SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
.abi to fasta/fastq conversion script/program? AppleInformatics General 12 08-26-2012 10:17 PM
csfasta --> fasta conversion doxologist SOLiD 35 05-15-2012 09:27 AM
File conversion on CisGenome ninino Bioinformatics 2 07-16-2010 01:38 PM
fastq to fasta conversion kwtennis311 Bioinformatics 4 06-11-2010 11:06 AM
Fasta to Ace conversion Farhat Bioinformatics 19 05-15-2010 06:08 PM

Reply
 
Thread Tools
Old 05-13-2011, 12:04 PM   #1
empyrean
Member
 
Location: EU

Join Date: Sep 2010
Posts: 52
Default EMBL like file to FASTA conversion..

Helo all, I wanted to parse aEMBL format like file to fasta. i cannot use bioperl because this is not complete EMBL format. so please suggest me how to get this done..

Code:
ID   013789-0068 
PS   TBD 
OO   huringiensis 
OS   ringiensis 
OX 
SI   68 
RA 
RL   2010. OKAYAMA UNIVERSITY,JAPAN LAMB CO LTD 
FT   source          1..1176 
MT 
AC   67106 
SV 
CT 
PN   013789 
PT   PROTEIN PRODUCTION METHOD, FUSION PROTEIN, AND ANTISERUM 
PA   AMA UNIVERSITY,JAPAN LAMB CO LTD. 
PI   HAYAKAWA TORU (JP) SAKAI, HIROSHI, HAYAKAWA, TORU 
P8 
P4   10013789 
P5   0 
PC   International Classification: \nUS Classification: \nEuropean Classification: C12N15/62; C07K14/47A25 
PR   80199166; 
PE   199166 
AN   09JP63603 
KC   1 
P1   ng the DNA into a host bacterium to transform the host bacterium; and (c) causing the expression of the fusion protein in the transformed host bacterium.; The method may further comprise a step of removing the peptide chain (B) from the fusion protein. \n \n 
P7 
P9   112 
PO 
PM   10013789; 
PB   10013789 
PQ   10013789; 
EM   esentative 
W1   PRT 
D1   0204 
D2   0217 
D3   0730 
D4   0801 
D5   0204 
HL   [L[P9_GQ;0;3,WO2010013789,45,67]] [L[PM_PN_GQNUC;0;12,WO2010013789]] [L[PQ_PN_GQNUC;0;12,WO2010013789]] 
CC   mer C1-1-f FH   Key             Location/Qualifiers Copyright (c)Inc. 2011 
LS   Application 
L2   Publ. Of int. appl. w4 
 
  MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQI 
  EQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIPLLAVQNYQVPLLSV 
  YVQAANLHLSVLRDVSVFGQRWGFDAATINSRYNDLTRLIGNYTDYAVRWYNTGLERVWGPDSRDWVRYNQFRRELTLTV 
  LDIVALFSNYDSRRYPIRTVSQLTREIYTNPVLENFDGSFRGMAQRIEQNIRQPHLMDILNSITIYTDVHRGFNYWSGHQ 
  ITASPVGFSGPEFAFPLFGNAGNAAPPVLVSLTGLGIFRTLSSPLYRRIILGSGPNNQELFVLDGTEFSFASLTTNLPST 
  IYRQRGTVDSLDVIPPQDNSVPPRAGFSHRLSHVTMLSQAAGAVYTLRAPTFSWQHRSAEFNNIIPSSQITQIPLTKSTN 
  LGSGTSVVKGPGFTGGDILRRTSPGQISTLRVNITAPLSQRYRVRIRYASTTNLQFHTSIDGRPINQGNFSATMSSGSNL 
  QSGSFRTVGFTTPFNFSNGSSVFTLSAHVFNSGNEVYIDRIEFVPAEVTFEAEYDLERAQKAVNELFTSSNQIGLKTDVT 
  DYHIDQVSNLVECLSDEFCLDEKQELSEKVKHAKRLSDERNLLQDPNFRGINRQLDRGWRGSTDITIQGGDDVFKENYVT 
  LLGTFDECYPTYLYQKIDESKLKAYTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRC 
  APHLEWNPDLDCSCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKR 
 
