Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Split a huge data into few different files?!

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Split a huge data into few different files?!
# 1  
Old 10-30-2009
Split a huge data into few different files?!
Input file data contents:
Code:
>seq_1
MSNQSPPQSQRPGHSHSHSHSHAGLASSTSSHSNPSANASYNLNGPRTGGDQRYRASVDA
>seq_2
AGAAGRGWGRDVTAAASPNPRNGGGRPASDLLSVGNAGGQASFASPETIDRWFEDLQHYE
>seq_3
ATLEEMAAASLDANFKEELSAIEQWFRVLSEAERTAALYSLLQSSTQVQMRFFVTVLQQM
ARADPITALLSPANPGQASMEAQMDAKLAAMGLKSPASPAVRQYARQSLSGDTYLSPHSA
>seq_4
TTLPPAPVSPTTTTQAEDAAAAATLASQRAKLKASSRISAPANILLGASGADGVKSPLWS
EKERVVERRSPSPSGRNVERPKSTGSTGEPAQPNNSHAGMNLSQSTGPPSASFLRSPAPD
>seq_5
FDSQLSPIVGGNWASMVNTPLMPMFGSKGGGEGGSFGGLASPGLDGATAKLGSWATGTTT
GQAGIVLDDVRKFRRSARISGSGATGFGGGALGGMYDDQPAQASTNGQQQRRVSPSQLNS
>seq_6
AQQNAINLGLAGLQQQQQQHQQQLRSGAASPGLSSQQAAVAAQQNWRNGLGSPAVDSSDQ
YSQHGMGAFGMGSPANLSANAQLANLFALQQQMMQQQQMQQLNMAAAAGIALTPVQMMGL
QQQQQQAMLSPGGRGFGMGMNGMGMNGMMGMGMGGMGSPRRSPRQSDRSPGGKTNLPSTV
.
.
.
.

Output file 1 contents:
Code:
>seq_1
MSNQSPPQSQRPGHSHSHSHSHAGLASSTSSHSNPSANASYNLNGPRTGGDQRYRASVDA
>seq_2
 AGAAGRGWGRDVTAAASPNPRNGGGRPASDLLSVGNAGGQASFASPETIDRWFEDLQHYE
>seq_3
ATLEEMAAASLDANFKEELSAIEQWFRVLSEAERTAALYSLLQSSTQVQMRFFVTVLQQM
ARADPITALLSPANPGQASMEAQMDAKLAAMGLKSPASPAVRQYARQSLSGDTYLSPHSA

Output file 2 contents:
Code:
>seq_4
TTLPPAPVSPTTTTQAEDAAAAATLASQRAKLKASSRISAPANILLGASGADGVKSPLWS
EKERVVERRSPSPSGRNVERPKSTGSTGEPAQPNNSHAGMNLSQSTGPPSASFLRSPAPD
>seq_5
FDSQLSPIVGGNWASMVNTPLMPMFGSKGGGEGGSFGGLASPGLDGATAKLGSWATGTTT
GQAGIVLDDVRKFRRSARISGSGATGFGGGALGGMYDDQPAQASTNGQQQRRVSPSQLNS
>seq_6
AQQNAINLGLAGLQQQQQQHQQQLRSGAASPGLSSQQAAVAAQQNWRNGLGSPAVDSSDQ
YSQHGMGAFGMGSPANLSANAQLANLFALQQQMMQQQQMQQLNMAAAAGIALTPVQMMGL
QQQQQQAMLSPGGRGFGMGMNGMGMNGMMGMGMGGMGSPRRSPRQSDRSPGGKTNLPSTV

If I have a long list data inside a file, how I can divide the data into different file?
I need three data inside each file.
For example, my data source got 300 sequence.
I need it to divide 3 sequence in a file. Total desired output are 100 files that content 3 sequence each.
Do anybody got idea to solve my trouble?
Thanks a lot for all of your guide.
Last edited by pludi; 10-30-2009 at 05:51 AM.. Reason: code tags, please...
# 2  
Old 10-30-2009
Code:
awk -F'>' '$2{c--} c<=0{f=$2; c=3; $0=FS$2} {print>f}' infile



