import re 
from obitools3.parsers.fasta import fastaNucIterator
from obitools3.parsers.fastq import fastqIterator

oligore = re.compile("^[ACGTRYSWKMBDHVN]+$",re.I)
tagre   = re.compile("^([ACGTRYSWKMBDHVN]+|-)(:([ACGTRYSWKMBDHVN]+)|-)?$",re.I)

def is_ngsfilter_line(line):
    try:
        parts = line.split()
        ok = tagre.match(parts[2])
        ok&= oligore.match(parts[3])
        ok&= oligore.match(parts[4])
        ok&= parts[5]=="F" | parts[5]=="T"
        return ok  
    except:
        return False

def entryIteratorFactory(lineiterator, 
                  int skip=0,
                  only=None,
                  bytes seqtype=b'nuc',
                  int qualityoffset=32,
                  bool noquality=False,
                  bool skiperror=True,
                  bool header=False,
                  bytes sep=None,
                  bytes dec=b'.',
                  bytes nastring=b"NA",
                  bool stripwhite=True,
                  bool blanklineskip=True,
                  bytes commentchar=b"#",
                  int buffersize=100000000):

    if isinstance(lineiterator,(str,bytes)):
        lineiterator=uopen(lineiterator)
    
    if isinstance(lineiterator, LineBuffer):
        lb=lineiterator
    else:
        lb=LineBuffer(lineiterator,buffersize)
        
    i = iter(lb)
        
    first=next(i)
    
    format="tab"
    
    if first[0]==">":
        format=b"fasta"
    if first[0]=="@":
        format=b"fastq"
    elif first[0:3]=='ID ':
        format=b"embl"
    elif first[0:6]=='LOCUS ':
        format=b"genbank"
    elif first[0:11]=='#@ecopcr-v2':
        format=b"ecopcrfile"
    elif is_ngsfilter_line(first):
        format=b"ngsfilter"
    else:
        format=b"tabular"
        
        
    if format==b'fasta':
        if seqtype == b'nuc':
            return (fastaNucIterator(lineiterator,
                                    skip,only,
                                    first),
                    Nuc_Seq)
        else:
            raise NotImplementedError()
    elif format=b'fastq':
            return (fastqIterator(lineiterator,
                                 skip,only,
                                 qualityoffset,
                                 first),
                    Nuc_Seq)
                    
            
    raise NotImplementedError('File format not yet implemented')