Source code for tools.parsers.FastqTools

import os

[docs]class FastqEntry(object) : """A single entry in the FastqEntry file""" def __init__(self, ident = "", seq = "", plus = "", qual = "") : self.values = {} self.values['identifier'] = ident self.values['sequence'] = seq self.values['+'] = plus self.values['qualities'] = qual def __getitem__(self, i): return self.values[i] def __setitem__(self, i, v) : self.values[i] = v def __str__(self): return "%s\n%s\n%s\n%s" %(self.values['identifier'], self.values['sequence'], self.values['+'], self.values['qualities'])
[docs]class FastqFile(object) : """ Represents a whole CSV file:: #reading f = FastqFile() f.parse('hop.csv') for line in f : print line['sequence'] #writing, legend can either be a list of a dict {field : column number} f = CSVFile(legend = ['name', 'email']) l = f.newLine() l['name'] = 'toto' l['email'] = "hop@gmail.com" f.save('myCSV.csv') """ def __init__(self, fil = None) : self.reset() if fil != None : self.parseFile(fil)
[docs] def reset(self) : """Frees the file""" self.data = [] self.currentPos = 0
[docs] def parseStr(self, st) : """Parses a string""" self.data = st.replace('\r', '\n') self.data = self.data.replace('\n\n', '\n') self.data = self.data.split('\n')
[docs] def parseFile(self, fil) : """Parses a file on disc""" f = open(fil) self.parseStr(f.read()) f.close()
def __splitEntry(self, li) : try : self.data['+'] return self.data except : self.data[li] = FastqEntry(self.data[li], self.data[li+1], self.data[li+2], self.data[li+3])
[docs] def get(self, li) : """returns the ith entry""" i = li*4 self.__splitEntry(i) return self.data[i]
[docs] def newEntry(self, ident = "", seq = "", plus = "", qual = "") : """Appends an empty entry at the end of the CSV and returns it""" e = FastqEntry() self.data.append(e) return e
[docs] def add(self, fastqEntry) : """appends an entry to self""" self.data.append(fastqEntry)
def save(self, filePath) : f = open(filePath, 'w') f.write(self.make()) f.close() def toStr(self) : st = "" for d in self.data : st += "%s\n%s" % (d[0], d[1]) return st def __iter__(self) : self.currentPos = 0 return self def next(self) : #self to call getitem, and split he line if necessary i = self.currentPos +1 #print i-1, self.currentPos if i > len(self) : raise StopIteration() self.currentPos = i return self[self.currentPos-1] def __getitem__(self, i) : """returns the ith entry""" return self.get(i) def __setitem__(self, i, v) : """sets the ith entry""" if len(v) != 2: raise TypeError("v must have a len of 2 : (header, data)") self.data[i] = v def __len__(self) : return len(self.data)/4