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Splitting a file in a directory!

 
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Top Forums UNIX for Dummies Questions & Answers Splitting a file in a directory!
# 1  
Old 12-14-2011
Error Splitting a file in a directory!
Hey guys!


So I have a directory with 82 genomes in it and I have to split them up, one by one, into genes. I tried using the split function, like

Code:
#!/usr/bin/perl

  use strict;
  use warnings;

  my $data = 'location';

  my @values = split('>', $data);

  foreach my $val (@values) {
    print "$val\n";
  }

  exit;

At first I was using it from my home directory and specifying the location, then I was using it in the directory, using just the file name. I keep returning errors though. Does anyone know how to fix it? And should I use files with the .faa extension or get rid of it and just use the file name?

Thanks Smilie
Last edited by radoulov; 12-14-2011 at 06:23 AM.. Reason: Code tags!
# 2  
Old 12-14-2011
I am afraid .. genomes ??? not understandable .. Pls be more clear and also post some input and expected output contents ..
# 3  
Old 12-14-2011
Okay so the genome has a load of genes in it, all just characters, and each new gene is represented by > Here's an example of three genes taken from a genome


Code:
>AFL2G_00003 | Aspergillus flavus hypothetical protein similar to branched-chain amino acid aminotransferase pro
tein (translation) (287 aa)
MTSMNKVFSGYYERKARLDNSGNRFAKGIAYVQGSFVRLADARVPLLDEGFMHSDLTYDV
PSVWDGRFFRLDDHLSRLEDSCEKMRLKIPLSRDEVKQTLREMVAKSGIEDAFVELIVTR
GLKGVRGNKPEDLFDNHLYLIVMPYVWVMEPAMQPTGGTAIIARTVRRTPPEGSGFNIVL
VKDGIIYTPDRGVLEGITRKSVFDIAQAKNIEVRVQMVPLEHAYHADEIFMCTTAGGIMP
ITKLDGKPIRNGKVGPLTTKIWDEYWAMHYDPKYSSAIDYKGHEGN*
>AFL2G_00004 | Aspergillus flavus hypothetical protein similar to MSF tranporter (translation) (366 aa)
MANSWIHERFGQRGIALLGTGMHVISYFATTQHPPFPLLITIFILAGLGNGIVDASWNAW
IGAMHNSSQLMGILHAFYGLGAALAPLTATYVITQRGCMWYHFYYIMGIAATIEFVTSVA
AFWSARGSLVEASELGVPGDNVQQDDRDSSRRNTTLKNPTLESLGLVSTWIISLFLLVYV
GIEVTVGGWVFTFLVDLRNTPPSVAGVVTFMYWGGLTVGRVCLGFITPYFKRQRLVIVVY
LLACVVCHIGFWLATELHLSMIAVTLLGFFLGPLYPEAVIAQAALLPKHLHVAAVGFACA
LGSAGGCIFPFITGAIAKAHGIKVLHPVVLAMLMLCLILWFALPGQRRGTKEAASPAWSS
SPTRS*
>AFL2G_00005 | Aspergillus flavus hypothetical protein similar to class III aminotransferase (translation) (466 
aa)
MGSAAEPAYLYKNVTHDPTVPSVKSAEGIYIFLENGQKILDATSGAAVSAIGHGVGRVKK
AIMSQLDQVEYCHPGFFPNTPAMDLADLLVESTGGKLSRACILGSGSEAVEAAMKLAYQY
FEEQSPNTRRTRFISRHGSWHGCTLGALALGDFKPRKTRFNSILTSNISHVSACDPYHGL
MENEDPETYVARLKDELDNEFQRLGPETVCAVFLEPMVGTALGCVTALPGYLQAVRDVCD
RYGALLVFDEIMCGMGRTGITHAWQEDGVAPDIELVGKGLAAGYGTISGLLVNDRVLDGL
RHGGGYFVHGQTYQSHPLGCAAAVEVQRIIKEENLVENCRKMGQYLGQQLKLHLGDHPYV
GDIRGRGLFWAVEFMADPPTKTPFSPAFTISKRMQSRGMERGYDICLFAATGAVDGCNGD
HVLLAPPYIVHKEDVDEIMDETGIMSVKQAIPTHGSSQKGGMNLQ*

So what I want to do is split it up whenever there's a > and give each gene a number. That way I can reassemble them with replacement and see which ones are going in and which are not. I'm basically splitting up a text fie to redo it, and I think starting with the split and then going on to number them would be the easiest way to do it!

Moderator's Comments:
Mod Comment Video tutorial on how to use code tags in The UNIX and Linux Forums.
# 4  
Old 12-14-2011
what does genomes and genes refer too??
# 5  
Old 12-14-2011
Genomes is pretty much a text file that contains genes. There's an unknown number of genes in the text file, and they're all separated by ">" I want to separate all the genes so I have, say, 1000 small text files, each called a unique number. I tried using a basic split function but it doesn't appear to be working so any help anyone can give would be greatly appreciated!
# 6  
Old 12-14-2011
Do you want the files named 'AFL2G_00003.txt', or just a unique (for that run of the script) number?
# 7  
Old 12-14-2011
Just a unique number, 1-1000 or something like that.
 
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