So I've got a bunch of files like the picture shows. I need to remove the plus sign in between each set of 8 characters, but the problem is that these are .fastq files, which are huge and have many copies of that string of characters. Is there a way to replace every instance (regardless of the letters) in each file? Some of these are 85mb + and I can't do just a find and replace in Word, since it crashes. Any help would be appreciated.

Here is the code that I'm using, I'm not very well-versed in programming/Linux. Code is in Python:

import os
import argparse

def get_arguments():
    parser = argparse.ArgumentParser()
    parser.add_argument('dir',
                        help='The full path of the directory containing the original FASTQ Files')
    parser.add_argument('keyFile',
                        help='The full path of the Key File containing a table with corresponding file names, sample names, and barcode sequences')
    parser.add_argument('--out', help='the path to the directory where the modified FASTQ files will be stored; if none is provided, files are written to original directories')

    args = parser.parse_args()

    return args.dir, args.out, args.keyFile


def store_key_info(keyF):
    try:
        assert os.path.exists(keyF)
    except AssertionError:
        raise Exception('The Key File [%s] doesn\'t exist. Please check the location of the file.' % keyF)

    f = open(keyF, 'rU')
    f.readline()

    kDict = {}
    for line in f:
        fName, sName, barcode = line.rstrip().split('\t')
        kDict[barcode] = fName

    return kDict


def find_all_files_in_dir_tree_with_ext(fqDir, extensionsList):
    filesList = []

    for root, dirnames, filenames in os.walk(fqDir):
        for filename in filenames:
            if filename.endswith(tuple(extensionsList)):
                filesList.append(os.path.join(root, filename))

    return filesList


def remove_ext_from_file_name(fName):

    return os.path.splitext(fName)[0]


def identify_barcode_in_file_name(fName):
    nameComponents = fName.split('_')
    bc = nameComponents[-4].replace('-','')
    return bc


def determine_new_fastq_name(fName, sampleID):
    nameComps = fName.split('_')[-4:]
    nameComps[0] = nameComps[0].replace('-', '')
    nameComps.insert(0, sampleID)
    nameComps.append('mod.fastq')
    newFileName = '_'.join(nameComps)
    return newFileName


def create_new_file(fName):
    try:
        f = open(fName, 'w')
    except:
        raise Exception('Something went wrong while trying to write new FASTQ files.')
    return f


def replace_barcode_sequence(line, sID):
    line = line.rstrip().split(':')
    line[-1] = sID
    line = ':'.join(line)
    line += '\n'
    return line

def modify_header(fName, sID, newFName):

    # open old file
    # open new file

    newF = create_new_file(newFName)
    oldF = open(fName, 'r')

    for idx, row in enumerate(oldF):
        if idx%4 == 0:
            newHeader = replace_barcode_sequence(row, sID)
            newF.write(newHeader)
        else:
            newF.write(row)
    oldF.close()
    newF.close()
    return True


if __name__ == "__main__":
    print("\n######################## Start ########################\n")
    fqExt = ['fq', 'fastq']

    oldDir, newDir, keyFile = get_arguments()

    # check if a new directory was provided
    writeToNewDir = False
    if newDir is not None:
        writeToNewDir = True
        print("Modified FASTQ files will be written to a new directory [%s]." % newDir)
        # check if the new directory exists, and if not, create it
        if not os.path.exists(newDir):
            os.makedirs(newDir)
    else:
        print("The modified FASTQ files will be written to the same directories as the original FASTQ files.")


    # import sample-barcode key information
    keyDict = store_key_info(keyFile)
    print('I have imported the sample-barcode table; it contains %s barcodes.' % len(keyDict))
    # look for FASTQ files in the user-specified directory
    print('Looking for FASTQ files in [%s] ...' % oldDir)
    fileList = find_all_files_in_dir_tree_with_ext(oldDir, fqExt)
    print('A total of %s FASTQ files were found and are being modified.' % len(fileList))

    usedBarcodes = []
    shelvedBarcodes = []
    for filePath in fileList:
        fileParentDir, fileName = os.path.split(filePath)
        oldFileName = remove_ext_from_file_name(fileName)
        barcode = identify_barcode_in_file_name(oldFileName)

        if barcode in keyDict:
            usedBarcodes.append(barcode)

            sampleID = keyDict[barcode]
            newFileName = determine_new_fastq_name(oldFileName, sampleID)
            # print(newFileName)
            if writeToNewDir:
                newFilePath = os.path.join(newDir, newFileName)
            else:
                newFilePath = os.path.join(fileParentDir, newFileName)

            return_status = modify_header(filePath, sampleID, newFilePath)
            if return_status:
                print('    %s -- written' % (newFilePath))
        else:
            shelvedBarcodes.append(barcode)

    print('Files have been modified.')
    print('\n##################################\n')
    usedBarcodes = list(set(usedBarcodes))
    shelvedBarcodes = list(set(shelvedBarcodes))
    print('Summary:')
    print('Of the %s barcodes, %s were encountered in the files.' % (len(keyDict),len(usedBarcodes)))
    print('Additionally, %s barcodes were encountered in the FASTQ files but were not found in the sample-barcode table.' % len(shelvedBarcodes))
    print("\n######################## End ########################\n")

The highlighted area needs to be replaced:

EDIT: Was told to move an answer to the original post:Here are the first 100 lines of one such document. I need to change the 2:N:0: AAAAAAAA+GGGGGGGG section in all instances, in all files with the above code. I don't think the code will work with the + in the middle of them. I can't do a find and replace since some of these have nearly 100,000 reads which takes too long for my text editor to do (upwards of 8 hours), plus that 2:N:0 line isn't the same per read, so it's not 100%. The + sign between lines signals a new read, which should stay.

