ImportError: Нет модуля с именем writers.SeqRecord.fasta - PullRequest
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ImportError: Нет модуля с именем writers.SeqRecord.fasta

0 голосов
/ 19 мая 2011 
# File Name RandonProteinSequences.py
# standard library
import os
import random

# biopython
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqRecord import SeqRecord
import Bio.writers.SeqRecord.fasta
from Bio import SeqIO
from sys import *

residueList1 = ["C","D","E","F","G","H","I"]
residueList2 = ["A","K","L","M","N","S"]
residueList3 = ["P","Q","R","T","V","W","Y"]
residueList4 = ["C","A","G","U"]
def getProteinSeqRecord(residue, seqcount):
    strSeq = ""
    for i in range(0,100,1):
        index = random.randint(0, len(residue)-1)
        strSeq += residue[index]

    sequence = Seq(strSeq, IUPAC.IUPACProtein)
    seqRec = SeqRecord(sequence, id = 'randSeq' + str(seqcount), description= 'A random sequence using Amino acid residues.')
    return seqRec

def getProteinSequence(residue):
    strSeq = ""
    for i in range(0,100,1):
        index = random.randint(0, len(residue)-1)
        strSeq += residue[index]

    sequence = Seq(strSeq, IUPAC.IUPACProtein)
    return sequence

def randomProteinSeqRecord(index):
    if(index%2)==0:
        return getProteinSeqRecord(residueList1, index)
    elif(index%3)==0:
        return getProteinSeqRecord(residueList2, index)
    else:
        return getProteinSeqRecord(residueList3, index)

#information
print '--- This is python based program to generate random sequences ---'
print '--- Provide number of random sequences to generate. Default 10 ---'
print '--- Inorder to save to a file provide file path or filename ---'
print '--- If none or invalid filepath is provided then results will be displayed to console ---'
print '--- The file will be created in fasta format ---'
print

filepathProvided = False
#raw_input received the user input as string
try:
    filepath = raw_input('Enter filepath to save sequences ... ')
    filepath = filepath + '.fasta'
    handle = open(filepath, "w")
    handle.close()

    filepathProvided = True
except IOError:
    print 'Invalid or No File provided will print results to console'
print
ranSeqCount = 10
try:
    ranSeqCount = int(raw_input('Enter number of random sequences to generate ... '))
except ValueError:
    ranSeqCount = 10
pass

if(filepathProvided):
    handle = open(filepath, "w")

if(filepathProvided):
    fasta_writer = Bio.writers.SeqRecord.fasta.WriteFasta(handle)
else:
    fasta_writer = Bio.writers.SeqRecord.fasta.WriteFasta(stdout)
print 'Sequence Count : '
print ranSeqCount

for i in range(0,ranSeqCount,1):
    fasta_writer.write(randomProteinSeqRecord(i+1))
if(filepathProvided):
    handle.close()
print 'File created at : ' + filepath

print
raw_input('Press any key to exit ...')
print

Получение этой ОШИБКИ: Traceback (последний вызов был последним): Файл "C: \ Users \ Hemant \ Desktop \ RandonProteinSeptions.py", строка 10, в импорт Bio.writers.SeqRecord.fasta Ошибка импорта: нет модуля с именем writers.SeqRecord.fasta

Ответы [ 2 ]

2 голосов
/ 23 мая 2011

Я уже упоминал об этом в вашем другом вопросе , и я скажу здесь еще раз:
Этот код нуждается в обновлении, начиная с Bio.writers.SeqRecord.fasta устарела .

Я быстро взглянул на документацию Biopython, пытаясь выяснить, как можно написать файл FASTA.
Попробуйте это: 

# File Name RandonProteinSequences.py
# standard library
import os
import random

# biopython
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from sys import *

residueList1 = ["C","D","E","F","G","H","I"]
residueList2 = ["A","K","L","M","N","S"]
residueList3 = ["P","Q","R","T","V","W","Y"]
residueList4 = ["C","A","G","U"]

def getProteinSeqRecord(residue, seqcount):
    strSeq = ""
    for i in range(0,100,1):
        index = random.randint(0, len(residue)-1)
        strSeq += residue[index]

    sequence = Seq(strSeq, IUPAC.IUPACProtein)
    seqRec = SeqRecord(sequence, id = 'randSeq' + str(seqcount), description= 'A random sequence using Amino acid residues.')
    return seqRec

def getProteinSequence(residue):
    strSeq = ""
    for i in range(0,100,1):
        index = random.randint(0, len(residue)-1)
        strSeq += residue[index]

    sequence = Seq(strSeq, IUPAC.IUPACProtein)
    return sequence

def randomProteinSeqRecord(index):
    if(index%2)==0:
        return getProteinSeqRecord(residueList1, index)
    elif(index%3)==0:
        return getProteinSeqRecord(residueList2, index)
    else:
        return getProteinSeqRecord(residueList3, index)

#information
print '--- This is python based program to generate random sequences ---'
print '--- Provide number of random sequences to generate. Default 10 ---'
print '--- Inorder to save to a file provide file path or filename ---'
print '--- If none or invalid filepath is provided then results will be displayed to console ---'
print '--- The file will be created in fasta format ---'
print

filepathProvided = False
#raw_input received the user input as string
try:
    filepath = raw_input('Enter filepath to save sequences ... ')
    filepath = filepath + '.fasta'
    #handle = open(filepath, "w")
    #handle.close()

    filepathProvided = True
except IOError:
    print 'Invalid or No File provided will print results to console'
print
ranSeqCount = 10
try:
    ranSeqCount = int(raw_input('Enter number of random sequences to generate ... '))
except ValueError:
    ranSeqCount = 10
    pass

print 'Sequence Count : '
print ranSeqCount

records = []
for i in range(0,ranSeqCount,1):
    records.append(randomProteinSeqRecord(i+1))

if(filepathProvided):
    SeqIO.write(records, filepath, "fasta")
    print 'File created at : ' + filepath

else:
    print 'Writing to console is actually not supported!  :/'

print
raw_input('Press any key to exit ...')
print

Обратите внимание: У меня не установлен Biopython, поэтому я не запускал этот код.
Я пытаюсь вам здесь помочь, но правда в том, что у меня есть дела поважнее.

0 голосов
/ 19 мая 2011

Возможно, вам придется изменить: 

import Bio.writers.SeqRecord.fasta

для: 

from Bio.writers.SeqRecord import fasta
...