codonoptimizer/KazusaSPSUMHandler.py at master · hoerldavid/codonoptimizer · GitHub

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'''
Created on 07.02.2015

@author: david
'''

from os import listdir
from os.path import join

from CUTable import CUTable

class KazusaSPSUMHandler(object):
    '''
    classdocs
    '''


    def __init__(self, path=""):
        '''
        Constructor
        '''

        self.taxidToCodonUsage = dict()
        self.descToTaxidAndNCDS = dict()

        if not path:
            pass
        else:
            self.loadSPSUMFromPath(path)


    def loadSPSUMFromPath(self, path):
        '''

        '''

        files = listdir(path)

        for f in files:
            if f.endswith(".spsum"):
                self.readSPSUMFile(join(path, f))
            elif f == "SPSUM_LABEL":
                self.readSPSUM_LABEL(join(path, f))


    def readSPSUMFile(self, file):
        fd = open(file)

        while True:

            descLine = fd.readline()
            if not descLine: break

            cu = fd.readline()

            # split into taxid:desc:nrCDS
            taxid = descLine.split(":", 1)[0].strip()
            desc = descLine.split(":", 1)[1].strip()
            ncds = desc.rsplit(":", 1)[1].strip()
            desc = desc.rsplit(":", 1)[0].strip()

            self.taxidToCodonUsage[taxid] = cu.strip()
            self.descToTaxidAndNCDS[desc] = (taxid, ncds)

        fd.close()

    def readSPSUM_LABEL(self, file):

        fd = open(file)
        fd.readline() # omit first line

        self.SPSUM_LABEL = fd.readline().strip()

        fd.close()


    def search(self, query):
        '''
        '''

        res = dict()

        for desc, taxidNCS in self.descToTaxidAndNCDS.items():
            if desc.find(query) != -1:
                res[desc] = taxidNCS

        return res

    def getCUTable(self, taxid):
        '''
        '''
        res = CUTable(self.SPSUM_LABEL, self.taxidToCodonUsage[taxid])
        return res