问题
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
回答1:
Python is sensitive to indentation. If your code is badly indented, it won't work.
My amazing googling powers tell me you've taken your code from this page, where unfortunately the code isn't properly formatted either.
But here, I took the effort. I'm not responsible if this will fail miserably though, because I didn't run it, not even mentally.
# 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
回答2:
Python depends on indentation to determine where functions (and other block structures) end. Presumably, the function that is causing your error should look like this:
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
回答3:
You have your intendation wrong
来源：https://stackoverflow.com/questions/6056675/return-outside-function