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Parser for PHD files output by PHRED and used by PHRAP and CONSED.
This module can be used used directly which will return Record objects which should contain all the original data in the file.
Alternatively, using Bio.SeqIO with the "phd" format will call this module internally. This will give SeqRecord objects for each contig sequence.
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Record Hold information from a PHD file. |
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Iterator Iterates over a file of multiple PHD records (DEPRECATED). |
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RecordParser Parses PHD file data into a Record object (DEPRECATED). |
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_Scanner Scans a PHD-formatted file (DEPRECATED). |
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_RecordConsumer Consumer that converts a PHD record to a Record object (DEPRECATED). |
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Reads the next PHD record from the file, returning it as a Record object. This function reads PHD file data line by line from the handle, and returns a single Record object. |
Iterates over a file returning multiple PHD records. The data is read line by line from the handle. The handle can be a list of lines, an open file, or similar; the only requirement is that we can iterate over the handle to retrieve lines from it. Typical usage: records = parse(handle) for record in records: # do something with the record object |
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