So basically you just want to parse a fasta file and put the contents in a header array and a sequence array? You can use BioPython's SeqIO module:

from Bio import SeqIO
import sys

headerList = []
seqList = []

inFile = open(sys.argv[1],'r')
for record in SeqIO.parse(inFile,'fasta'):
   headerList.appendrecord.id)
   seqList.append(str(record.seq))

If you don't want to use BioPython you can:

import sys

inFile = open(sys.argv[1],'r')

headerList = []
seqList = []
currentSeq = ''
for line in inFile:
   if line[0] == ">":
      headerList.append(line[1:].strip())
      if currentSeq != '':
         seqList.append(currentSeq)

      currentSeq = ''
   else:
      currentSeq += line.strip()

seqList.append(currentSeq)

When I wrote a FASTA reshuffle routine some time ago (to layout contigs as mapped by BLAT) I used Perl and (if memory permits) just threw all sequences itself in a hash with the key being the unique fasta header/identifyer.

For reshuffle and display in particular order I just had to skip through some ordered list of fasta headers and get the corresponding sequences from the hash.

In Python I think you can relatively easily do the same using the python alternative to hashes..dictionaries (I believe...not a python export). Together with the clues of Robert you should get there. Even though I usually prefere regular expressions but thats just preference.

i needed to reset the string

def Name_Organizer(FASTA,output):

import os
import re

in_file=open(FASTA,'r')
dir,file=os.path.split(FASTA)
temp = os.path.join(dir,output)
out_file=open(temp,'w')

data=''
name_list=[]
seq_list=[]

for line in in_file:

    line=line.strip()
    for i in line:
        if i=='>':
            name_list.append(line)
            if data:
                seq_list.append(data)
                data=''
            break
        else:
            line=line.upper()
    if all([k==k.upper() for k in line]):
        data=data+line

print seq_list

You are going in the right direction! You should add a piece of code that puts your data string into a "sequence_list" when the line starts with a ">". And further more to make sure that there are no empty data objects added to your sequence_list you should put this in a if statement (if data != ''). After doing this you want to reset your data object (data = '').

Furthermore your 2nd for loop (for i in line) is not required. You can just check the ">" with line[0] == >.

I hope that helps you to solve the problem yourself.