conkit.io.a3m module

Parser module specific to HH-suite A3M sequence files

Credits

Stefan Seemayer and his A3MIO project [https://github.com/sseemayer/BioPython-A3MIO]

class A3mParser[source]

Bases: conkit.io._parser.SequenceFileParser

Parser class for A3M sequence files

Methods

read(f_handle[, f_id, remove_insert]) Read a sequence file
write(f_handle, hierarchy) Write a sequence file instance to to file
read(f_handle, f_id=’a3m’, remove_insert=True)[source]

Read a sequence file

Parameters:

f_handle

Open file handle [read permissions]

f_id : str, optional

Unique sequence file identifier

remove_insert : bool, optional

Remove insert states [default: True]
Returns:

SequenceFile
write(f_handle, hierarchy)[source]

Write a sequence file instance to to file

Parameters:

f_handle

Open file handle [write permissions]

hierarchy : SequenceFile, Sequence