Hii I am getting the following error in Biopython: 'return' outside function (filename.. line 26) Below is the code of myfile PLEASE HELP
# 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