"""
This module provides simple parsers for the FASTA and FASTQ sequence
data formats.

The FASTQ parser is not strictly conformant since it assumes the input
to be in a line oriented form (which is usually true).
"""

__docformat__ = 'restructuredtext'

import os
import os.path
import subprocess
import uuid

def readFasta(file):
    """
    Read textual input from the file object `file`, which is assumed to
    be in FASTA format.  Yields the sequence of (name, sequence) tuples.
    """
    nm = None
    seq = []
    for l in file:
        l = l.strip()
        if len(l) and l[0] == '>':
            if nm is not None:
                yield (nm, ''.join(seq))
            nm = l[1:].strip()
            seq = []
        else:
            seq.append(l)
    if nm is not None:
        yield (nm, ''.join(seq))

def readFastq(file):
    """
    Read textual input from the file object `file`, which is assumed
    to be in line-oriented FASTQ format (not full multi-line FASTQ).
    Yields the sequence of (name, sequence, label, quality) tuples.
    """
    grp = []
    for l in file:
        l = l.strip()
        grp.append(l)
        if len(grp) == 4:
            yield tuple(grp)
            grp = []
    if grp == 4:
        yield tuple(grp)

def readFastqBlock(file, n=1024):
    """
    Read textual input from the file object `file`, which is assumed
    to be in line-oriented FASTQ format (not full multi-line FASTQ).
    Yields a block of sequences at a time.
    """
    grps = []
    grp = [None, None, None, None]
    i = 0
    for l in file:
        l = l.strip()
        grp[i] = l
        i += 1
        if i == 4:
            grps.append(grp)
            if len(grps) == n:
                yield grps
                grps = []
            grp = [None, None, None, None]
            i = 0
    if i == 4:
        grps.append(grp)
    if len(grps) > 0:
        yield grps

def openFile(fn, mode='r'):
    """
    Open a file "cleverly".

    If the file name ends with ".gz" or ".bz2", it is compressed
    or uncompressed on the fly (according to the mode).

    In read mode (mode='r'), the filename '-' is interpreted as stdin.

    In write mode (mode='w'), the filename '-' is interpreted as stdout.
    """
    if mode == 'r':
        if fn == "-":
            return sys.stdin
        if fn.endswith(".gz"):
            p = subprocess.Popen(['gunzip', '-c', fn],
                                 bufsize=1024*1024,
                                 stdout=subprocess.PIPE)
            return p.stdout
        if fn.endswith(".bz2"):
            p = subprocess.Popen(['bunzip2', '-c', fn],
                                 bufsize=1024*1024,
                                 stdout=subprocess.PIPE)
    if mode == 'w':
        if fn == "-":
            return sys.stdout
        if fn.endswith(".gz"):
            p = subprocess.Popen(['gzip', '-9', '-', '>', fn],
                                 bufsize=1024*1024,
                                 stdin=subprocess.PIPE,
                                 shell=True)
            return p.stdin
        if fn.endswith(".bz2"):
            p = subprocess.Popen(['bzip2', '-9', '-', '>', fn],
                                 bufsize=1024*1024,
                                 stdout=subprocess.PIPE,
                                 shell=True)
        return p.stdin
    return open(fn, mode)

_tmpfiles = []

class _AutoRemover:
    def __init__(self):
        _tmpfiles.append(set([]))

    def __enter__(self):
        return None

    def __exit__(self, _t, _v, _tb):
        assert len(_tmpfiles) > 0
        fns = _tmpfiles.pop()
        for fn in fns:
            if os.path.isfile(fn):
                os.remove(fn)

def autoremove():
    """
    Enable auto-removal of temporary files.
    Use in a with statement:
        with autoremove():
            my_code()
    """
    return _AutoRemover()

def tmpfile(suffix = ''):
    """
    Create a unique filename for temporary storage. If auto-remove
    is enabled (see `autoremove`), the file will be removed when
    the __exit__() method of the autoremove object is invoked (i.e.
    by exiting a with block).
    """
    fn = os.getenv('TMPDIR', '/tmp') + '/' + str(uuid.uuid4()) + suffix
    if len(_tmpfiles):
        _tmpfiles[-1].add(fn)
    return fn


@@ -3315,32 +3315,36 @@
 l=True)%0A        
+    
 return p.stdin%0A 

Fix a trivial bug.