+++ /dev/null
-"""Utilities for working with FASTA-formatted sequences (OBSOLETE).
-
-Classes:
-Record Holds FASTA sequence data.
-Iterator Iterates over sequence data in a FASTA file.
-RecordParser Parses FASTA sequence data into a Record object.
-SequenceParser Parses FASTA sequence data into a SeqRecord object.
-
-For a long time this module was the most commonly used and best documented
-FASTA parser in Biopython. However, we now recommend using Bio.SeqIO instead.
-
-In view of this, while you can continue to use Bio.Fasta for the moment, it is
-considered to be a legacy module and should not be used if you are writing new
-code. At some point Bio.Fasta may be officially deprecated (with warning
-messages when used) before finally being removed.
-
-If you are already using Bio.Fasta with the SequenceParser to get SeqRecord
-objects, then you should be able to switch to the more recent Bio.SeqIO module
-very easily as that too uses SeqRecord objects. For example,
-
-from Bio import Fasta
-handle = open("example.fas")
-for seq_record in Fasta.Iterator(handle, Fasta.SequenceParser()) :
- print seq_record.description
- print seq_record.seq
-handle.close()
-
-Using Bio.SeqIO instead this becomes:
-
-from Bio import SeqIO
-handle = open("example.fas")
-for seq_record in SeqIO.parse(handle, "fasta") :
- print seq_record.description
- print seq_record.seq
-handle.close()
-
-Converting an existing code which uses the RecordParser is a little more
-complicated as the Bio.Fasta.Record object differs from the SeqRecord.
-
-from Bio import Fasta
-handle = open("example.fas")
-for record in Fasta.Iterator(handle, Fasta.RecordParser()) :
- #record is a Bio.Fasta.Record object
- print record.title #The full title line as a string
- print record.sequence #The sequence as a string
-handle.close()
-
-Using Bio.SeqIO instead this becomes:
-
-from Bio import SeqIO
-handle = open("example.fas")
-for seq_record in SeqIO.parse(handle, "fasta") :
- print seq_record.description #The full title line as a string
- print seq_record.seq.tostring() #The sequence as a string
-handle.close()
-
-
-
-"""
-from Bio import Seq
-from Bio import SeqRecord
-from Bio import Alphabet
-
-
-class Record:
- """Holds information from a FASTA record.
-
- Members:
- title Title line ('>' character not included).
- sequence The sequence.
-
- """
- def __init__(self, colwidth=60):
- """__init__(self, colwidth=60)
-
- Create a new Record. colwidth specifies the number of residues
- to put on each line when generating FASTA format.
-
- """
- self.title = ''
- self.sequence = ''
- self._colwidth = colwidth
-
- def __str__(self):
- s = []
- s.append('>%s' % self.title)
- i = 0
- while i < len(self.sequence):
- s.append(self.sequence[i:i+self._colwidth])
- i = i + self._colwidth
- #Was having a problem getting the tests to pass on windows...
- #return os.linesep.join(s)
- return "\n".join(s)
-
-class Iterator:
- """Returns one record at a time from a FASTA file.
- """
- def __init__(self, handle, parser = None, debug = 0):
- """Initialize a new iterator.
- """
- self.handle = handle
- self._parser = parser
- self._debug = debug
-
- #Skip any text before the first record (e.g. blank lines)
- while True :
- line = handle.readline()
- if not line or line[0] == ">" :
- break
- if debug : print "Skipping: " + line
- self._lookahead = line
-
- def __iter__(self):
- return iter(self.next, None)
-
- def next(self):
- """Return the next record in the file"""
- line = self._lookahead
- if not line:
- return None
- assert line[0]==">", line
- lines = [line.rstrip()]
- line = self.handle.readline()
- while line:
- if line[0] == ">": break
- if line[0] == "#" :
- if self._debug : print "Ignoring comment line"
- pass
- else :
- lines.append(line.rstrip())
- line = self.handle.readline()
- self._lookahead = line
- if self._debug : print "Debug: '%s' and '%s'" % (title, "".join(lines))
- if self._parser is None:
- return "\n".join(lines)
- else :
- return self._parser.parse_string("\n".join(lines))
-
-class RecordParser:
- """Parses FASTA sequence data into a Fasta.Record object.
- """
- def __init__(self, debug = 0):
- pass
-
- def parse_string(self, text) :
- text = text.replace("\r\n","\n") #Crude way of dealing with \r\n
- assert text[0] == ">", text
- text = text.split("\n>",1)[0] # Only do the first record if more than one
- title, sequence = text.split("\n", 1)
- title = title[1:]
- rec = Record()
- rec.title = title
- rec.sequence = sequence.replace("\n","")
- return rec
-
- def parse(self, handle):
- return self.parse_string(handle.read())
-
-class SequenceParser:
- """Parses FASTA sequence data into a SeqRecord object.
- """
- def __init__(self, alphabet = Alphabet.generic_alphabet, title2ids = None,
- debug = 0):
- """Initialize a Scanner and Sequence Consumer.
-
- Arguments:
- o alphabet - The alphabet of the sequences to be parsed. If not
- passed, this will be set as generic_alphabet.
- o title2ids - A function that, when given the title of the FASTA
- file (without the beginning >), will return the id, name and
- description (in that order) for the record. If this is not given,
- then the entire title line will be used as the description.
- """
- self.alphabet = alphabet
- self.title2ids = title2ids
-
- def parse_string(self, text) :
- text = text.replace("\r\n","\n") #Crude way of dealing with \r\n
- assert text[0] == ">", text
- text = text.split("\n>",1)[0] # Only do the first record if more than one
- title, sequence = text.split("\n", 1)
- title = title[1:]
-
- seq = Seq.Seq(sequence.replace("\n",""), self.alphabet)
- rec = SeqRecord.SeqRecord(seq)
-
- if self.title2ids:
- seq_id, name, descr = self.title2ids(title)
- rec.id = seq_id
- rec.name = name
- rec.description = descr
- else:
- rec.description = title
-
- return rec
-
- def parse(self, handle):
- return self.parse_string(handle.read())
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