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Probably some stupid mistake...

 
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Top Forums UNIX for Dummies Questions & Answers Probably some stupid mistake...
# 1  
Old 01-28-2011
[solved]Probably some stupid mistake...
Hi everyone !

I have a file wich look like this :

>Sis01
[lots of ATCG stuff]

> Sis02
[lots of ATCG stuff]

...

>Sis44
[lots of ATCG stuff]


I want to separe each paragraphe in a different file, so I decide to use the "FOR" loop + sed.

Code:
for f in {01..44}
do
(
   sed -n '/^>Sis `echo $f'/,/^>/p' Sis_110125.fasta | sed '$d' > Sis_110125_contig`echo $f`
)
done

I get empty files, i think due to the space between ^> and the echoed $f


I try a lot of thing, but I was unable to find a solution !

Thanks for your help !
Last edited by sluvah; 01-28-2011 at 02:10 PM.. Reason: Solved
# 2  
Old 01-28-2011
Code:
awk '/Sis/{close(f);f=sprintf("Sis%02d",++c)}{print > f}' file

# 3  
Old 01-28-2011
You are a god !

Thank you so mutch !

Could you just help me to understand the line ? I prefer to understand what I use, at least it help me to improve my bash !

What I understand :
Code:
awk  ==> Awk program, the one to use with a table

'/Sis/{ ==> ??? Pattern to search in my file ?

close(f); ==> Empty F variable ?

f=sprintf("Sis%02d",++c)} ==> what my f variable is : Sis + number in two digit, increasing each time by one

{print > f}' ==> Print my paragraphe ? How did this paragraphe get selected by awk ???

file ==> Obviously, my file name

Thanks !
# 4  
Old 01-28-2011
Quote:
Originally Posted by sluvah
Could you just help me to understand the line ? I prefer to understand what I use, at least it help me to improve my bash !
Sure.
Code:
awk '/Sis/{close(f);f=sprintf("Sis%02d",++c)}{print > f}' file

Explanation:

/Sis/ search for the pattern and if it matches:
{close(f) close the opened file (if there was one opened) and...
f=sprintf("Sis%02d",++c)} fill the variable f with "Sis" and an increased number in 2 digits
{print > f} open a file (if it wasn't) and print the line to the file f

Hope this helps.
# 5  
Old 01-28-2011
Great !

Thanks !
# 6  
Old 01-29-2011
Code:
awk -F \> '/Sis/ {f=$2}{print > f}' Sis_110125.fasta

 
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