NAME

Bio::SeqIO::phd - phd file input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

This object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::Quality objects. The phd format is described in section 10 at this url: http://www.phrap.org/phredphrap/phred.html

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR Chad Matsalla

Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS

Jason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.fr

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

Title   : next_seq()
Usage   : $swq = $stream->next_seq()
Function: returns the next phred sequence in the stream
Returns : Bio::Seq::Quality object
Args    : NONE

write_header

Title   : write_header()
Usage   : $seqio->write_header()
Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file
Returns : nothing
Args    : a Bio::Seq::Quality object
Notes   : These are the comments that reside in the header of a phd file
          at the present time. If not provided by the Bio::Seq::Quality object,
          the following default values will be used:

    CHROMAT_FILE          : $swq->id()
    ABI_THUMBPRINT        : 0
    PHRED_VERSION         : 0.980904.e
    CALL_METHOD           : phred
    QUALITY_LEVELS        : 99
    TIME                  : <current time>
    TRACE_ARRAY_MIN_INDEX : 0
    TRACE_ARRAY_MAX_INDEX : unknown
    CHEM                  : unknown
    DYE                   : unknown

write_seq

Title   : write_seq()
Usage   : $seqio->write_seq($swq);
Function: Write out a phd file.
Returns : Nothing.
Args    : a Bio::Seq::Quality object

attribute

Title   : attribute()
Usage   : swq->attribute(name[,value]);
Function: Get/Set the name attribute.
Returns : a string if 1 param, nothing else.
Args    : a name or a pair name, value

chromat_file

Title   : chromat_file
Usage   : swq->chromat_file([filename]);
Function: Get/Set the CHROMAT_FILE attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a filename

abi_thumbprint

Title   : abi_thumbprint
Usage   : swq->abi_thumbprint([value]);
Function: Get/Set the ABI_THUMBPRINT attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

phred_version

Title   : phred_version
Usage   : swq->phred_version([value]);
Function: Get/Set the PHRED_VERSION attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value 

call_method

Title   : call_method
Usage   : swq->call_method([value]);
Function: Get/Set the CALL_METHOD attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value 

quality_levels

Title   : quality_levels
Usage   : swq->quality_levels([value]);
Function: Get/Set the quality_levels attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

trace_array_min_index

Title   : trace_array_min_index
Usage   : swq->trace_array_min_index([value]);
Function: Get/Set the trace_array_min_index attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

trace_array_max_index

Title   : trace_array_max_index
Usage   : swq->trace_array_max_index([value]);
Function: Get/Set the trace_array_max_index attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

chem

Title   : chem
Usage   : swq->chem([value]);
Function: Get/Set the chem attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

dye

Title   : dye
Usage   : swq->dye([value]);
Function: Get/Set the dye attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

time

Title   : time
Usage   : swq->time([value]);
Function: Get/Set the time attribute.
Returns : a string if 1 param, nothing else.
Args    : none or a value

touch

Title   : touch
Usage   : swq->touch();
Function: Set the time attribute to current time.
Returns : nothing
Args    : none

cpanm BioPerl

perl -MCPAN -e shell
install BioPerl