0400 +++ b/get_edge_data.py Fri Jan 31 05:44:03 2014 -0500 @@ -4,7 +4,7 @@ import optparse import sys -class GetData: +class GetData(object): def __init__(self, gbkid, fnafile, pttfile, rntfile, gfffile): self.gbkid = gbkid @@ -14,9 +14,6 @@ self.gfffile = gfffile self.ftpurl = 'ftp.ncbi.nlm.nih.gov' self.folder = '/genomes/Bacteria/' - - def getData(self): - """ """ strainName = self._getStrainName() print strainName if not strainName: @@ -25,7 +22,7 @@ ftp.login() newDir = self.folder + strainName ftp.cwd(newDir) - + directoryFiles = [] ftp.retrlines('NLST', directoryFiles.append) for fileName in directoryFiles: @@ -58,7 +55,7 @@ ftp = FTP(self.ftpurl) ftp.login() ftp.cwd(self.folder) - + straindirectories = [] ftp.retrlines("NLST " , straindirectories.append) #print "scanning directories..." @@ -77,7 +74,6 @@ def __main__(): - """ main function """ parser = optparse.OptionParser() parser.add_option('-i', dest='gbkid', help='RefSeq Genomic Accession ID') parser.add_option('--fna', dest='fnafile', help='Output FASTA file name') @@ -87,9 +83,8 @@ (options, args) = parser.parse_args() if len(args) > 0: parser.error('Wrong number of arguments') - - S = GetData(options.gbkid, options.fnafile, options.pttfile, options.rntfile, options.gfffile) - S.getData() + + GetData(options.gbkid, options.fnafile, options.pttfile, options.rntfile, options.gfffile) if __name__ == "__main__":