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Primer3.py

# Copyright 2008 Michiel de Hoon.
# Revisions copyright 2009 Leighton Pritchard.
# Revisions copyright 2010 Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
"""Code to parse output from the EMBOSS eprimer3 program.

As elsewhere in Biopython there are two input functions, read and parse,
for single record output and multi-record output. For primer3, a single
record object is created for each target sequence and may contain
multiple primers.

i.e. If you ran eprimer3 with a single target sequence, use the read
function. If you ran eprimer3 with multiple targets, use the parse
function to iterate over the retsults.
"""

# --- primer3

00022 class Record:
    """Represent information from a primer3 run finding primers.

    Members:

    primers  - list of Primer objects describing primer pairs for
               this target sequence.
    comments - the comment line(s) for the record
    """
    def __init__(self):
        self.comments = ""
        self.primers = []

00035 class Primers:
    """A primer set designed by Primer3.

    Members:

    size
    forward_seq
    forward_start
    forward_length
    forward_tm
    forward_gc
    reverse_seq
    reverse_start
    reverse_length
    reverse_tm
    reverse_gc
    """
    def __init__(self):
        self.size = 0
        self.forward_seq = ""
        self.forward_start = 0
        self.forward_length = 0
        self.forward_tm = 0.0
        self.forward_gc = 0.0
        self.reverse_seq = ""
        self.reverse_start = 0
        self.reverse_length = 0
        self.reverse_tm = 0.0
        self.reverse_gc = 0.0


def parse(handle):
    """Iterate over primer3 output as Bio.Emboss.Primer3.Record objects.
    """
    # Skip blank lines at head of file
    while True:
        line = handle.readline()
        if line.strip():
            break # Starting a record

    # Read each record
    record = None
    primer = None
    while True:
        if line.startswith('# EPRIMER3') or line.startswith('# PRIMER3'):
            # Record data
            if record is not None:
                yield record
            record = Record()
            record.comments += line
            primer = None
        elif line.startswith('#'):
            if line.strip() != '#                      Start  Len   Tm     GC%   Sequence':
                record.comments += line
        elif not line.strip():
            pass
        elif line[5:19]=="PRODUCT SIZE: ":
            primer = Primers()
            primer.size = int(line[19:])
            record.primers.append(primer)
        elif line[5:19]=="FORWARD PRIMER":
            words = line.split()
            if not primer or primer.size==0:
                primer = Primers()
                record.primers.append(primer)
            primer.forward_start = int(words[2])
            primer.forward_length = int(words[3])
            primer.forward_tm = float(words[4])
            primer.forward_gc = float(words[5])
            primer.forward_seq = words[6]
        elif line[5:19]=="REVERSE PRIMER":
            words = line.split()
            if not primer or primer.size==0:
                primer = Primers()
                record.primers.append(primer)
            primer.reverse_start = int(words[2])
            primer.reverse_length = int(words[3])
            primer.reverse_tm = float(words[4])
            primer.reverse_gc = float(words[5])
            primer.reverse_seq = words[6]
        elif line[5:19]=="INTERNAL OLIGO":
            words = line.split()
            if not primer or primer.size==0:
                primer = Primers()
                record.primers.append(primer)
            primer.internal_start = int(words[2])
            primer.internal_length = int(words[3])
            primer.internal_tm = float(words[4])
            primer.internal_gc = float(words[5])
            primer.internal_seq = words[6]
        try:
            line = handle.next()
        except StopIteration:
            break
    if record:
        yield record


def read(handle):
    """Parse primer3 output into a Bio.Emboss.Primer3.Record object.

    This is for when there is one and only one target sequence. If
    designing primers for multiple sequences, use the parse function.
    """
    iterator = parse(handle)
    try:
        first = iterator.next()
    except StopIteration:
        raise ValueError("No records found in handle")
    try:
        second = iterator.next()
    except StopIteration:
        second = None
    if second is not None:
        raise ValueError("More than one record found in handle")
    return first

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