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Shell Programming and Scripting
Extract specific content from a file
Post 302361812 by patrick87 on Wednesday 14th of October 2009 07:00:23 AM
10-14-2009
Log file data extraction
Hi danmero,
My input file:
Code:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
>ABC_6
SAASASASASASASTSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
>SDF_7
TASDASDAFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
My desired output file:
Code:
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>ABC_6
SAASASASASASASTSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
>SDF_7
TASDASDAFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
If I got a long list of file, how I can use your script or program to extract only the contents of sequence_2,ABC_6,SDF_7?
Do you have any idea how I can extract specific content only from a long list of file?
As I try, the awk script that you suggested only can extract sequence_2 from a long list of file.
Thanks again
My input file:
Code:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
>ABC_6
SAASASASASASASTSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
>SDF_7
TASDASDAFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
My desired output file:
Code:
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>ABC_6
SAASASASASASASTSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
>SDF_7
TASDASDAFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
If I got a long list of file, how I can use your script or program to extract only the contents of sequence_2,ABC_6,SDF_7?
Do you have any idea how I can extract specific content only from a long list of file?
As I try, the awk script that you suggested only can extract sequence_2 from a long list of file.
Thanks again
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