labblouin.SeqMask module
Get the amino acid sequence from a landmark file, align this profile to more sequences if required
using muscle, and mask the membership vector into this alignment.
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labblouin.SeqMask.InferSeqs_landmarks(prefix)[source]
Given a landmark file, return a dictionary with the name as key and the
sequence as value
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labblouin.SeqMask.InferSingleLettterCode(threlettercode)[source]
Convert the amino acid three letter code, into a single letter code
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labblouin.SeqMask.MaskAln(fastafilename, modulename, mem, tuples)[source]
Strip the module in an alignment (fasta) file
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labblouin.SeqMask.Mem2List2tuple(prefix)[source]
Read the membership vector, and returns a list and a dictionary with tupples for
each module, indicating the indexes
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labblouin.SeqMask.dict2fasta(outfilename, dic)[source]
Convert the dictionary return by InferSeqs_landmarks fuction
and writes a fasta file. The dictionary should have the seq name as
key and a string as value containing the sequence
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labblouin.SeqMask.fasta2dict(fastafilename)[source]
convert a fasta file into a python dictionary, being the keys the name of the sequence
and the values the sequence itself, in a list
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labblouin.SeqMask.modseq2Fasta(prefix, modseq, names)[source]
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labblouin.SeqMask.str2list(string)[source]
returns a list of a string that have no spaces between elements