[Bioperl-l] Creating a fastq format file?
dan.bolser at gmail.com
Wed Apr 22 09:36:03 EDT 2009
Cheers Mark - I was having difficulty understanding that module... I
should read more and post less ;-) I got it figured out now...
Here is my working code, based on the example kindly posted by Phillip
my ($seq_infile,$qual_infile) =(scalar @ARGV == 1)
#Create input objects for both a seq (fasta) and qual file
my $in_seq_obj =
Bio::SeqIO->new( -file => $seq_infile,
-format => 'fasta',
my $in_qual_obj =
Bio::SeqIO->new( -file => $qual_infile,
-format => 'qual',
my $out_fastq_obj =
Bio::SeqIO->new( -format => 'fastq'
## create objects for both a seq and its associated qual
my $seq_obj = $in_seq_obj->next_seq || last;
my $qual_obj = $in_qual_obj->next_seq;
#use seq and qual object methods feed info for new BSQ object
my $bsq_obj =
Bio::Seq::Quality->new( -seq => $seq_obj->seq(),
-qual => $qual_obj->qual(),
2009/4/22 Mark A. Jensen <maj at fortinbras.us>:
> Dan- There is a fastq module under Bio::SeqIO. Do something like
> use Bio::Seq::Quality;
> use Bio::SeqIO;
> # from Bio::Seq::Quality synopsis...
> my $qual = '0 1 2 3 4 5 6 7 8 9 11 12';
> my $trace = '0 5 10 15 20 25 30 35 40 45 50 55';
> my $seq = Bio::Seq::Quality->new
> ( -qual => $qual,
> -trace_indices => $trace,
> -seq => 'atcgatcgatcg',
> -id => 'human_id',
> -accession_number => 'S000012',
> -verbose => -1 # to silence deprecated methods
> # typical Bio::SeqIO call
> $seqio = Bio::SeqIO( -file => ">your_file", -format=>'fastq');
> ----- Original Message ----- From: "Dan Bolser" <dan.bolser at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, April 22, 2009 6:49 AM
> Subject: [Bioperl-l] Creating a fastq format file?
>> Creating a fastq format file from fasta and 'fasta quality file'?
>> I'm sure this is easy, but I'm still not able to 'think bioperl'...
>> I have a 'fasta quality file' and a fasta file, and I would like to
>> output a fastq file. I followed the discussion on the previous thread
>> With the conclusion seeming to be 'just do it'. Could someone point me
>> at a way to do this, or was that suggestion an error? i.e. the poster
>> was working out a way to create a fastq the only way possible...
>> I get the feeling that this should be a one-liner, but perhaps the
>> above thread was demonstrating the code I need to copy.
>> Thanks for any suggestions,
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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