---------- Post updated at 02:31 AM ---------- Previous update was at 01:57 AM ----------

shell equivalent:
Code:
c=2
while read line; do
  case $line in
    \>*) c=$((c+1));;          # if label is found then increase counter
  esac
  if [ $c -eq 3 ]; then        # if 3 labels have been found then
    exec>${line#>}             # redirect output to file "label"
    c=0                        # reset counter
  fi
  echo $line                   # print output to current output file
done<infile

Last edited by Scrutinizer; 10-30-2009 at 07:40 AM..
# 3  
Old 10-30-2009
Hi,

Thanks a lot for your suggestion.
But it seem like it only split two sequence and put the third sequence header read as the file name?
Can I know what is the problem going on?
Thanks again for your kindly help and advice Smilie
# 4  
Old 10-30-2009
With the input you provided it creates two output files, seq_1 and seq_4;
Code:
$> cat seq_1
>seq_1
MSNQSPPQSQRPGHSHSHSHSHAGLASSTSSHSNPSANASYNLNGPRTGGDQRYRASVDA
>seq_2
AGAAGRGWGRDVTAAASPNPRNGGGRPASDLLSVGNAGGQASFASPETIDRWFEDLQHYE
>seq_3
ATLEEMAAASLDANFKEELSAIEQWFRVLSEAERTAALYSLLQSSTQVQMRFFVTVLQQM
ARADPITALLSPANPGQASMEAQMDAKLAAMGLKSPASPAVRQYARQSLSGDTYLSPHSA

$> cat seq_4
>seq_4
TTLPPAPVSPTTTTQAEDAAAAATLASQRAKLKASSRISAPANILLGASGADGVKSPLWS
EKERVVERRSPSPSGRNVERPKSTGSTGEPAQPNNSHAGMNLSQSTGPPSASFLRSPAPD
>seq_5
FDSQLSPIVGGNWASMVNTPLMPMFGSKGGGEGGSFGGLASPGLDGATAKLGSWATGTTT
GQAGIVLDDVRKFRRSARISGSGATGFGGGALGGMYDDQPAQASTNGQQQRRVSPSQLNS
>seq_6
AQQNAINLGLAGLQQQQQQHQQQLRSGAASPGLSSQQAAVAAQQNWRNGLGSPAVDSSDQ
YSQHGMGAFGMGSPANLSANAQLANLFALQQQMMQQQQMQQLNMAAAAGIALTPVQMMGL
QQQQQQAMLSPGGRGFGMGMNGMGMNGMMGMGMGGMGSPRRSPRQSDRSPGGKTNLPSTV

Do your real headers contain spaces?
# 5  
Old 10-30-2009
Yup.
You are right.
My other sequence of header contains space and some got ":" inside the header.
But after I using sed to substitute all of this spaces and ":" with "_".
Like:
Code:
sed 's/ /_/g' file_data > file_data.out 
sed 's/:/_/g' file_data.out > file_data.final.txt

By using the command that you suggested, end up all of my file name will got the "?" at the end of the file name. Smilie
Besides that, after I look at the contents of each file produced, it only contains two sequence instead of three sequences inside each file.
Really thanks of your advice Smilie
# 6  
Old 11-01-2009
Hi Scrutinizer, do you have any idea to get my desired output result?
I try to replace the space of header with "_" and try your suggested code.
Unfortunately, it still can't work Smilie
Thanks a lot for your advise.
# 7  
Old 11-02-2009
Quote:
Originally Posted by patrick87
Hi Scrutinizer, do you have any idea to get my desired output result?
I try to replace the space of header with "_" and try your suggested code.
Unfortunately, it still can't work Smilie
Thanks a lot for your advise.
Hi patrick87,

The problem is, I put random spaces and : characters inside the labels of your input examples you gave and both scripts still work as expected. I have to assume your real world data sets somehow do not correspond with the input format you provided. You would have to take a small part (say 7 records) of an actual, anonymized, file, then run my scripts on them to see if they also produce the strange results and then post that example input file here, and also list the strange resulting file names and their content, so I can have a look.

