[Bioperl-l] Merging separate sequence and quality files to FASTQ ?

[Dan Bolser]

Hi, can someone test the script here on zero length fasta / qual files?

http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ


It seems the output has an extra newline in the sequence part of the
output (which throws off scripts that rely on the 'four lines per
record' structure of the fastq (although I'm not sure if it's illegal
fastq).

Here is what I see

BEGIN
$ head one.fna
>FVF7ZWH02PFOVG length=0 xy=2116_2074 region=2
$ head one.qual
>FVF7ZWH02PFOVG length=0 xy=2116_2074 region=2
$ createFastq.plx one.fna one.qual
@FVF7ZWH02PFOVG


+FVF7ZWH02PFOVG

END


Currently I just put in a clause in the script to skip any zero length
sequences, but I think the Qual shouldn't output an extra newline like
this.


Cheers,
Dan.


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JHB: Bioinformatics is Biology and Biology is Bioinformatics.