// 
 
ID   0223489-0068 
PS   TBD 
OO   huringiensis 
OS   ringiensis 
OX 
SI   68 
RA 
RL   2010. OKAYAMA UNIVERSITY,JAPAN LAMB CO LTD 
FT   source          1..1176 
MT 
AC   67106 
SV 
CT 
PN   013789 
PT   PRN METHOD, FUSION PROTEIN, AND ANTISERUM 
PA   AMERSITY,JAMB CO LTD. 
PI   HAYAKAWA TORU (JP) SAKAI, HIROSHI, HAYAKAWA, TORU 
P8 
P4   10013789 
P5   0 
PC   International Classification: \nUS Classification: \nEuropean Classification: C12N15/62; C07K14/47A25 
PR   80199166; 
PE   199166 
AN   09JP63603 
KC   1 
P1   ng the DNA into a host bacterium to transform the host bacterium; and (c) causing the expression of the fusion protein in the transformed host bacterium.; The method may further comprise a step of removing the peptide chain (B) from the fusion protein. \n \n 
P7 
P9   112 
PO 
PM   10013789; 
PB   10013789 
PQ   10013789; 
EM   esentative 
W1   PRT 
D1   0204 
D2   0217 
D3   0730 
D4   0801 
D5   0204 
HL   [L[P9_GQ;0;3,WO2010013789,45,67]] [L[PM_PN_GQNUC;0;12,WO2010013789]] [L[PQ_PN_GQNUC;0;12,WO2010013789]] 
CC   mer C1-1-f FH   Key             Location/Qualifiers Copyright (c)Inc. 2011 
LS   Application 
L2   Publ. Of int. appl. w4 
 
  VLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQI 
  EQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIPLLAVQNYQVPLLSV 
   
 LLGTFDECYPTYLYQKIDESKLKAYTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRC 
  APHLEWNPDLDCSCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKR

The output should be in fasta format which consists of lines starting with ID, PT, PA and Sequence. "//" the two slashes are dividing lines between two EMBL genes.

Code:
>013789-0068 ;  PROTEIN PRODUCTION METHOD, FUSION PROTEIN, AND ANTISERUM PA ;   AMA UNIVERSITY,JAPAN LAMB CO LTD. 
MDNNPNINECIPYNCLSNPEVEVLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQI 
  EQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIPLLAVQNYQVPLLSV 
  YVQAANLHLSVLRDVSVFGQRWGFDAATINSRYNDLTRLIGNYTDYAVRWYNTGLERVWGPDSRDWVRYNQFRRELTLTV 
  LDIVALFSNYDSRRYPIRTVSQLTREIYTNPVLENFDGSFRGMAQRIEQNIRQPHLMDILNSITIYTDVHRGFNYWSGHQ 
  ITASPVGFSGPEFAFPLFGNAGNAAPPVLVSLTGLGIFRTLSSPLYRRIILGSGPNNQELFVLDGTEFSFASLTTNLPST 
  IYRQRGTVDSLDVIPPQDNSVPPRAGFSHRLSHVTMLSQAAGAVYTLRAPTFSWQHRSAEFNNIIPSSQITQIPLTKSTN 
  LGSGTSVVKGPGFTGGDILRRTSPGQISTLRVNITAPLSQRYRVRIRYASTTNLQFHTSIDGRPINQGNFSATMSSGSNL 
  QSGSFRTVGFTTPFNFSNGSSVFTLSAHVFNSGNEVYIDRIEFVPAEVTFEAEYDLERAQKAVNELFTSSNQIGLKTDVT 
  DYHIDQVSNLVECLSDEFCLDEKQELSEKVKHAKRLSDERNLLQDPNFRGINRQLDRGWRGSTDITIQGGDDVFKENYVT 
  LLGTFDECYPTYLYQKIDESKLKAYTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRC 
  APHLEWNPDLDCSCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKR 
 
>0223489-0068 ; PRN METHOD, FUSION PROTEIN, AND ANTISERUM PA  ; AMERSITY,JAMB CO LTD. 
VLGGERIETGYTPIDISLSLTQFLLSEFVPGAGFVLGLVDIIWGIFGPSQWDAFPVQIMNSALTTAIPLLAVQREEMRIQLE 
  EQLINQRIEEFARNQAISRLEGLSNLYQIYAESFREWEADPTNPALREEMRIQFNDMNSALTTAIPLLAVQNYQVPLLSV 
  LLGTFDECYPTYLYQKIDESKLKAYTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRC 
  APHLEWNPDLDCSCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKR
I hope i am making sense..
empyrean is offline   Reply With Quote
Old 05-14-2011, 12:49 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

You got several answers to your question here:
http://biostar.stackexchange.com/que...o-fasta-format

It is nice to mention you've asked the question elsewhere, and report back with any solution, so that people here don't waste their time.
maubp is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:23 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO