:>"^ @sdZddlmZddlmZdddddd d d d d ddg ZGdddeZddZddZ dS)aRParser for PHD files output by PHRED and used by PHRAP and CONSED. This module can be 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. )Seq) generic_dnaZ CHROMAT_FILEZABI_THUMBPRINTZ PHRED_VERSIONZ CALL_METHODZQUALITY_LEVELSZTIMEZTRACE_ARRAY_MIN_INDEXZTRACE_ARRAY_MAX_INDEXZTRIMZTRACE_PEAK_AREA_RATIOZCHEMZDYEc@s"eZdZdZddZdS)Recordz!Hold information from a PHD file.cCsUd|_i|_x!tD]}d|j|jszread..)rrrrrztimerr )r!r"r#r$)r%r&) startswithrrstripr ValueErrorstripsplitr rintfloatlenr appendtuplerjoinrr r ) handlelinerecordkeywordvaluefirstlastZprobpartsrrrread4s|             ,        .r=ccs&xt|}|sdS|VqWdS)aIterate over a file yielding 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 N)r=)r5r7rrrparses  r>N) rZBiorZ Bio.Alphabetrrobjectrr=r>rrrrs"  [