diff utils/fastqreader.py @ 18:e4d75f9efb90 draft

planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils/fastqreader.py	Thu Feb 02 18:44:31 2017 -0500
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+import os
+__version__ = '0.5'
+
+
+class FastqReadGenerator(object):
+  """A simple FASTQ parser that returns reads one at a time.
+  Handles multi-line read/quality values.
+  Usage:
+  fastq = FastqReadGenerator('/home/user/sequence.fq')
+  for read in fastq:
+    print "There is a read with this identifier: "+read.id
+    print "(Its full name is "+read.name+".)"
+    print "Its sequence is: "+read.seq
+    print "Its quality is:  "+read.qual
+  All values (id, name, seq, qual) are whitespace-stripped.
+  """
+
+  def __init__(self, filepath):
+    if not os.path.isfile(filepath):
+      raise IOError('File not found: "'+filepath+'"')
+    self.filepath = filepath
+    self.name = None
+    self.id = None
+
+  def __iter__(self):
+    return self.reads()
+
+  def reads(self):
+    with open(self.filepath, 'rU') as filehandle:
+      read = None
+      line_type = 'first'
+      for line_raw in filehandle:
+        line = line_raw.strip()
+        if not line:
+          continue  # allow empty lines
+        # Determine what kind of line we're in
+        if line.startswith('@'):
+          if line_type == 'first':
+            line_type = 'name'
+          elif line_type == 'plus':
+            line_type = 'qual'
+          elif line_type == 'qual':
+            # Determine if it's another qual line or a name line.
+            # If the quality scores observed so far already cover the whole read, we've seen all
+            # the quality information already. It should be a name line.
+            if len(read.qual) >= len(read.seq):
+              line_type = 'name'
+            else:
+              line_type = 'qual'
+          else:
+            raise FormatError('"@" starts line in wrong context:\n'+line_raw)
+        elif line.startswith('+'):
+          if line_type == 'seq':
+            line_type = 'plus'
+          elif line_type == 'qual':
+            pass
+          else:
+            raise FormatError('"+" starts line in wrong context:\n'+line_raw)
+        elif line_type == 'name':
+          line_type = 'seq'
+        elif line_type == 'plus':
+          line_type = 'qual'
+        elif line_type == 'first':
+          raise FormatError('First line must start with a "@":\n'+line_raw)
+        else:
+          raise FormatError('Invalid parser state: line_type "{}", first char "{}":\n{}'
+                            .format(line_type, line[0], line_raw))
+        if line_type == 'name':
+          # Return the previous read.
+          if read is not None:
+            yield read
+          read = Read()
+          read.name = line[1:]  # remove ">"
+          if read.name:
+            read.id = read.name.split()[0]
+          else:
+            read.id = ''
+        elif line_type == 'seq':
+          read.seq += line
+        elif line_type == 'qual':
+          read.qual += line
+      # Return the last read.
+      if read is not None:
+        yield read
+
+
+class Read(object):
+  def __init__(self):
+    self.seq = ''
+    self.qual = ''
+    self.id = ''
+    self.name = ''
+
+
+class FormatError(Exception):
+  def __init__(self, message=None):
+    if message:
+      Exception.__init__(self, message)