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src/m/g/mgtaxa-HEAD/MGT/FastaSplitters.py   mgtaxa(Download)
def mapFastaRecordsToTaxaTree(inSeqs,taxaTree,giToTaxa,
        storeHeader=False,storeSeq=False,storeSeqLen=False):
    from MGT.FastaIO import FastaReader
    if taxaTree is None:
        taxaTree = loadTaxaTree()
    if giToTaxa is None:
        giToTaxa = loadGiTaxBin()
    taxMis = Struct()
    for inSeq in inSeqs:
        inpSeq = FastaReader(inSeq)
def splitFastaFilesByTaxa(inSeqs,outStore,taxaTree=None,giToTaxa=None,filt=None):
    """@param outStore SeqDbFasta instance"""
    from MGT.FastaIO import FastaReader
    if taxaTree is None:
        taxaTree = loadTaxaTree()
    def _multi_iter():
        for inSeq in inSeqs:
            inpSeq = FastaReader(inSeq)
            for rec in ncbiFastaRecordsWithTaxa(fastaReader=filt(inpSeq),
                    taxaTree=taxaTree,
    will be skipped
    """
    from MGT.FastaIO import FastaReader
    if not modelsMeta:
        checkTaxa = False

src/m/g/mgtaxa-HEAD/MGT/Proj/HctApp.py   mgtaxa(Download)
 
from MGT.Taxa import *
from MGT.FastaIO import FastaReader
from MGT.App import *
 
        else:
            inFasta = pjoin(options.refSeqDataDir,"%s.genomic.fna.gz" % orgType)
        inp = FastaReader(inFasta)
        for rec in inp.records():
            line = rec.header()[1:]
    def loadProtIdsOrgType(self,db,idGenSeq,inserterSeq,orgType):
        """Load Fasta deflines for protein sequences generated by pullSeq, parse and insert them into SQL table.
        """
        inFasta = self.store.getFilePath('%s.protein.cat.gz' % orgType)
        inp = FastaReader(inFasta)

src/m/g/mgtaxa-HEAD/MGT/Proj/GbFeatApp.py   mgtaxa(Download)
 
from MGT.Taxa import *
from MGT.FastaIO import FastaReader
from MGT.App import *
 
                normPolicy=NORM_POLICY.FREQ)
        for fastaFile in self.store.getFilePaths("*.fasta.gz"):
            inpFasta = FastaReader(fastaFile)
            iRec = 0
            for rec in inpFasta.records():

src/m/g/mgtaxa-HEAD/bin/gosToSvm.py   mgtaxa(Download)
from MGT.Common import *
from MGT.Svm import *
from MGT.FastaIO import FastaReader
#from MGT.SampDb import *
#from MGT.SampDbKmer import *
    elif opt.outFormat == "fasta":
        svmWriter = SvmFastaFeatureWriterTxt(outName,lineLen=opt.fastaLineLen)
    inpSeq = FastaReader(inFileFasta)
    if opt.degenLen >= 0:
        symCompr = SymbolRunsCompressor('N',opt.degenLen)