@M04574:62:000000000-BMHJ4:1:1101:20437:3142 2:N:0:GCTCATGA+ACTGCAAA
TNGTTTAAAGCCAGTACGTCAACATCCTAAGCGCAGATAAGGAGAAACAACCGACTGAAAGGGAACGGAGATAATCGAACGGAAGCTACGGGCACAAGAACAACATAAAGGGCAGAGAGGGGAACCGGAAAAGCTAACCGTAAAAAGAGACAAGAACGGGAAGCAGAAGCACCGGCGAGTAAAAAACGTAAGGAGGAGAAAGAGGCGACCACGACGGAACCAGCGGAAGAAAAACAAGATGGGTGCAAAAAGCAAACAGGGGGGAGAACAGTAAGAAGGCAAGAGGAGGCAGGGAGCGCGC
+
-#8---9;<@,,6,;@CC;EFBFGFGGGFG<FB@@@+,,6;,,;F,C,<@AFCC@+8C9<F8:D,C,,87@,,66CB,,,+,666B,:,,,4+48B,,,,:9,,9,:5A,,++++A=4+4B++8++++++3A8,,,3,3>8++8DF7+,,,6=,,,,3@+@B*@,54,,,@53*******,,511=3*2*//5=*/18=5C**)/*)07)/*)))))8)))))())01()((.7().(2*)).,-.))6.:((4(,(.,4((((073<04(.)))..,((.310((,41(-31(-1(((-(
@M04574:62:000000000-BMHJ4:1:1101:23391:4717 2:N:0:GCGCATGA+ACTGCAAA
TNGTTTAAAGCCATTATGCCAAGAGCGTAAGCATGTTACGTGGGCGAAACGCGACCAAAAAGACATAGTGAGTACATCGAGGGCAATGGCCGCATACGATAAAAGGATAAAACACACACGAAGAGGCCACAGACCTCAAAGCCTGAACCGACGGTCAAAATCGATGGTGAACCGGCAAAACAGGAAATGAAACAAGCAGAAGCAAGGCGGAAGACCAGAAGAGGCGAATGACTGCAAGCGGTGCACAGTCAACAAGGTAACGTACTGGTGGACGGTAGGTGCAAAGATAGTTTCATCGTGA
+
8#88-66@@A,,666;,;=,CC,C,,+78;C6666C,C,,,6,+,6+6++,8C7C@C,C<CF,:6:,,<C<E,,,,,6BE,++,:?:,4B,@+:8B9BF+CF,C54,,:,9A<A,AC++@FFEE,=43=+D,,,83AFFE,8>,,6,6>BECEC6*>:=;,,436@*37><7:;*1:CE,4ACCCCF,<,=+,4:C4C00;98ACC7)11/7))0)770<9<)4)57)(0--*1:77)(0(((()9*(-)..)58,()-))-(.)--,61:3(((,((-.).4).4()--)).)6))4(((
@M04574:62:000000000-BMHJ4:1:1101:18653:4992 2:N:0:GCTCATGA+ACTGCATA
TNGTTTAAAGCCATTACGTCATGGAGGATAACATGATTCATTGAAATTTCCCTCCTCGTTGAATCGGTTCCTACCCGCTTTGCCAGCCACACCGGCAGAGCCACCGGGCCATGGGAACAACTTTCAGCAACCAGCAGCCGCAACAGGGGCAATGCCTGGTCCATACGTGCCTGCTGCCACGAGCAATGCATCCGCCTGGCGTCCCCACGGAATGTCTCATCAGCCGTTGGCCATAGAATACCACTTCCGAGCACCCCTGGTCCTCAAGAACCGCTGTGAGCCTAAAACGGGAAAGGACAAA
+
-#86-9C<<E9C@;@,CC;EBEE<C<,6;C<FFG<@E,6CD,C<DE,6C@FEEC@F,BC,@@<6@F@8@@CCFG86@@CF7@@,BF?FFF@,6C:=FFDEG,BFGDC@FGGBF,DE49AEF8,9EE,CEDF<C=FEGG:C74BFGEDCE7+@,@8D,383@@EC=C:@D:87@@,@C:DFC>*@5D8,@<==C*1*3;D*8*)01;*:CCDGFF6C+13:A=63A>ADFFF@F)7ACE)@<>FF7=?7BF>F(3((--3:(:))9.).48(441((4(6<7((),.8848(4(,82(380:
@M04574:62:000000000-BMHJ4:1:1101:8566:5003 2:N:0:GGTCATGA+ACTGCTTA
TNGTTTAAAGCCATTACGTCAACATCCTCTGCCTCTTTTATACATCTTACTTTGCTTACGTACTGCTGCGGTCTTCTCTCTTTTTTACCCTTTTCTTTTAGTTTACAAACCCAGTTCACAACTTTCTCACCTTTCTGTCCCGTTTTCCCTCTCATCAAGCTTCTATATACTACTTACTCGTAGGCCGAACTCTTCCTCCACTGATTTCTTTATTATCTCCAATACTGACTTCGATCCTTCCCCTTTTGACACTTTCCCGTACTGTTTTGCTCCCATTTCACGGTTCTTTACCTCTTTCCCC