Text Manipulation


 
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# 1  
Old 04-30-2010
Data Text Manipulation

Greetings. Iīm a biologist and I donīt have mucho knowledge on Unix/Linux, but I need to use Cygwin to change some documents from a GenBank format to a FASTA format. GenBank format goes somthing like this:

LOCUS NM_013964 2568 bp mRNA linear PRI 26-APR-2009
DEFINITION Homo sapiens neuregulin 1 (NRG1), transcript variant HRG-alpha,
mRNA.
ACCESSION NM_013964
VERSION NM_013964.2 GI:116006963
KEYWORDS .
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
TITLE Genetic variation in the schizophrenia-risk gene neuregulin 1
correlates with brain activation and impaired speech production in
a verbal fluency task in healthy individuals
JOURNAL Hum Brain Mapp (2009) In press
HRGA; NDF;
SMDF"
polyA_site 2568
/gene="NRG1"
/gene_synonym="ARIA; GGF; GGF2; HGL; HRG; HRG1; HRGA; NDF;
SMDF"
ORIGIN
1 gcgcctgcct ccaacctgcg ggcgggaggt gggtggctgc ggggcaattg aaaaagagcc
61 ggcgaggagt tccccgaaac ttgttggaac tccgggctcg cgcggaggcc aggagctgag
121 cggcggcggc tgccggacga tgggagcgtg agcaggacgg tgataacctc tccccgatcg
181 ggttgcgagg gcgccgggca gaggccagga cgcgagccgc cagcggtggg acccatcgac



But all I would need to get a FASTA format is this:

>NM_013964
1 gcgcctgcct ccaacctgcg ggcgggaggt gggtggctgc ggggcaattg aaaaagagcc
61 ggcgaggagt tccccgaaac ttgttggaac tccgggctcg cgcggaggcc aggagctgag
121 cggcggcggc tgccggacga tgggagcgtg agcaggacgg tgataacctc tccccgatcg
181 ggttgcgagg gcgccgggca gaggccagga cgcgagccgc cagcggtggg acccatcgac


This is just the ">" symbol, followed by the LOCUS ID and, in a separate line the sequence of the gen wich goes from the ORIGEN till the end of the document. How can I achieve this? Can you please help me??? Smilie
# 2  
Old 04-30-2010
Code:
$ sed '/^DEFINITION/,/^ORIGIN/d' input | sed '/LOCUS /s//>/' | awk '/^>/{print $1} NR>1'
>NM_013964
1 gcgcctgcct ccaacctgcg ggcgggaggt gggtggctgc ggggcaattg aaaaagagcc
61 ggcgaggagt tccccgaaac ttgttggaac tccgggctcg cgcggaggcc aggagctgag
121 cggcggcggc tgccggacga tgggagcgtg agcaggacgg tgataacctc tccccgatcg
181 ggttgcgagg gcgccgggca gaggccagga cgcgagccgc cagcggtggg acccatcgac
$

This User Gave Thanks to pseudocoder For This Post:
# 3  
Old 04-30-2010
No words to thank you, it worked perfectly! I really appreciate your help. THANK YOU!!!!
 
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