ipyrad/assemble/refmap.py
def split_merged_reads(outhandles, input_derep):
    """
    Takes merged/concat derep file from vsearch derep and split it back into 
    separate R1 and R2 parts. 
    - sample_fastq: a list of the two file paths to write out to.
    - input_reads: the path to the input merged reads
    """

    handle1, handle2 = outhandles
    splitderep1 = open(handle1, 'w')
    splitderep2 = open(handle2, 'w')

    with open(input_derep, 'r') as infile: 
        ## Read in the infile two lines at a time: (seqname, sequence)
        duo = itertools.izip(*[iter(infile)]*2)

        ## lists for storing results until ready to write
        split1s = []
        split2s = []

        ## iterate over input splitting, saving, and writing.
        idx = 0
        while 1:
            try:
                itera = duo.next()
            except StopIteration:
                break
            ## split the duo into separate parts and inc counter
            part1, part2 = itera[1].split("nnnn")
            idx += 1

            ## R1 needs a newline, but R2 inherits it from the original file            
            ## store parts in lists until ready to write
            split1s.append("{}{}\n".format(itera[0], part1))
            split2s.append("{}{}".format(itera[0], part2))

            ## if large enough then write to file
            if not idx % 10000:
                splitderep1.write("".join(split1s))
                splitderep2.write("".join(split2s))
                split1s = []
                split2s = [] 

    ## write final chunk if there is any
    if any(split1s):
        splitderep1.write("".join(split1s))
        splitderep2.write("".join(split2s))

    ## close handles
    splitderep1.close()
    splitderep2.close()
def split_merged_reads(outhandles, input_derep):
    """
    Takes merged/concat derep file from vsearch derep and split it back into 
    separate R1 and R2 parts. 
    - sample_fastq: a list of the two file paths to write out to.
    - input_reads: the path to the input merged reads
    """

    handle1, handle2 = outhandles
    splitderep1 = open(handle1, 'w')
    splitderep2 = open(handle2, 'w')

    with open(input_derep, 'r') as infile: 
        ## Read in the infile two lines at a time: (seqname, sequence)
        duo = itertools.izip(*[iter(infile)]*2)

        ## lists for storing results until ready to write
        split1s = []
        split2s = []

        ## iterate over input splitting, saving, and writing.
        idx = 0
        while 1:
            try:
                itera = duo.next()
            except StopIteration:
                break
            ## split the duo into separate parts and inc counter
            part1, part2 = itera[1].split("nnnn")
            idx += 1

            ## R1 needs a newline, but R2 inherits it from the original file            
            ## store parts in lists until ready to write
            split1s.append("{}{}\n".format(itera[0], part1))
            split2s.append("{}{}".format(itera[0], part2))

            ## if large enough then write to file
            if not idx % 10000:
                splitderep1.write("".join(split1s))
                splitderep2.write("".join(split2s))
                split1s = []
                split2s = [] 

    ## write final chunk if there is any
    if any(split1s):
        splitderep1.write("".join(split1s))
        splitderep2.write("".join(split2s))

    ## close handles
    splitderep1.close()
    splitderep2.close()
def split_merged_reads ( outhandles , input_derep ) : handle1 , handle2 = outhandles splitderep1 = open ( handle1 , 'w' ) splitderep2 = open ( handle2 , 'w' ) with open ( input_derep , 'r' ) as infile : ## Read in the infile two lines at a time: (seqname, sequence) duo = itertools . izip ( * [ iter ( infile ) ] * 2 ) ## lists for storing results until ready to write split1s = [ ] split2s = [ ] ## iterate over input splitting, saving, and writing. idx = 0 while 1 : try : itera = duo . next ( ) except StopIteration : break ## split the duo into separate parts and inc counter part1 , part2 = itera [ 1 ] . split ( "nnnn" ) idx += 1 ## R1 needs a newline, but R2 inherits it from the original file             ## store parts in lists until ready to write split1s . append ( "{}{}\n" . format ( itera [ 0 ] , part1 ) ) split2s . append ( "{}{}" . format ( itera [ 0 ] , part2 ) ) ## if large enough then write to file if not idx % 10000 : splitderep1 . write ( "" . join ( split1s ) ) splitderep2 . write ( "" . join ( split2s ) ) split1s = [ ] split2s = [ ] ## write final chunk if there is any if any ( split1s ) : splitderep1 . write ( "" . join ( split1s ) ) splitderep2 . write ( "" . join ( split2s ) ) ## close handles splitderep1 . close ( ) splitderep2 . close ( )
Takes merged/concat derep file from vsearch derep and split it back into 
    separate R1 and R2 parts. 
    - sample_fastq: a list of the two file paths to write out to.
    - input_reads: the path to the input merged reads
Takes merged / concat derep file from vsearch derep and split it back into separate R1 and R2 parts . - sample_fastq : a list of the two file paths to write out to . - input_reads : the path to the input merged reads