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Rafidah_080312 Permalink
December 02, 2015, 02:32

Hi Guys,

Need some help here.
I have 2 files.
File1=list of all pattern that I want.
File2=original file with wanted and unwanted pattern.

I am trying to search for this wanted pattern from File1 in File2 and put the match pattern and its line below into new file but until now I did not find the correct command.
I am using shell script.
Hope someone can help.
Thank you.

Below is the excerpt from both file:
File 1:
>aka:TKWG_16035
>amim:MIM_c14350
>cbaa:SRAA_2322
>cbab:SMCB_2338
>lch:Lcho_3755
>rme:Rmet_1511
>rge:RGE_36020
>rfr:Rfer_1393
>pna:Pnap_1982
>cnc:CNE_2c13480
>reh:H16_B1390
>reh:PHG422_cbbFp
>rpj:N234_28310
>cti:RALTA_B1696
>pdx:Psed_1418
>aza:AZKH_p0228
>bbag:E1O_14830
>mpt:Mpe_A2788
>vap:Vapar_3026
>vpd:VAPA_1c30920
>mph:MLP_19560

File2:
>aka:TKWG_16035 inositol phosphatase/fructose-1,6-bisphosphatase; K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MILNIALVCRRISHAIACGALAGVNGSADSTNVQGEDQKKLDILSNDLFIEGNQWGGQLA
GMVSEELDEPYSIPKPYSRGRYLLLFDPLDGSSNIDVNVAVGSIFSVLRTPDSRRTTTVK
DYLQPGVKQVAAGYAIYGPSTMLVLSVGNGVHAFTLCPLVGEFMLTHPNLQVPEDTNEFA
INTSNSRFWDEPVRRYVDECIAGKTGERGKDFNMRWIASLVAEAHRILMRGGVFLYPRDN
KLPARNGRLRLLYEANPIGFIMEQAGGRASTGHEPVLQVVPTEIHQRIGFIFGSKNEVER
IEEYHKHPRRVDSPNPLFHERSLFTESPNML
>amim:MIM_c14350 fbp1; fructose-1,6-bisphosphatase class 1 (EC:3.1.3.11); K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MQTPQRPTLTQFLIDERRRFPEAGGDFNSVILNIALVCRRISHAIACGALAGVNGSADST
NVQGEDQKKLDILSNDLFIEGNQWGGQLAGMVSEELDEPYSIPKPYTRGRYLLLFDPLDG
SSNIDVNVSVGSIFSVLRAPDSRRATKAEDYLQPGVEQVAAGYAIYGPATMLVLSVGTGV
HAFTLCPLVGEFMLTHPNLKVPEDTSEFAINTSNSRFWEEPVRRYVDECIAGKTGERGKD
FNMRWIASLVAEAHRILMRGGVFLYPRDNKQPARNGRLRLLYEANPIGFIMEQAGGRAST
GHEPVMQVKPTDIHQRIGFIFGSKNEVERIEQYHKHPRRVDSPNPLFHERSLFTETPNMQ
>app:CAP2UW1_0957 Inositol phosphatase/fructose-16-bisphosphatase; K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MLCGRTNVNKFLIEEQRRNPALAGDFSMLISDVVRSCKAIAQGVSRGSLAGVLGDHGSEN
VQGEAQKKLDVLANQAFIHHCEWGGHLAAMASEEMDDIYPIPAENPRGKYLLVFDPLDGS
SNIDVNLSVGSIFSVLRCPEKGSAGTPTAADFLQPGSRQVAAGYALYGPSAMLVLTVGNG
THGFTLDRNIGEFLLTHPNLVIAADTHEFAINASNERFWEKPVQRYVAECLAGKTGVRGK
DFNMRWVASMVAEVHRILMRGGVFLYPRDSKDTSKPGRLRLMYEANPMAMIVGQAGGLAS
TGNERILDVQPTSLHQRVPVILGSRDEVERIERYHREHETGEDQPFRSPLFSTRTLFRDD
>aza:AZKH_p0228 fbp; inositol phosphatase/fructose-1,6-bisphosphatase; K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MFDIERTTLTEYLIAQRRLHPGATGEFNALILQVAQACKAISRAVEHGALAGVLGSLDTE
NVQGETQKKLDVLADRIFLRATHWGGELAGMVSEENDAPIPLPEGTRRGKYLLVFDPLDG
SSNIDVNVSVGSIFSVLRAPTPGEDAKPEDFLQPGTRQVAAGYAIYGPSTMLVLTVGDGV
AGFTFDPIIGEFFLTHPEIGIPTTTREFAINAANSRFWEPPVRRYVDECLAGRSGPRESD
FNMRWVASLVAETHRILMRGGVFLYPRDRKDPAKPGRLRLLYECNPIGMIIEQAGGRAST
GEGPVLDVQPTSLHQRIGFVFGSREEVERIERYHAEPAPQPDSDLPLFHSRSLFRQN
>bbag:E1O_14830 fructose-1,6-/sedoheptulose-1,7-bisphosphatase; K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MLEKKITLTQFLIEERRRFPQASGAFNSILLNIALACKAISRKVAYGALSGIHGAVGNTN
VQGESQQKLDVLADDTFLHCLQWSGHARGLLSEERDEPWINETEGEGEYLVAFDPLDGSS
NIDVNVSVGSIFSILRAPEGGRRAKIEDFLRPGSEQVAAGYAVYGPTTMLVLTVGRGVQG
FTLDPELGEFVLTHPQMTIPAATKEFAINASNSRFWEAPVRAYIEECLAGVNGPRGKDFN
MRWVASLVAEAHRILTRGGVFLYPRDTKDLKKPGRLRLLYEANPIGMLIEQAGGRASTGY
GPMLAVQPESTHQRIGFVFGSREEVERIERYHAETPAAAGGSDTPLFNARGLFRE
>cbaa:SRAA_2322 fbp1; fructose-1,6-bisphosphatase; K01086 fructose-1,6-bisphosphatase I / sedoheptulose-1,7-bisphosphatase [EC:3.1.3.11 3.1.3.37] (A)
MLQTNRSTLTQFLIEERRRFPGATGDFNALILDVTLACKAIASAVAYGELGGAMGNHAPE
AGGSVNVQGETQKKLDVLSNEVFMQRTEWSGHLAGMASEEMDLPHQIPAQYPRGHYLLVF
DPLDGSSNIDVNVSVGSIFSVLRAPQAVIDSGRDVVEADFLQPGATQMAAGYALYGPTTM
LILTVGRGVNGFTLDPNLGEFMLTHPDMKIPPDTQEFAINASNARFWEAPVKRYVDECLA
GKTGPRGKDFNMRWIASMVAEAHRILMRGGVFLYPRDTKDPLKPGRLRLLYEANPVGMIM
EQAGGRASTGREPMMGVVPTSLHQRIGLVFGSKNEVERIERYHREPAQAKEGEPLFATRS
LFRD

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