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to print output using shell command

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# 1  
Old 07-30-2007
to print output using shell command
suppose u have 2 files ; where both files have one line in common.
say one file like that
Code:
>gi|62859953|ref|NP_001017322.1| plexin B2 [Xenopus tropicalis]
MKEKERTKAITEIYLTRLLSVKGTLQQFVDNFFQSVLNSNQVVPPAVKYFFDFLDEQAEKYEIKDEDTVHIWKTNSLSLR
FWVNILKNPHFIFDVHVHQVVDASLSVIAQTFMDACSRTEHKLSRESPSNKLLYAKEISTYKKMVEDYYKGIRQMVQVSD
QDMNTHLAEISRAHTESLNTLVALHQLYQYTNKYYDEIINALEEDPAAQRMQLAYRLQQIAAALENKVTDL
>gi|114670186|ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTQFIILSGFMVVFSLFLLYGLSLVALAFLM
SILVKKSFLTGLVVFLLTVFWGCLGFTSLYRHLPASLEWILSLLSPFAFMLGMAQLVHLDYDLNSNAFPHPSDGSNLIVA
>gi|149723613|ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]
MSKREISVCQQTWALLCKNFLKKWRMKREPLLEWLNSFLLLLCLYLYPNNHQLNDFSSLPTMDLGRVDSFNESKFAIAYT
PVTNTTQQIMNKVASASFMKDREVLGLPDEESIKELTANYPEEIVRVIFTNTFSYHLKFLLGHRIPTKKEHRDHTAHCYE
TIEDIDCEVSEFWKKGFVALQAAINAAIIEITTNHSVMEKLMSVTGKNMKIYPFVSQGGVFTDFFVFFCIISFSPFTYYA
SVNVTRERKRMKRMMTMMGLRDSAFWLSWGLLYASFIFIMAFFLTLVIKSVQFVILTGVMVVFTLFLLYGLSLVTLAFLM
SVLIKKSFLTGLVVFLLTVFWGSLGFMALYRNLPASLEWMLSLFSPFAFTLGMSQLLHLDYDLNSNAFPDPSDLSNLIIA
>gi|73965429|ref|XP_548020.2| PREDICTED: similar to ATP-binding cassette, sub-family A member 8 [Canis familiaris]
MTKRQISVCQQTWALFCKNLLKKWRMRRESFMEWFNPLLLLLCLYLFPTNHKVNDFSSLPDMDLGPVDSFKDSLFSIVYT
PITNTTQQIMDKVALASFMKDKKVLGLSNEESIKEVMTHYPEEIIQVIFTNTFSYHLKFTLGHRIPTRREHRDHEAHCYN
LSEGVKCQVSKYWKQGFVALQAAINAAIIETTTNHSVMEELMSVTGKNMKIHPFIRQGGIVADFFIFFCIISFSSFTYYA
SINVTRERKKMKVLMKMMGLRDSAFWLSWGLLYAVFIFIMALFLALIIKSVQFVILTGFMAIFTLFFLYGLSLIALAFLM
SVLVKKSFLTGLIVFLLTIFWGSLGFTALYRHLPTSLEWILSFLSPFAFSLGMAQLLHLDYDLNSNAFPYPSDDSKLIIA
TNFMLAFDLFFYVALTIYFEKILPNEHGHEYPPLFFLKPSFWSRQHKADHVALEDEIDSNPSSNDSFEPMPPEFHGKEAI

contuining so many list of proteins as very big file

so another file just have input
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]

so have a output like that 
with using 2nd file to search the first file and extract and so have a output like that 
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTQFIILSGFMVVFSLFLLYGLSLVALAFLM
SILVK
>gi|149723613|ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]
MSKREISVCQQTWALLCKNFLKKWRMKREPLLEWLNSFLLLLCLYLYPNNHQLNDFSSLPTMDLGRVDSFNESKFAIAYT
PVTNTTQQIMNKVASASFMKDREVLGLPDEESIKELTANYPEEIVRVIFTNTFSYHLKFLLGHRIPTKKEHRDHTAHCYE
TIEDIDCEVSEFWKKGFVALQAAINAAIIEITTNHSVMEKLMSVTGKNMKIYPFVSQGGVFTDFFVFFCIISFSPFTYYA
SVNVTRERKRMKRMMTMMGLRDSAFWLSWGLLYASFIFIMAFFLTLVIKSVQFVILTGVMVVFTLFLLYGLSLVTLAFLM
SVLIKKSFLTGLVVFLLTVFWGSLGFMALYRNLPASLEWMLSLFSPFAFTLGMSQLLHLDYDLNSNAFPDPSDLSNLIIA
KSFLTGLVVFLLTVFWGCLGFTSLYRHLPASLEWILSLLSPFAFMLGMAQLVHLDYDLNSNAFPHPSDGSNLIVA
>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

# 2  
Old 07-30-2007
try this
Code:
while read line
do
  grep "$line" source_big_file 2>/dev/null
done < source_file_with_patterns

# 3  
Old 07-30-2007
Another way:
Code:
grep -f pattern_file big_file 2>/dev/null

# 4  
Old 07-30-2007
dear matrixmadhan,
u have give code like this
while read line
do
grep "$line" source_big_file 2>/dev/null
done < source_file_with_patterns

so i shud proceed with that
while read line
do
grep "$line" file2 2>/dev/null
done < file1

and in the .sh command
thanks
# 5  
Old 07-30-2007
Power
dear shell_life
this is not wht i want
having second file which is like
say >gi|114577921|ref|XP_00113.....
>gi|114583129|ref|XP_516070.2| PREDICTED: ATP-bind....
so using tht file to search for first file as shown in the first original post
so output shud be like that

>gi|114577921|ref|XP_001136060.1| PREDICTED: hypothetical protein [Pan troglodytes]
MQSISGPVFTPALSLEEAPGGDAESRCAPSAGSLLHQDVGLEWPLTHLEISLH
>gi|114583129|ref|XP_516070.2| PREDICTED: ATP-binding cassette, sub-family A, member 12 isoform 4 [Pan troglodytes]
MASLFHQLQILVWKNWLGVKRQPLWTLVLILWPVIIFIILAITRTKFPPTAKPTCYLAPRNLPSTGFFPFLQTLLCDTDS
KCKDTPYGPQDLLRRKGIDDALFKDSEILRKSSNLDKDSSLSFQSTQVPERRHASLATVFPSPSSDLEIPGTYTFNGSQV
LARILGLEKLLKQNSTSEDIRRELCDSYPGYIVDDAFSWTFLGRNVFNKFCLSNKTLLESSLQELNKQFSQLSSDPNNQK
IVFQEIVRMLSFFSQVQEQKAVWQLLSSFPNVFQNDTSLSNLFDVLRKANSVLLVVQKVYPHFATNEGFRTLQKSVKHLL
thanks
cdfd123
# 6  
Old 07-30-2007
Cdfd,
You already posted the same issue yesterday:
https://www.unix.com/shell-programmin...#post302129161

Did you try the solution I gave to you:
Code:
csplit -f xyz input_file /^>/ {99}
for mFile in `egrep -l -f reference_file xyz*`
do
  cat ${mFile}
done

# 7  
Old 07-30-2007
Quote:
Originally Posted by cdfd123
dear matrixmadhan,
u have give code like this
while read line
do
grep "$line" source_big_file 2>/dev/null
done < source_file_with_patterns

so i shud proceed with that
while read line
do
grep "$line" file2 2>/dev/null
done < file1

and in the .sh command
thanks

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
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