deleting the spaces in a line while reading a text file

[aboxylica]

I have a file which contains something like this

>ref|NC_001133| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=I]
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA
CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
ACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAAC
CACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC
CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATAC
TGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCT
TACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC
CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATG
CACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTAT
CCACATTTTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAAT
ACATACGTTATACCACTTTTGCACCATATACTTACCACTCCATTTATATACACTTATGTC
AATATTACAGAAAAATCCCCACAAAAATCACCTAAACATAAAAATATTCTACTTTTCAAC
AATAATACATAAACATATTGGCTTGTGGTAGCAACACTATCATGGTATCACTAACGTAAA
AGTTCCTCAATATTGCAATTTGCTTGAACGGATGCTATTTCAGAATATTTCGTACTTACA
CAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCTTTATTCACCGAGC
AATAATACGGTAGTGGCTCAAACTCATGCGGGTGCTATGATACAATTATATCTTATTTCC
ATTCCCATATGCTAACCGCAATATCCTAAAAGCATAACTGATGCATCTTTAATCTTGTAT
GTGACACTACTCATACGAAGGGACTATATCTAGTCAAGACGATACTGTGATAGGTACGTT
ATTTAATAGGATCTATAACGAAATGTCAAATAATTTTACGGTAATATAACTTATCAGCGG
CGTATACTAAAACGGACGTTACGATATTGTCTCACTTCATCTTACCACCCTCTATCTTAT
TGCTGATAGAACACTAACCCCTCAGCTTTATTTCTAGTTACAGTTACACAAAAAACTATG
CCAACCCAGAAATCTTGATATTTTACGTGTCAAAAAATGAGGGTCTCTAAATGAGAGTTT
GGTACCATGACTTGTAACTCGCACTGCCCTGATCTGCAATCTTGTTCTTAGAAGTGACGC
ATATTCTATACGGCCCGACGCGACGCGCCAAAAAATGAAAAACGAAGCAGCGACTCATTT
TTATTTAAGGACAAAGGTTGCGAAGCCGCACATTTCCAATTTCATTGTTGTTTATTGGAC
ATACACTGTTAGCTTTATTACCGTCCACGTTTTTTCTACAATAGTGTAGAAGTTTCTTTC
TTATGTTCATCGTATTCATAAAATGCTTCACGAACACCGTCATTGATCAAATAGGTCTAT
AATATTAATATACATTTATATAATCTACGGTATTTATATCATCAAAAAAAAGTAGTTTTT
TTATTTTATTTTGTTCGTTAATTTTCAATTTCTATGGAAACCCGTTCGTAAAATTGGCGT
TTGTCTCTAGTTTGCGATAGTGTAGATACCGTCCTTGGATAGAGCACTGGAGATGGCTGG
CTTTAATCTGCTGGAGTACCATGGAACACCGGTGATCATTCTGGTCACTTGGTCTGGAGC
AATACCGGTCAACATGGTGGTGAAGTCACCGTAGTTGAAAACGGCTTCAGCAACTTCGAC
TGGGTAGGTTTCAGTTGGGTGGGCGGCTTGGAACATGTAGTATTGGGCTAAGTGAGCTCT
GATATCAGAGACGTAGACACCCAATTCCACCAAGTTGACTCTTTCGTCAGATTGAGCTAG
AGTGGTGGTTGCAGAAGCAGTAGCAGCGATGGCAGCGAC
 

while reading this file.. i dont want the first line , and there are spaces between the line. i am going to read this file in my program which does many things with this. but while reading it should not have spaces between these characters(as in the "\n" in the file.. i want it to be stored like a a continuous sequence of letters
this is the code I have written what changes should i make

def readfasta():
    file=open("chr01.fsa","r")
    print file
    file_content=file.readlines()
    seq_s=""
    for z,seq_ in enumerate(file_content):
        if seq_=="\n":
            seq_s+=seq_
        #print seq_
        #for line in file_content:
            #while not line.startswith(">"):
               # print line
 
k=readfasta()
 

waiting for ur reply
cheers!

[bartonc]

I've broken this down into fairly simple steps for you.
I hope that it's not too complicated.

# def...
    for line in file_content:
        if line.startswith('>ref'):
            continue   # back to top of loop
        parts = line.strip().split()  # strip of \n and split at the space
        try:
            seq = parts[0] + parts[1]   # put the parts together if they exist
        except IndexError:
            seq = line   # else use the line as is

[aboxylica]

Thanks for that.It helped me !
cheers!

[bartonc]

Thanks for that.It helped me !
cheers!

I'm glad to be of help. I hope that you are catching on (it looks like it) and have a good reference book handy.

[ghostdog74]

you can also use the replace() function.

[bartonc]

you can also use the replace() function.

Yes, yes! Great suggestion.

If you know how many spaces, instead of split() use

line = line.replace(" ", "")