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Saving file edited whith sed

 
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# 1  
Old 06-26-2010
Data Saving file edited whith sed
HI!
I have a file that looks like this:

Code:
>ANKRD30_2kb
AAGTAACCAATGCAGGAAACCGAGAGGAGAGGTTTGGAAGGTGGTTTAGTGAGGTAATCCATCTTTTCT
AGTGATAAACTGGCACCCAGTCAATTTATTCATCAGAAGGGAATACATCAGCCTGGCGTGGTGGCTCGC
CCCCGACCCTGTCAGCGTCACCAGCAGCGCGGATCCATGGGCCAGAAGCCTCTAGGGCGCCTAAGTCAG
Number of residues in the repeat = 3
AAG
[ 1 to 3 ]
[ 38 to 40 ]
[ 106 to 108 ]
----------------------------------------------------------------------
Number of residues in the repeat = 3
AGA
[ 23 to 25 ]
----------------------------------------------------------------------
Number of residues in the repeat = 3
AGC
[ 119 to 121 ]
[ 152 to 154 ]
[ 161 to 163 ]
----------------------------------------------------------------------
Number of residues in the repeat = 3
>C3orf24_2kb
TTGTGGTGTGTGTTCTATAGTTTGTAAAATGCAAGGGCAATTCTGGGTGTACAAGGGAAGGCCAAGTAG
GCCATTAGTTACTTCCTCCCACAAATACTGCACACTGCCAGACATGGCAATAGCCAGGTACTGGGAATA
CAGACATCAGCTGGGTAGACTCCTCCCTTCCCTCAGCCATCCAGGGTCATTATTTTAAGTGATGATTAC
Number of residues in the repeat = 3
AAA
[ 26 to 28 ]
[ 27 to 29 ]
[ 92 to 94 ]
----------------------------------------------------------------------
Number of residues in the repeat = 3
AAG
[ 33 to 35 ]
[ 53 to 55 ]
----------------------------------------------------------------------
Number of residues in the repeat = 3

All I want to get from this file is:

Code:
>ANKRD30_2kb
AAG
AGA
AGC
>C3orf24_2kb
AAA
AAG

I've tried to use this command:
Code:
sed '/\[/,/^N/d' file|grep -v "^N"|sed '/^.\{50\}/d'

If I look with it using the head command it seems to work, but when I try to save it into a new file (>newfile) all I get is an empty file!!!. What am I doing wrong???Smilie
Thanks
Last edited by Scott; 06-27-2010 at 06:22 AM.. Reason: Code tags, please...
# 2  
Old 06-26-2010
Code:
egrep '>|^[A-Z][A-Z][A-Z]$' infile

This User Gave Thanks to pseudocoder For This Post:
vanesa1230
# 3  
Old 06-26-2010
Quote:
Originally Posted by pseudocoder
Code:
egrep '>|^[A-Z][A-Z][A-Z]$' infile

That's even much more elegant. ThanksSmilie
# 4  
Old 06-26-2010
pseudocoder - doesn't alternation usually require '(pattern1|pattern2)' - the surrounding parentheses? I've never tried it that way....
# 5  
Old 06-26-2010
Code:
egrep '^>|^[A-Z]{3}$' infile

Code:
egrep '^(>|[A-Z]{3}$)' infile

This User Gave Thanks to Scrutinizer For This Post:
vanesa1230
# 6  
Old 06-26-2010
Code:
egrep '>|^[A,G,C]*$' infile

This User Gave Thanks to EAGL€ For This Post:
vanesa1230
# 7  
Old 06-26-2010
Hi Eagl€, you probably mean:
Code:
egrep '>|^[AGC]*$' infile

But I do not think that works here, since then you filtering on the fact that there happens to be no T present on the lines with 3 characters, otherwise it would match lines with more than 3 of those characters as well.
This User Gave Thanks to Scrutinizer For This Post:
vanesa1230
 
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