---
name: "Bio::SeqIO::phd"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::SeqIO::phd"
---

# Bio::SeqIO::phd(3pm)

phd file input/output stream

## 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
```