S.
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Solaris

Split huge File System

Gents I have huge NAS File System as /sys with size 10 TB and I want to Split each 1TB in spirit File System to be mounted in the server. How to can I do that without changing anything in the source. Please your support. (1 Reply)
Discussion started by: AbuAliiiiiiiiii
1 Replies

2. UNIX for Advanced & Expert Users

File comaprsons for the Huge data files ( around 60G) - Need optimized and teh best way to do this

I have 2 large file (.dat) around 70 g, 12 columns but the data not sorted in both the files.. need your inputs in giving the best optimized method/command to achieve this and redirect the not macthing lines to the thrid file ( diff.dat) File 1 - 15 columns File 2 - 15 columns Data is... (9 Replies)
Discussion started by: kartikirans
9 Replies

3. Shell Programming and Scripting

Split JSON to different data files

Hi Gurus, I have below JSON file, now I want to rewrite this file into a new file. I will appreciate if anyone can help me to provide the solution...I can't use jq. { "_id": "3ad893cb4cf1560add7b4caffd4b6126", "_rev": "1-1f0ce165e1d210319cf6e9f9c6ff654f", "name":... (4 Replies)
Discussion started by: manas_ranjan
4 Replies

4. Shell Programming and Scripting

Split a folder with huge number of files in n folders

We have a folder XYZ with large number of files (>350,000). how can i split the folder and create say 10 of them XYZ1 to XYZ10 with 35,000 files each. (doesnt matter which files go where). (12 Replies)
Discussion started by: AlokKumbhare
12 Replies

5. UNIX for Dummies Questions & Answers

Split a huge 7 GB File Based on Pattern into 4 files

Hi, I have a Huge 7 GB file which has around 1 million records, i want to split this file into 4 files to contain around 250k messages each. Please help me as Split command cannot work here as it might miss tags.. Format of the file is as below <!--###### ###### START-->... (6 Replies)
Discussion started by: KishM
6 Replies

6. Shell Programming and Scripting

Split a file into several files using a data

Hi All, I have file(File1) with data like below: 102100|LName|Gender|Company|Branch|Bday|Salary|Age 102100|bbbb|male|cccc|dddd|19900814|15000|20| 102101|asdg|male|gggg|ksgu|19911216||| 102102|bdbm|male|kkkk|acke|19931018||23| 102102|kfjg|male|kkkc|gkgg|19921213|14000|24|... (2 Replies)
Discussion started by: sarav.shan
2 Replies

7. Shell Programming and Scripting

how to split a huge file by every 100 lines

into small files. i need to add a head.txt and tail.txt into small files at the begin and end, and give a name as q1.xml q2.xml q3.xml .... thank you very much. (2 Replies)
Discussion started by: dtdt
2 Replies

8. Shell Programming and Scripting

Help- counting delimiter in a huge file and split data into 2 files

I’m new to Linux script and not sure how to filter out bad records from huge flat files (over 1.3GB each). The delimiter is a semi colon “;” Here is the sample of 5 lines in the file: Name1;phone1;address1;city1;state1;zipcode1 Name2;phone2;address2;city2;state2;zipcode2;comment... (7 Replies)
Discussion started by: lv99
7 Replies

9. Shell Programming and Scripting

Problem running Perl Script with huge data files

Hello Everyone, I have a perl script that reads two types of data files (txt and XML). These data files are huge and large in number. I am using something like this : foreach my $t (@text) { open TEXT, $t or die "Cannot open $t for reading: $!\n"; while(my $line=<TEXT>){ ... (4 Replies)
Discussion started by: ad23
4 Replies

10. Shell Programming and Scripting

Perl script error to split huge data one by one.

Below is my perl script: #!/usr/bin/perl open(FILE,"$ARGV") or die "$!"; @DATA = <FILE>; close FILE; $join = join("",@DATA); @array = split( ">",$join); for($i=0;$i<=scalar(@array);$i++){ system ("/home/bin/./program_name_count_length MULTI_sequence_DATA_FILE -d... (5 Replies)
Discussion started by: patrick87
5 Replies
Login or Register to Ask a Question