MSA File

This module defines functions and classes for parsing, manipulating, and analyzing multiple sequence alignments.

class prody.sequence.msafile.MSAFile(msa, mode='r', format=None, aligned=True, **kwargs)

Handle MSA files in FASTA, SELEX, CLUSTAL and Stockholm formats.

close()

Close the file. This method will not affect a stream.

property closed

True for closed file.

property format

Format of the MSA file.

getFilename()

Returns filename, or None if instance is handling a stream.

getFilter()

Returns function used for filtering sequences.

getFormat()

Returns file format.

getSlice()

Returns object used to slice sequences.

getTitle()

Returns title of the instance.

isAligned()

Returns True if MSA is aligned.

reset()

Returns to the beginning of the file.

setFilter(filter, filter_full=False)

Set function used for filtering sequences. filter will be applied to split sequence label, by default. If filter_full is True, filter will be applied to the full label.

setSlice(slice)

Set object used to slice sequences, which may be a slice() or a list() of numbers.

setTitle(title)

Set title of the instance.

write(seq)

Write seq, an Sequence instance, into the MSA file.

prody.sequence.msafile.parseMSA(filename, **kwargs)

Returns an MSA instance that stores multiple sequence alignment and sequence labels parsed from Stockholm, SELEX, CLUSTAL, PIR, or FASTA format filename file, which may be a compressed file. Uncompressed MSA files are parsed using C code at a fraction of the time it would take to parse compressed files in Python.

prody.sequence.msafile.splitSeqLabel(label)

Returns label, starting residue number, and ending residue number parsed from sequence label.

prody.sequence.msafile.writeMSA(filename, msa, **kwargs)

Returns filename containing msa, a MSA or MSAFile instance, in the specified format, which can be SELEX, Stockholm, or FASTA. If compressed is True or filename ends with .gz, a compressed file will be written. MSA instances will be written using C function into uncompressed files.

Can also write CLUSTAL or PIR format files using Python functions.