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Full Discussion: grep until a space
Top Forums UNIX for Dummies Questions & Answers grep until a space Post 302404544 by kkohl78 on Tuesday 16th of March 2010 08:55:53 PM
Old 03-16-2010
Data grep until a space
This is probably common knowledge, but I am a beginner at bioinformatics!

I want a list of my sequence names, without sequence or any of the free text after the space. This is some example file:

>cow|68989024|dbj|AB107582.1| Uncultured bacterium gene for 16S rRNA, partial se
quence, clone: 2-G12
AGAGTTTGATCCTGGCTCAGGACGAACGCGGCGGCGTGCCTAACACATGCAAGTCGAACGGAGATATACG
CTGATTTGATGAAAGCTTGCTTTTGGATTTTCTTGTGTATCTTAGTGGCGGACGGGCGAGTAACGCGTGA
>cow|68989023|dbj|AB107581.1| Uncultured bacterium gene for 16S rRNA, partial se
quence, clone: 1-H07
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAACCACTTC
GGTGGTGAGCGGCGAACGGGTGAGTAACACGTAGGTGATCTGCCCATCAGACGGGGACAACGATTGGAAA

And I want the output to look like this:

>cow|68989024|dbj|AB107582.1|
>cow|68989023|dbj|AB107581.1|

I assume there is some way of using grep and terminating how much is returned? but I have no idea.

Thanks so much!
 

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PSTOPDF(1)							      ConTeXt								PSTOPDF(1)

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SYNOPSIS

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DESCRIPTION

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OPTIONS

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       --convert
	      Convert EPS to PDF.  This option is assumed if none is given.

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	      What  method  to use for bounding boxes when converting to PDF.  Specify one of crop, bounded (the default), or raw.  Older versions
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SEE ALSO

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