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# 22  
Old 02-23-2011
if your entries are 1 long line (so that it is displayed on multi lines but containing no "\n", this should do the work (assuming you don't want *.10 or *.11 entries ) :
Code:
grep POPTR_1855s00200\.1\| infile

Code:
nawk -v RS=">" -v FS="" '/POPTR_1855s00200\.1\|/'  infile

or
Code:
nawk -v RS=">" -v FS="" '/POPTR_1855s00200\.1\|/{printf "%s",$0}' infile

Last edited by ctsgnb; 02-23-2011 at 09:45 AM..
# 23  
Old 02-23-2011
perl is also powerful!!
PHP Code:
cat ufile|perl -p -ne 's/(?:(?<==)PAC)/PT/;' 
# 24  
Old 02-23-2011
but your code is not working POPTR_1855s00201 this file contains set of different values.If I use it just return following
Code:
POPTR_1855s00200.1|PACid:18205976
ATGCTGTCGCACAATTTCTGTCCCTTGGTATCAACTGGGATGAACATGACACAGACTGCTGAAATAGCCATCAGGACCTC
AAACAGGATGATGGCTTCTGTAATCTGGCAGCTAGTCACCAGGCCAACTGCCACAAGAGGACATATCATGCCACCAACCT
TCCCCGCAGCATTTGCAGCTCCAGCACCAGTTGCCCTGACGGATGTCGGATATAACTGTTGGGGATTCCGACTCCCCATG
CGCGGACCGGTGGTGTTCTGA

I need to get all the paragraphs which contains *.1 values.
# 25  
Old 02-23-2011
Then just remove POPTR_1855s00200 and give a try to :
Code:
grep \.1\| infile

Code:
nawk -v RS=">" -v FS="" '/\.1\|/'  infile

Code:
nawk -v RS=">" -v FS="" '/\.1\|/{printf "%s",$0}' infile

Last edited by ctsgnb; 02-23-2011 at 09:46 AM..
This User Gave Thanks to ctsgnb For This Post:
shen
# 26  
Old 02-23-2011
hi justlooks your code output contains
Code:
>POPTR_0005s00710.3|PACid:18208427
ACAAAACAAAAACAAAAGAGAAAGAGAGAAAGAAAGCACTTTCTTTTGTGTATTGTATTGGAAGGCAGCTTGTTGTGTTA
TTGCCCACAAAAATGGATCTGTCTTCCCCACCTTCTCTCTCCACTGTCTGATCCTCAGCTCCTCTTCCTCATCTCCACCT
TCAAAACGGCATCTTCTTTAATACCCAGGATTTTTTCCGGCTTAATTGGTAATGTGTAATTGCATTGAAGTTCAAGAGTA
AGACAGAATAATTTGTTCTTGTCTAACAAATGGGTTCTGTGGGCGTGGCACCTTCTTCGGGATTAAGAGAAGCTAGTGCC
CATAATGCTGGTGTGGATAAGTTACCTGAGGAAATGAATGACATGAAAATTAGAGATGACAAAGAAATGGAGGCAACAGT

values ,I just wanted to extract *.1 paragraphs.

---------- Post updated at 08:46 AM ---------- Previous update was at 08:39 AM ----------

great,This means I can use any one of the three functions.
# 27  
Old 02-23-2011
Quote:
Originally Posted by shen
I need to get all the paragraphs which contains *.1 values.
Try this:
Code:
awk 'f && /^>POP/{f=0} /^>POP.*\.1\|/{f=1}f' file

This User Gave Thanks to Franklin52 For This Post:
shen
# 28  
Old 02-23-2011
my code output does not contain *.3 stuff, only *.1 :
(i based my test on the sample you gave)

