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to print output using shell command

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Top Forums Shell Programming and Scripting to print output using shell command
# 8  
Old 07-30-2007
dear shell_life
when i use ur code
Code:
csplit -f file1 input_file /^>/ {99}
for mFile in `egrep -l -f reference_file file2`
do
 cat ${mFile}
done

it shows display
Code:
shell_life.sh: line 1: /: Is a directory
cat: invalid option -- l
Try `cat --help' for more information.

Thanks
# 9  
Old 07-30-2007
Cdfd,
Please, run exactly my code below:
Code:
csplit -k -f xyz input_file '/^>/' {99} 1,2>/dev/null
for mFile in `egrep -l -f reference_file xyz*`
do
  cat ${mFile}
done

Where:
xyz: Is a prefix to be used to generate split files.
input_file: Your large file.
reference_file: Your reference file with patterns.
Last edited by Shell_Life; 07-30-2007 at 04:09 PM.. Reason: Add single quotes, '-k' and /dev/null.
# 10  
Old 08-02-2007
Dear shell_life,
i have exactly follows urs code tht is
csplit -k -f xyz file1 '/^>/' {99} 1,2>/dev/null
for mFile in 'egrep -l -f file3 xyz*'
do
cat ${mFile}
done

where file1
Code:
>O94911|ABCA8_HUMAN ATP-binding cassette sub-family A member 8 - Homo sapiens (Human)
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLL
TMDLGRVDTFNESRFSVVYTPVTNTTQQIMNKVASTPFLAGKEVLGLPDEESIKEFTANY
PEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYETNEDVYCEVSVFWKEGFVAL
QAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSSFIYYA
>gi|114670186|ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA
>gi|109117480|ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8 isoform 2 [Macaca mulatta]
MRKREISVCQQTWALLCKNFLKKWRMKRESLMEWLNSFLLLLCLYIYPHSHQVNDFSSLLTTDLGRVDTFNESRFSVAYT
PVTNTTQQIMNKVASAPFLAGKEVLGLPDEESIKEFTANYPEEIVRVIFTNTYSYQLKFLLGHEMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSPFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTLFIILSGFMVVFSLFLLYGLSLIALAFLM
SILVKKSFLTGLVVFLLTVFWGSLGFTALYRYLPASLEWILSLLSPFAFMLGMAQLLHLDYDLNSNAFPHPLDGSNIIVA
TNFMLAFDTCLYLALAIYFEKILPNEYGHRRSPLFFLKSSFWSQTQKADHVALEDEMDADPSSHDSFEPVPPEFHGKEAI
RIRN
>gi|114670192|ref|XP_001165871.1| PREDICTED: similar to KIAA0822 protein isoform 2 [Pan troglodytes]
MNHTSRFLASIFPEEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYTPVTNTTQQIMNKVASIPF
LAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYETNEDVYCEVSVFWKEGFV
ALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYASVNVTRERKRMKGLMTMM
GLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTQFIILSGFMVVFSLFLLYGLSLVALAFLMSILVKKSFLTGLVVFLLT
VTKEYKGKPDKIEALKDLVFDIYEGQITAILGHSGAGKSTLLNILSGLSTPTKGSVTIYNNKLSEVADLENLSKLT


And File 3 is
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
>ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8[Macaca mulatta]
>ref|XP_001165871.1| PREDICTED: similar to KIAA0822 protein isoform 2 [Pan troglodytes]
>ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]

While running this code this shows the error 
csplit: 1,2: invalid pattern
Try `cat --help' for more information.

