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Deleting certain new lines from a file with shell

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# 1  
Old 02-16-2011
Deleting certain new lines from a file with shell
Good morning!!! Im a newbie with shell programing and i was wondering if there is a way to delete certain new lines from a file, here is an example of my current file:
Code:
>seq_0
GTGAGATTGCTAATGAGCTGCTTTTAGGGGGCGTGTTGTGCTTGCTTTCC
AACTTTTCTAGATTGATTCTACGCTGCCTCCAGCAGCCACCCCTCCCATC
ACCATTCCCATCACCATCCAGTCCCGTTGGCTCCCAGTCACAGTATTACA
CGTATGCAAATTAAGCCGAAGTTCAATTGCGACCGCAGCAACAACACGAT
>seq_1
TTATGTCTCGATTCCAGCTAAATTGTCGCCTAAAGACGCCTCCGCCGGCG
TTGAGCGCCGAGCAGCATCTGGCACGCATCGAGGTTTTCAATTCGCTGGC
CGTGACAGCACCCCAAATCGAGGTGGACCGCCTGCGCTACGATAGGCGGC
ACAACATGAGCGGTAAGTGGATGCCACCAGCGGTTGGATCTGTGGGCGTG
GCAGTGGGAGTGGGAGTACGTGCCAGTCACGGCTGCCGTACCACCCGAAA
TCTGGTAAACAACGCTAATGCCACATGGTCACACTCCGGGACAGCTGATT
TGAAGAAGAAGAAGCAGCACGTGCACGTTGTTGTCAAATTTCAAATTAAC
TTTATTTGAAGCCAGCTTTTAAGTTAATTTCATCTTGCTGACACATCAAG
>seq_2
ACCAAAATAAATCTGGGAACTGAATAATCGAAAATAACTGGATGTGCATC
ATAAGATCTTCTTTTGAAGACTGACTACAGTTTGCAGCTCAGCGAGCTCG
GGCCGGCAACTCAAGCCGGTCAACTCAAGTCAGGCGCCAATTCGCTGCTC
CCACTCGCTCAGCTCTCTCAGTCACTCAAAATGGCAACGAGAGCAGAACG
GTTCTTTTGCAAAATACTTTATGACCGGAGCAGAAGCAGAATCGGACCTC
TGTCGCGGTCGCAGTCGCTGCCAGTGCTGACGGCGCTGTTGCGGCCGACG

And i was wondering if i can delete all the new lines from the letters sequences, so i can get one line with the >seq_# and only one line for all the letters, example:
Code:
>seq_0
GTGAGATTGCTAATGAGCTGCTTTTAGGGGGCGTGTTGTGCTTGCTTTCCAACTTTTCTAGATTGA...
>seq_1
TTATGTCTCGATTCCAGCTAAATTGTCGCCTAAAGACGCCTCCGCCGGCGTTGAGCGCCGAGCAGC...
>seq_2
ACCAAAATAAATCTGGGAACTGAATAATCGAAAATAACTGGATGTGCATCATAAGATCTTCTTTTG...

Thanks for your help Smilie
Last edited by Scott; 02-16-2011 at 02:11 PM.. Reason: Please use code tags
# 2  
Old 02-16-2011
Code:
nawk '/^>/{printf("%c%s\n",(FNR==1)?"":"\n",$0);next}{printf $0}END{print}' myFile

# 3  
Old 02-16-2011
Thanks!!! im trying to save it to a new file

Code:
 
nawk '/^>/{printf("%c%s\n",(FNR==1)?"":"\n",$0);next}{printf $0}END{print}' myFile >> newfile

But i cant get it recognized as a text file, am i doing something wrong? thanks!
# 4  
Old 02-16-2011
Quote:
Originally Posted by machalita
Thanks!!! im trying to save it to a new file

Code:
 
nawk '/^>/{printf("%c%s\n",(FNR==1)?"":"\n",$0);next}{printf $0}END{print}' myFile >> newfile

But i cant get it recognized as a text file, am i doing something wrong? thanks!
Hmmm... I'm having hard time understanding what's wrong - the above looks fine.
What error/warning messages are you seeing?
Anything in the 'newfile'?
# 5  
Old 02-16-2011
The new file its not being recognized as a text file, when i try to open it, i get the error: Gedit has not been able to detect the character coding, please check that you are not trying to open a binary file.
# 6  
Old 02-16-2011
Quote:
Originally Posted by machalita
The new file its not being recognized as a text file, when i try to open it, i get the error: Gedit has not been able to detect the character coding, please check that you are not trying to open a binary file.
Sorry, don't know much about Gedit.
Can you 'cat' a file or use other editor?
# 7  
Old 02-16-2011
Can you change >> newfile to > newfile while you are at it?

And show the output of file myFile (the input file)
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