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- delN(fsaD)
- Fasta.delN(fsaD)
----------------
Remove any entries in the Fasta-derived dictionary that have any DNA
ambiguity codes within. Reports ids of deleted sequences.
- fasta2dict(filename, want_dict='YES', key_func=None)
- Fasta.fasta2dict(filename, want_dict = 'YES',key_func=None)
----------------------------------------------------------
Very fast Fasta Loader. Used internally. You should be using
Fasta.load() or Fasta.seqs() instead.
- file2dict(filename, key_func=None)
- Fasta.file2dict(filename,key_func=None)
--------------------------------------
Synonymous with Fasta.load(). See documentation for Fasta.load().
- find(name, pathhint=None)
- Fasta.find(name,pathhint=None)
------------------------------
Find a ".fsa" file with a similar name to the supplied file.
For example, given "GAL4_YPD.meme," this function will look in
the current directory, then the parent directory or the
optinal "hint" directory for a file with the name "GAL4_YPD.fsa"
- ids(filename, key_func=None)
- Fasta.ids(filename,key_func=None)
---------------------------------
Return the ids in a Fasta file. Same as Fasta.keys(file,key_func=None)
key_func is a function (or lambda expression that extracts the key.
Default is to take first word separated by whitespace.
For example:
key_func=lambda x: x.split('|')[3]
Would use the 4th token separated by the "|" symbol
- keys(filename, key_func=None)
- Fasta.keys(filename,key_func=None)
----------------------------------
Return the ids in a Fasta file. Same as Fasta.ids(file,key_func=None)
key_func is a function (or lambda expression that extracts the key.
Default is to take first word separated by whitespace.
For example:
key_func=lambda x: x.split('|')[3]
Would use the 4th token separated by the "|" symbol
- load(filename, key_func=None)
- Fasta.load(filename,key_func=None)
---------------------------------
Load the file "filename" as a dictionary of sequences, indedex according
to key_func. Default is to take first word separated by whitespace.
For example:
key_func=lambda x: x.split('|')[3]
Would use the 4th token separated by the "|" symbol
- random_split(filename_or_seqD, frac=0.5)
- Fasta.random_split(filename_or_seqD,frac=0.5)
--------------------------------------------
Randomly partition a fasta-derived dictioary. The input may be either
a filename or a dictionary of sequences. The "frac" argument
specifies the ratio of number of sequences.
Returns two dictionaries.
- random_subset(filename_or_seqD, target_count=30)
- Fasta.random_subset(filename_or_seqD,target_count=30)
-----------------------------------------------------
Pick a subset of entries at random from the specificied
input, and return a dictionary. The input may be either
a filename or a dictionary of sequences.
"target_count" is the desired size of the subset.
- seqs(filename)
- Fasta.seqs(filename)
--------------------
Return a list of the sequences contained in the file.
- text(D, toupper=0, linelen=70)
- Fasta.text(D,toupper=0,linelen=70)
----------------------------------
Utility fucntion for generating Fasta-formatted output from a dictonary
of sequences. toupper specifies if all sequences should be capitalized,
and linelen specifies how many sequence characters are allowed on each line.
Returns a single string.
- write(D, filename, linelen=70)
- Fasta.write(D,filename,linelen=70)
----------------------------------
Write dictionary of sequences out to a file. Optional
linelen argument specifies how many sequence characters
are allowed on each line.
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