Code:
# cat tst
>POPTR_1446s00200.20|PACid:18205974
KGIAEIKNRLQNRKVLVILDDVDNLKQLHFLAVDWKWFLPGSRIIITSRDKNLLSTHAVDGIYEAEELNDDDALVLLSRK
AFKKDQPIEGYWELCKSVLGHARGLPLAARVLGSSLCGRSMDFWESFIKRLNEIPNRDVMAVLKLSFDGLEELEKKIFLD
IACFFKGMNKDQVSRILNQCGFHANYGIQILQDKSLICVSNDTLSMHDLLQAMGREVVRQESTAEPGRRSRLWANGSLTW
YQSLDDQAGTEEIESIALDWPNPEDVEGTMLKTKRSAWNTGVFSKMSRLRLLRIRNACFDSGPEYLSNELRLILKGCRRL
SEVHSSIGHHNKLIYVNLIDCKSLTSLPSRISGLKLLEELHLSGCSKLKEFPEIVGNKKCLRKLCLDQTSIEELPLSIQY
LVGLISLSLKDCKKLARLPSSINGLKSLKTLHLSGCSELDNLPENLGQLECLNELDVRAVPNDIGYLSSLRHLDLSCNKF
VSLPTSIDQLSGLQFLRMEDCKMLQSLPELPSNLEEFRGPPNLIESFSVIIPGSEIPTWFSHQSEGSSVSVQTPPHSHEN
DEWLGYAVCASLGYPDFPPNVFRSPMQCFFNGDGNESESIYVRLKPCEILSDHLWFLYFPSRFKRFDRHVRFRFEDNCSQ
TKVIKCGVRLVYQQDVEELNRMTNLYENSTFEGVDECFQESGGALVKRLGHTNDVGEASGSVSSDEQPPTKKLKQI*
>POPTR_1855s00205.1|PACid:18205975
MVMPRLSWRWLLAVSCLPAFALLLFYSHVPESPRYLCMKGRINDAYNILEKIALLNQSKLPPGELVPDSTIGLDEESATS
EYTPLLSTTEKMDLDFRSGFQSFLMLFSSKVIRTTLLLWELLFGNVFSYYAIILLTSELSSWQSRCGSNLLKSENPDSLY
INVFISNLAGIACLLSSSLCN*
>POPTR_1855s00200.1|PACid:18205976
MLSHNFCPLVSTGMNMTQTAEIAIRTSNRMMASVIWQLVTRPTATRGHIMPPTFPAAFAAPAPVALTDVGYNCWGFRLPM
RGPVVFYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNRLVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKA
>POPTR_0005s16590.4|PACid:18205977
FKINAVNLGGWLVTEGWIKPSLFDGITNKDFLDGTGLQFKSVTVGKYLCAEAGGGNIIVANRTSASGWETFSLWRINETN
FNFRVFNKQFAGLDTNGNGIDIVAVSSTPGRSETFEIVRNSNDTSRVRIKASNGFFLQAKTEELVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKAL
DNAFLWAQNYGLQVVIDLHAAPGSQNGWEHSSSRDGSQEWGQTDENIRQTVDVIDFLTARYAKSPSLYAVELMNEPRAPG
ASLDSMTKYYKGGYDAVRKHSSTAYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNR
SGQLNYVTTSNGPLTFVGEWVAEWTVQGATKEDYQRFAEAQLKVFGRATFGWAYWTLKNVNNHWSLEWMIKNGYIKI*

Code:
# nawk -v RS=">" -v FS="" '/\.1\|/' tst
POPTR_1855s00205.1|PACid:18205975
MVMPRLSWRWLLAVSCLPAFALLLFYSHVPESPRYLCMKGRINDAYNILEKIALLNQSKLPPGELVPDSTIGLDEESATS
EYTPLLSTTEKMDLDFRSGFQSFLMLFSSKVIRTTLLLWELLFGNVFSYYAIILLTSELSSWQSRCGSNLLKSENPDSLY
INVFISNLAGIACLLSSSLCN*

POPTR_1855s00200.1|PACid:18205976
MLSHNFCPLVSTGMNMTQTAEIAIRTSNRMMASVIWQLVTRPTATRGHIMPPTFPAAFAAPAPVALTDVGYNCWGFRLPM
RGPVVFYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNRLVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKA

Code:
# nawk -v RS=">" -v FS="" '/\.1\|/{printf "%s",$0}' tst
POPTR_1855s00205.1|PACid:18205975
MVMPRLSWRWLLAVSCLPAFALLLFYSHVPESPRYLCMKGRINDAYNILEKIALLNQSKLPPGELVPDSTIGLDEESATS
EYTPLLSTTEKMDLDFRSGFQSFLMLFSSKVIRTTLLLWELLFGNVFSYYAIILLTSELSSWQSRCGSNLLKSENPDSLY
INVFISNLAGIACLLSSSLCN*
POPTR_1855s00200.1|PACid:18205976
MLSHNFCPLVSTGMNMTQTAEIAIRTSNRMMASVIWQLVTRPTATRGHIMPPTFPAAFAAPAPVALTDVGYNCWGFRLPM
RGPVVFYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNRLVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKA

Last edited by ctsgnb; 02-23-2011 at 10:03 AM..
This User Gave Thanks to ctsgnb For This Post:
shen
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