Awk script

shen · February 23, 2011, 2:47am

It works perfectly,Thank you.I have one more question.
I have fatsa file something like this

>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*

I just want to extract following out put "*.1" results only

>POPTR_1855s00200.1|PACid:18205976
MLSHNFCPLVSTGMNMTQTAEIAIRTSNRMMASVIWQLVTRPTATRGHIMPPTFPAAFAAPAPVALTDVGYNCWGFRLPM
RGPVVFYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNRLVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKA

Can you help me to do that.

ctsgnb · February 23, 2011, 3:12am

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 ) :

grep POPTR_1855s00200\.1\| infile

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

or

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

justlooks · February 23, 2011, 3:13am

perl is also powerful!!

cat ufile|perl -p -ne 's/(?:(?<==)PAC)/PT/;'

shen · February 23, 2011, 8:34am

but your code is not working POPTR_1855s00201 this file contains set of different values.If I use it just return following

POPTR_1855s00200.1|PACid:18205976
ATGCTGTCGCACAATTTCTGTCCCTTGGTATCAACTGGGATGAACATGACACAGACTGCTGAAATAGCCATCAGGACCTC
AAACAGGATGATGGCTTCTGTAATCTGGCAGCTAGTCACCAGGCCAACTGCCACAAGAGGACATATCATGCCACCAACCT
TCCCCGCAGCATTTGCAGCTCCAGCACCAGTTGCCCTGACGGATGTCGGATATAACTGTTGGGGATTCCGACTCCCCATG
CGCGGACCGGTGGTGTTCTGA

I need to get all the paragraphs which contains *.1 values.

ctsgnb · February 23, 2011, 8:39am

Then just remove POPTR_1855s00200 and give a try to :

grep \.1\| infile

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

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

shen · February 23, 2011, 8:46am

hi justlooks your code output contains

>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.

Franklin52 · February 23, 2011, 8:48am

Try this:

awk 'f && /^>POP/{f=0} /^>POP.*\.1\|/{f=1}f' file

ctsgnb · February 23, 2011, 8:49am

my code output does not contain *.3 stuff, only *.1 :
(i based my test on the sample you gave)

# 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*

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

POPTR_1855s00200.1|PACid:18205976
MLSHNFCPLVSTGMNMTQTAEIAIRTSNRMMASVIWQLVTRPTATRGHIMPPTFPAAFAAPAPVALTDVGYNCWGFRLPM
RGPVVFYVVMSNRLSSDDPREFFPLASGLTGSVIDVHYYNLFSDEFNSMSVQQNIDFINTNRLVTADYAGDNKWGDDDP
SVFVMTIAGRLQGEFQVTNGYGPKLAPKVMRDHWRTFIVEDDFKFISQNGINAVRIPVGWWIASDPTPPQPYVGGSLKA

# 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

shen · February 23, 2011, 8:56am

perfect,Thank you it works fine

---------- Post updated at 08:56 AM ---------- Previous update was at 08:55 AM ----------

Great It works nicely,I meant "justlooks" perl code it gave me *.3 out not yours.
Thank you very much.

ctsgnb · February 23, 2011, 9:04am

You might want to keep the leading ">" :

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