My output is just like searching for file3 in file1 
shoulld give that 
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA

contiuning those which are in file3 with single ine

One question wht prefix u have written xyz is not understood to me .
if possible
Thanks
Last edited by cdfd123; 08-02-2007 at 03:46 AM..
# 11  
Old 08-02-2007
Power
Quote:
Originally Posted by matrixmadhan
As per the example you had provided,

this is file 1

Code:
1.>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
2.>ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]
3. >ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8[Macaca mulatta]

and the other big file is file 2


Please use CODE tags Smilie


Dear matrixpradhan,
i have exactly follow the same code
still it give no output means blank results .....
thanks u......
i have written question again as u can see in this part
regards
cdfd123
# 12  
Old 08-02-2007
Quote:
Originally Posted by Shell_Life
Cdfd,
Please, run exactly my code below:
Code:
csplit -k -f xyz input_file '/^>/' {99} 1,2>/dev/null
for mFile in `egrep -l -f reference_file xyz*`
do
  cat ${mFile}
done

Where:
xyz: Is a prefix to be used to generate split files.
input_file: Your large file.
reference_file: Your reference file with patterns.

Dear shell_life,
i have exactly follows urs code tht is
csplit -k -f xyz file1 '/^>/' {99} 1,2>/dev/null
for mFile in 'egrep -l -f file3 xyz*'
do
cat ${mFile}
done

where file1
Code:
>O94911|ABCA8_HUMAN ATP-binding cassette sub-family A member 8 - Homo sapiens (Human)
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLL
TMDLGRVDTFNESRFSVVYTPVTNTTQQIMNKVASTPFLAGKEVLGLPDEESIKEFTANY
PEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYETNEDVYCEVSVFWKEGFVAL
QAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSSFIYYA
>gi|114670186|ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA
>gi|109117480|ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8 isoform 2 [Macaca mulatta]
MRKREISVCQQTWALLCKNFLKKWRMKRESLMEWLNSFLLLLCLYIYPHSHQVNDFSSLLTTDLGRVDTFNESRFSVAYT
PVTNTTQQIMNKVASAPFLAGKEVLGLPDEESIKEFTANYPEEIVRVIFTNTYSYQLKFLLGHEMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSPFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTLFIILSGFMVVFSLFLLYGLSLIALAFLM
SILVKKSFLTGLVVFLLTVFWGSLGFTALYRYLPASLEWILSLLSPFAFMLGMAQLLHLDYDLNSNAFPHPLDGSNIIVA
TNFMLAFDTCLYLALAIYFEKILPNEYGHRRSPLFFLKSSFWSQTQKADHVALEDEMDADPSSHDSFEPVPPEFHGKEAI
RIRN
>gi|114670192|ref|XP_001165871.1| PREDICTED: similar to KIAA0822 protein isoform 2 [Pan troglodytes]
MNHTSRFLASIFPEEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYTPVTNTTQQIMNKVASIPF
LAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYETNEDVYCEVSVFWKEGFV
ALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYASVNVTRERKRMKGLMTMM
GLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTQFIILSGFMVVFSLFLLYGLSLVALAFLMSILVKKSFLTGLVVFLLT
VTKEYKGKPDKIEALKDLVFDIYEGQITAILGHSGAGKSTLLNILSGLSTPTKGSVTIYNNKLSEVADLENLSKLT


And File 3 is
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
>ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8[Macaca mulatta]
>ref|XP_001165871.1| PREDICTED: similar to KIAA0822 protein isoform 2 [Pan troglodytes]
>ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]

While running this code this shows the error
csplit: 1,2: invalid pattern
Try `cat --help' for more information.

My output is just like searching for file3 in file1
shoulld give that
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA

contiuning those which are in file3 with single ine

One question wht prefix u have written xyz is not understood to me .
if possibleSmilieSmilieSmilie
Thanks
# 13  
Old 08-02-2007
Cdfd,
Please, try the following version -- my bad with '1,2':
Code:
csplit -k -f xyz file1 '/^>/' {99} 1>/dev/null 2>&1
for mFile in `egrep -l -f file3 xyz*`
do
  cat ${mFile}
done

# 14  
Old 08-02-2007
Tools
Quote:
Originally Posted by Shell_Life
Cdfd,
Please, try the following version -- my bad with '1,2':
Code:
csplit -k -f xyz file1 '/^>/' {99} 1>/dev/null 2>&1
for mFile in `egrep -l -f file3 xyz*`
do
  cat ${mFile}
done

Thanks tht code works
it runs like a zoooom....
aha.....
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