Add code

FastqReader.py

+# -*- coding: utf-8 -*-
+
+"""
+@package    Sekator
+@brief      Contain an iterator function to read fastq files and return FastqSeq objects
+@copyright  [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
+@author     Adrien Leger - 2014
+* <adrien.leger@gmail.com>
+* <adrien.leger@inserm.fr>
+* <adrien.leger@univ-nantes.fr>
+* [Github](https://github.com/a-slide)
+* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
+"""
+
+# Standard library imports
+from gzip import open as gopen
+
+# Local imports
+from FastqSeq import FastqSeq
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+# FUNCTIONS
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+
+def FastqReader (fastq_file):
+    """ Simple fastq reader returning a generator over a fastq file """
+    try:
+
+        # Open the file depending of the compression status
+        fastq = gopen(fastq_file, "rb") if fastq_file[-2:] == "gz" else open(fastq_file, "rb")
+        i=0
+
+        # Iterate on the file until the end
+        while True:
+
+            # Extract informations from the fastq file
+            name, seq, sep, qual= next(fastq), next(fastq), next(fastq), next(fastq)
+
+            # Try to generate a valid FastqSeq object
+            try:
+                yield FastqSeq(
+                name = name.rstrip()[1:].split()[0],
+                seq = seq.rstrip(),
+                qualstr = qual.rstrip())
+
+                i+=1
+
+            except AssertionError as E:
+                print(E)
+                print ("Skipping the sequence")
+
+    except IOError as E:
+        print(E)
+        print ("Error while reading {} file".format(fastq_file))
+        exit()
+
+    except StopIteration:
+        raise StopIteration("\t{} sequences parsed".format(i))

FastqSeq.py

+# -*- coding: utf-8 -*-
+
+"""
+@package    Sekator
+@brief      Contain a class to model a fastq sequence and an iterator function to read fastq files
+@copyright  [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
+@author     Adrien Leger - 2014
+* <adrien.leger@gmail.com>
+* <adrien.leger@inserm.fr>
+* <adrien.leger@univ-nantes.fr>
+* [Github](https://github.com/a-slide)
+* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
+"""
+
+# Third party imports
+import numpy as np
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+class FastqSeq (object):
+    """
+    Simple Representation of a fastq file. The object support slicing and addition operations
+    The quality score is a numpy array to facilitate further data manipulation
+    Only works with illumina 1.8+ Phred 33 quality encoding
+    """
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+
+
+    #~~~~~~~FUNDAMENTAL METHODS~~~~~~~#
+
+    def __init__ (self, name, seq, qualstr, descr=""):
+        """
+        @param name Name of the sequence (without spaces)
+        @param seq DNA sequence string
+        @param qual string of quality encoded in illumina 1.8+ phred +33
+        @param descr Facultative description
+        """
+        self.name = name
+        self.seq = seq
+        self.qual = np.array([ord(x)-33 for x in qualstr])
+        self.descr = descr
+
+        assert len(self.seq) == len(self.qual), "Sequence length and quality string length are not equal."
+
+    def __repr__(self):
+        return "<Instance of {} from {} >".format(self.__class__.__name__, self.__module__)
+
+    def __str__(self):
+        if len(self) > 20:
+            return "{} : {}...{}  {}...{}".format(self.name, self.seq[:10], self.seq[-10:], self.qual[:10], self.qual[-10:])
+        else:
+            return "{} : {}  {}".format(self.name, self.seq, self.qual)
+
+    #~~~~~~~PROPERTIES~~~~~~~#
+
+    @property
+    def qualstr(self ):
+        """Compute the quality string from the numpy int array """
+        qualstr_phred = ""
+        for i in self.qual:
+            qualstr_phred += str(unichr(i+33))
+        return qualstr_phred
+
+    @property
+    def fastqstr(self):
+        """Return string formated as a fastq sequence"""
+        if self.descr:
+            return "@{} {}\n{}\n+\n{}\n".format(self.name, self.descr, self.seq, self.qualstr)
+        else:
+            return "@{}\n{}\n+\n{}\n".format(self.name, self.seq, self.qualstr)
+
+
+    #~~~~~~~MAGIC METHODS~~~~~~~#
+
+    def __len__ (self):
+        """Support for len method"""
+        return len(self.seq)
+
+    def __getitem__( self, item ):
+        """Support for slicing operator"""
+        return FastqSeq(name = self.name, seq = self.seq[ item ], qual = self.qual[ item ])
+
+    def __add__(self, other):
+        """Support for concatenation of fastqSeq objects = + operator"""
+        return FastqSeq(
+            name = "{}_{}".format(self.name, other.name),
+            seq = self.seq+other.seq,
+            qual = np.concatenate((self.qual, other.qual)),
+            descr = self.descr+other.descr)

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-

README.md

-# pyFastq
-Simple python 2.7 tools to parse fastq files
+# pyFastq 0.1
+
+**Simple python 2.7 libraries to parse fastq files and handle illumina 1.8+ fastq sequences**
+
+**Creation : 2015/04/02**
+
+**Last update : 2015/04/02**
+
+## FastqReader
+Parsing function that reads a fastq file and generates an iterator of FastqSeq object.
+When the file is empty the generator raise a StopIteration exception indicating the number of valid sequence parsed. If a fastq sequence is invalid, this sequence is skipped.
+Any part of the sequence name following a blank space will be removed
+
+## FastqSeq : Simple object representing a Fastq sequence
+FastqSeq is a simple python object class generating a object representing a fastq sequence. The object is initialised with a name, a DNA sequence, an **illumina 1.8+ Phred +33** encoded quality sequence (same size than the DNA sequence) and eventually a short text description. After creation the object has the following fields:
+
+* name = name of the sequence without @.
+* seq = The DNA sequence of the fastq sequence store as a simple string.
+* qual = An numpy integer array representing the Phred Quality of bases (support all np.array methods)
+* descr = A description of the fastq sequence.
+* qualstr = A string of letters corresponding to the sequence quality in illumina 1.8+ Phred 33 encoding
+* fastqstr = The field "descr" will be included in the output fastq sequence name after a space if present
+
+The object support slicing([0:10]), concatenation(seq1+seq2) and the len method
+
+## Authors and Contact
+
+Adrien Leger - 2015
+
+* <adrien.leger@gmail.com> - <adrien.leger@inserm.fr> - <adrien.leger@univ-nantes.fr>
+* [Github](https://github.com/a-slide)
+* [Atlantic Gene Therapies - INSERM 1089](http://www.atlantic-gene-therapies.fr/)

__init__.py

+# -*- coding: utf-8 -*-
+"""
+@package    pyFastq
+@brief      **Simple python 2.7 libraries to parse fastq files and handle fastq sequences**
+* FastqReader : Parsing function reading a fastq file and generating an iterator of FastqSeq object
+* FastqSeq : Simple object representing a Fastq sequence
+
+@copyright  [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
+@author     Adrien Leger - 2015
+* <adrien.leger@gmail.com>
+* <adrien.leger@inserm.fr>
+* <adrien.leger@univ-nantes.fr>
+* [Github](https://github.com/a-slide)
+* [Atlantic Gene Therapies - INSERM 1089] (http://www.atlantic-gene-therapies.fr/)
+"""
+
+__all__ = ["FastqReader", "FastqSeq"]
+__version__ = 0.1