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parsing data and incorporating it into another file

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# 1  
Old 09-09-2010
parsing data and incorporating it into another file
Hi,
I have a folder that contains many (multiple) files

1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files

Each such file have data in the following format
for example:
vi 1.fasta

Code:
>AB_1 gi|15835212|ref|NP_296971.1| preprotein translocase subunit SecE
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA
>AB_4 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_5 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_6 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE

I would to have a output file in the following format

Code:
1 AB_6 gi|76789043|ref|YP_328129.1| preprotein translocase subunit SecE 
2 AB_6 gi|76788923|ref|YP_328009.1| OppD 
3 AB_6 lcl|CP001890.1_cdsid_ADH20660.1 [gene=E11023_01035] [protein=oligopeptide transport ATPase
4 AB_6 gi|15604921|ref|NP_219705.1| oligopeptide transport AT

Pase

where the first coulmn would be the digit associated with the file name (1 for 1.fasta) and second coulmn will be the header (begins with ">") on the 6th > (here it is AB_6), but don't want ">" in the output file

I would like to know how to do it in a speedy watyusing awk or sed where it goes in all the files in the folder and gives the above shown tab delimited text file.
Please let me know
# 2  
Old 09-09-2010
Code:
awk 'FNR==1{a=0}/>/{a++;if(a==6){split(FILENAME,n,"\\.");sub("^>","");print n[1]" "$0}}' * > output.txt

Last edited by bartus11; 09-09-2010 at 03:09 PM.. Reason: Added the "6th occurence of >"
This User Gave Thanks to bartus11 For This Post:
Lucky Ali
# 3  
Old 09-16-2010
Dear Scottn,
Sorry for the confusion. I am using only the same type example data but this time it was different question.
LA
# 4  
Old 09-16-2010
Code:
awk -F \> '/>AB_6 / {split(FILENAME,f,".");print f[1], $2}' *.fasta

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