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Help with file splitting

 
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# 1  
Old 06-23-2010
Help with file splitting
Hey everyone,
I would really appreciate some help with a problem I have filing away some data I have. I have multiple fasta files that have different pieces of information in each. I want to split each file into parts, and then file away each separate part into its own file. Here is an example file:

Code:
                 >mhp001
atgcaaacaaataaaaataatttaaaggttagaacacagcaaattaggcaacaaattga
aaatttattaaatgatcgaatgttgtataacaacttttttagcacaatttatgtactca
acgagacagaaactgaaattattatagattttacagacttaatcgcgaaacaggaagtg
atttcacgctgagttgatacggttgaaaaagctattaaaaatcttgaaatttcaaaaat
cctaacttttaacaatacaaataattataccattaattcaaaagaaagccaaaactttt
ccataaaaaataaatattgcagctttaatattaacaatgttttaaacaaatttaccttt
agaaattttataaaatcaagttataatttccaaatttttagtatttatgacgcaatagt
cgcaaattcaagactaaattactcaccaatttttatttcaggaccatcaggaattggaa
aaacgcattttattaatgcgattggaaatttacttgtagaaaaacagaagaaagttttc
tacattaacgactataaatttatcagttgcgtttcttcctggatgcaaaatggtcaaaa
tgaaaaaattagtgaatttttaaactgattgtctcaagttgacgcttttctttttgatg
atatccaaggtttggctaacaaacaacaaacttcaattgttgcacttgaaattttaaat
agatttatcgaagaggataaaacagtgataataacatctgataaatcgccttctttact
tggtggatttgaagaaagatttataacgcgatttagttcagggttgcacattaaattaa
acaagccgaaaaaagaagactttttgcggatttttaagcataaattagttgaagaaaaa
ttagaaaaacatatttgaacaaatgatgcttttgaatttttgtcaaagcattttcgaaa
ttcgattcgtgagcttgaaggtgcgctaaaatcaattgttttttatatccaaacaaata
aaaataaatttgaggatgaaatttattttgataagaaaaaaatgtttgaaatttttgtt
gaaaaatatgaaatcgaacaaacaatcacccctgatttaatcattgaggttgtctcaaa
atattatggcgtctcaattttagatataaaaagtgaaaaaagaggcaaaaatattgtgc
atgcccgcgatattgcaatctgattaattaaaaatattctggatttaactcataatagc
gtaggaactttttttaacaacagaagacattcaacaataatttctacccttaaaaaaat
tgatactttaaaacaaagcaacaataatgaacttgaaattgcccttaaccatatttata
aacaattaaactgaagttttaaacagcgaaaataa
>mhp001_mycohypo
atgcaaacaaataaaaataatttaaaggttagaacacagcaaattagAcaacaaattga
aaatttattaaatgatcgaatgttgtataacaacttttttagcacaatttatgtactca
acgagacagaaactgaaattattatagattttacagacttaatcgcgaaacaggaagtg
atttcacgctgagttgatacggttgaaaaagctattaaaaatcttgaaatttcaaaaat
cctaacttttaacaatacaaataattataccattaattcaaaagaaagTcaaaactttt
ccataaaaaataaatattgcagctttaatattaacaatgttttaaacaaatttaccttt
GgaaaCtttataaaatcaagttataatttccaaatttttagtatttatgaTgcaatagt
cgcaaattcaCgactaaattactcaccaatttttatttcaggaccatcaggaattggaa
aaacgcattttattaatgcgattggaaatttacttgtGgaaaaacagaagaaaAttttc
tacattaaTgactataaatttatcagCtgcgtttcttcctggatgcaaaaCggtcaaaa
tgaaaaaattagtgaatttttaaactgattgtctcaagttgacgcttttctttttgatg
atatccaaggtttggctaacaaacaacaaacttcaattgttgcGcttgaaattttaaat
agatttatcgaagaggataaaGTagtgataataacatctgaCaaatcAccttctttact
tggtggatttgaagaaagatttataacTcgatttagttcagggttgcacattaaattaa
acaagccgaaaaaagaGgactttttgcggatttttaagcataaattagttgaagaaaaa
ttagaaaaacatatttgaacaaatgatgcttttgaatttttgtcaaaAcattttcgaaa
ttcgattcgCgagcttgaaggtgcgctaaaatcaattgttttttatatccaaacaaata
aaaataaatttgaAAatgaaatttattttgataagaaaaaaatgtttgaaatttttgtt
gaaaaatatgaaatcgaacaaacaatTacccctgatttaatcattgaggttgtctcaaa
atattatggcgtctcaattttagatataaaaagtgaaaaaagaggcaaaaatattgtgc
atgcccgcgatattgcaatctgattaattaaaaatattctggatttaactcataatagc
gtaggaactttttttaacaacagaagacattcaacaataatttctacccttaaaaaaat
tgatactttaaaacaaagcaacaataatgaacttgaaattgcccttaaccatatttata
aacaattaaactgaagttttaaacagcgaaaataa

What I want to do is to split the file at the '>' marks and put each piece into a different file. I'm a newbie to linux, so I really have no idea how to write the script for this.

Thanks for your help!
Last edited by vgersh99; 06-23-2010 at 04:38 PM.. Reason: code tags, please!
# 2  
Old 06-23-2010
Code:
 awk '
     /^>/ {if(length(f)>0){close(f)}; f=substr($0,2) }
    {print $0 > f } ' filename

This creates filenames named after the string following the ">"
# 3  
Old 06-23-2010
Ok!
That works great! Now how do I do that for say, 700 files, and put all the generated files into separate folders according to what file they originated from?
# 4  
Old 06-23-2010
Hint: tell us all of what you want at the very beginning.... it is easier for all of us.

Define what you want by directory, i.e., how do you determine the directory name based on an originating directory.
# 5  
Old 06-23-2010
Sorry
Sorry about that, this is my first time on here, so I didn't think my question through as much as I should have the first time through.

Also, I'm not sure what you're asking? Basically, the directory created should be named the same as the original file, so that all the components are held within.
# 6  
Old 06-23-2010
You want the splits to go into the same directory the file came from.
/path/to/files is the top directory for your file tree.
Code:
#!/bin/ksh
awkit()
{
    awk '
     /^>/ {if(length(f)>0){close(f)}; f=substr($0,2) }
    {print $0 > f } '  $1
}
find /path/to/files -type d |
while read dirname
do
      cd $dirname
      for i in *
      do
           [[ -f $i  ]] && awkit $i
      done 
done

# 7  
Old 06-24-2010
One more thing
Ok, thanks for all you help, it is working well. The only problem is, that when I use the script, the output is just as a "file". I didn't think this was a big deal what kind of file the output was, but I am trying to do some things with a program that needs all of the output to be in fasta format ( .fa ). So, how does the script you gave need to be changed to do that as it outputs?
 
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