UNIX for Dummies Questions & Answers

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!

Try:

Code:

awk -F"|"  '/^>/ { OFS="|"; $NF=""; print;}' file

Using sed

Code:

sed 's/\(.*| \)\(.*\)/\1/g;/^>cow/!d' input

Here the input file contains your input data.

You dont need to use the second reg-exp grouping...

Code:

 
sed 's/\(.*| \).*/\1/g;/^>cow/!d'  file

Code:

 
cat file | cut -d'|' -f 1-4  | sed '2d' | grep ">"

See the following code to match the pattern and give the following Output:

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

Code:

egrep --color -o "^[>cow|](.*?[|])" fine_name

Code:

cat file | cut -d'|' -f 1-4

can be written as

Code:

 
cut -d'|' -f 1-4  file

Uselesss use of cat (UUOC) . Very useful to read a posting of one of our unix.com member "era"

Useless Use of Cat Award