pyFastqSplitter

pyFastqSplitter is part of the pyCRAC package. Splits a merged fastq file (pyFastqJoiner output) in to two files.

Example:

Here the ":" character was used to separate the two sequences. By using the -c flag you can tell pyFastqSplitter where to split the sequences.
This character is ignored by pyFastqDuplicateRemover


@FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
+
`efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
@FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
+
^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
@FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
+
bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg

Result:

Forward reaction:

@FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
+
`efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
@FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
+
^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
@FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
+
bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
@FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
+
cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW
Reverse reaction:

@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
+
YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
+
YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
+
PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg

Parameter list

Options:

-f fastq_file, --filename=fastq_file
                    To provide the names of two raw data files separated
                    by a single space. Default = standard input
--file_type=FASTQ
                    Can split joined fasta and fastq files. Fastq is default
                    If there isn't a specific character splitting the two reads
                    the tool assumes that the two reads were of equal length
-o splitfastq, --outfile=splitfastq
                    Provide the name of the output files (WITHOUT file
                    extension). By default the data will be printed to the
                    standard output
-c :, --character=:
                    If the joined sequences were separated by a specific
                    character then the program can divide the sequences by
                    looking for that character