Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/afe1db2a19a2 Дата изменения: Unknown Дата индексирования: Tue Oct 2 07:20:47 2012 Кодировка:

# HG changeset patch
# User boris
# Date 1288800500 -10800
# Node ID afe1db2a19a285568b49f352bdcc116b8d95bf29
# Parent 45573ee4884449b931505b4225cc84786b196199
some local var name changes

diff -r 45573ee48844 -r afe1db2a19a2 lib/project.py
--- a/lib/project.py Wed Nov 03 19:01:50 2010 +0300
+++ b/lib/project.py Wed Nov 03 19:08:20 2010 +0300
@@ -33,9 +33,9 @@
"""overloaded constructor

Project() -> new empty Project
- Project(sequences, alignment) -> new Project with sequences and
- alignment initialized from arguments
- Project(fasta_file) -> new Project, read alignment and sequences
+ Project(sequences, body) -> new Project with sequences and
+ body initialized from arguments
+ Project(fasta_file) -> new Project, read body and sequences
from fasta file

"""
@@ -102,12 +102,12 @@
monomer_kind is class, inherited from MonomerType

>>> import project
- >>> sequences,alignment=project.Project.from_fasta(open("test.fasta"))
+ >>> sequences,body=project.Project.from_fasta(open("test.fasta"))
"""
import re

sequences = []
- alignment = {}
+ body = {}

raw_sequences = file.read().split(">")
if len(raw_sequences) <= 1:
@@ -137,17 +137,17 @@
piece_without_whitespace_chars = re.sub("\s", "", piece)
string += piece_without_whitespace_chars
monomers = [] #convert into Monomer objects
- alignment_list = [] #create the respective list in alignment dict
+ body_list = [] #create the respective list in body dict
for current_monomer in string:
if current_monomer not in ["-", ".", "~"]:
monomers.append(monomer_kind.from_code1(current_monomer).instance())
- alignment_list.append(monomers[-1])
+ body_list.append(monomers[-1])
else:
- alignment_list.append(None)
+ body_list.append(None)
sequence = sequence.Sequence(monomers, name, description)
sequences.append(sequence)
- alignment[sequence] = alignment_list
- return sequences, alignment
+ body[sequence] = body_list
+ return sequences, body


@staticmethod
@@ -181,7 +181,7 @@
self.save_fasta(tmp_file)
tmp_file.close()
os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})
- sequences, alignment = Project.from_fasta(open(tmp_file.name))
+ sequences, body = Project.from_fasta(open(tmp_file.name))
for sequence in self.sequences:
try:
new_sequence = [i for i in sequences if sequence==i][0]
@@ -190,7 +190,7 @@
sequence.name)
old_monomers = iter(sequence.monomers)
self.body[sequence] = []
- for monomer in alignment[new_sequence]:
+ for monomer in body[new_sequence]:
if not monomer:
self.body[sequence].append(monomer)
else: