Importerror: No Module Named Writers.seqrecord.fasta

# 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 SeqRe

Solution 1:

I've already mentioned this in your other question and I'll say it here again: This code is in need of an update, since Bio.writers.SeqRecord.fasta is deprecated.

I took a quick look at Biopython's documentation trying to figure out how you can write a FASTA file. Try this:

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

# biopythonfrom 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"]

defgetProteinSeqRecord(residue, seqcount):
    strSeq = ""for i inrange(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

defgetProteinSequence(residue):
    strSeq = ""for i inrange(0,100,1):
        index = random.randint(0, len(residue)-1)
        strSeq += residue[index]

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

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

#informationprint'--- 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 stringtry:
    filepath = raw_input('Enter filepath to save sequences ... ')
    filepath = filepath + '.fasta'#handle = open(filepath, "w")#handle.close()

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

records = []
for i inrange(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

Please note: I don't have Biopython installed, so I didn't run this code. I'm trying to help you here, but the truth is I've got better things to do.

Solution 2:

Maybe you have to change:

import Bio.writers.SeqRecord.fasta

for:

fromBio.writers.SeqRecordimport fasta