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# 1  
Old 05-02-2011
Awk problem
Hello everyone.

I have a file with this structure :

>[something near random]
[Lots of letters, several lines]
>[something near random]
[Lots of letters, several lines]
>[something near random]
[Lots of letters, several lines]
>[something near random]
[Lots of letters, several lines]
.......

I want to separate each file on this basis :
Title is what is after the ">"
File information is evrything from one > to another >

What I have tried :

Code:
awk 'BEGIN{RS=">";FS="\n";OFS="\n"}{close(f);f=$1}{print>f}' [name of my loooooong file]

And, I get an error : awk: (FILENAME=[file name] FNR=1> fatal: expression for '>' redirection has null string value

Help ?
(Thank you !!!)
# 2  
Old 05-02-2011
Code:
awk 'BEGIN{i=0; f="file"} /^>/{f=sprintf("file_%d,i++ )} {print $0>f}'  [name of my loooooong file]

This will produce a bunch of files: file1, file2.... filen

You really should consider using csplit, it is meant for this. It is possible with awk to exceed your open file limit

Code:
$ -f "file" is the prefix of the split out file set  -n 8 gives 00000000 9999999 files
csplit  -f "file" -n 8  inputbigfilename  '/^>/'

you get file00000000 -> file99999999
This User Gave Thanks to jim mcnamara For This Post:
sluvah
# 3  
Old 05-03-2011
Thank you for your response.

I didn't know this command, but after reading man, I think it's the best one !
Gonna try this one tomorrow. Thank you !

---------- Post updated 03-05-11 at 03:11 AM ---------- Previous update was 02-05-11 at 02:58 PM ----------

I just found how it work !

here is the code I used :

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/^>/' '{*}'

I think the '{*}' is to told the csplit to search for my pattern as much as possible.

Thank you, I get my hundreds of files Smilie Smilie


Hello,

I just tried the csplt command :

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/^>/'

Or

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/>/'

None of them worked well : It print a "0" meanig everything is okay, but instead of 2700 files, I get only two... One empty, and one with the same information my big file have...

I'm still trying to find the answer with google, but if you can help me I would appreciate Smilie

Thank you !
Last edited by sluvah; 05-03-2011 at 05:21 AM..
# 4  
Old 05-03-2011
Quote:
Originally Posted by sluvah
Code:
awk 'BEGIN{RS=">";FS="\n";OFS="\n"}{close(f);f=$1}{print>f}' [name of my loooooong file]

And, I get an error : awk: (FILENAME=[file name] FNR=1> fatal: expression for '>' redirection has null string value
The error is due to the empty line (appearing at first) that is getting processed, to nullify it use "NR > 1". So, here is the modified code:
Code:
awk 'BEGIN {RS=">"; FS=OFS="\n"} NR > 1 {close(f); f=$1; print > f}' [name of my loooooong file]

---------- Post updated at 03:59 PM ---------- Previous update was at 03:15 PM ----------

Quote:
Originally Posted by sluvah
Thank you for your response.

I didn't know this command, but after reading man, I think it's the best one !
Gonna try this one tomorrow. Thank you !

---------- Post updated 03-05-11 at 03:11 AM ---------- Previous update was 02-05-11 at 02:58 PM ----------

I just found how it work !

here is the code I used :

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/^>/' '{*}'

I think the '{*}' is to told the csplit to search for my pattern as much as possible.

Thank you, I get my hundreds of files Smilie Smilie


Hello,

I just tried the csplt command :

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/^>/'

Or

Code:
csplit -n 4 -f "LAL14.1-" no_space_Sis_110407_amino.fasta '/>/'

None of them worked well : It print a "0" meanig everything is okay, but instead of 2700 files, I get only two... One empty, and one with the same information my big file have...

I'm still trying to find the answer with google, but if you can help me I would appreciate Smilie

Thank you !
Code:
sed 's/>/\n&/g' infile | sed 1d > out
csplit -f "f" -n 8 out '/^>/' {*}

This works for me, but I don't know how to suppress the formation of file f00000000 with empty contents!! Smilie
 
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