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counting characters

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# 1  
Old 07-02-2010
counting characters
Hi All,
I need some help in counting the number of letters in a big file with separations.

Following is the file I have

Code:
>AB_1
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA

Likewise it goes down.

I would like to count the number of alphabeths each subsections have (subsections are separated with the header starting with >).

It would be great if I could get an tab delimited output file in the following format:
AB_1 number of alphabets
AB_2 number of alphabets
AB_3 number of alphabets

I don't want to count the letters on the header.

Also it would be great if we could omit the ">" on the output file.

Please let me know the best way to do it using awk or sed

LA
# 2  
Old 07-02-2010
Code:
awk '/^>/{sub(">","");p=$0;next}{a[p]}+=length($0)}END{for (i in a) printf "%s\t%s\n",i,a[i]}' file

# 3  
Old 07-02-2010
Code:
 nawk '/^>/ {if(n) print n,l;n=substr($0,2);next} {l+=length}END{print n,l}' myFile

# 4  
Old 07-02-2010
Thanks.

When I did it I got the following error message

Code:
awk: syntax error at source line 1
 context is
     >>> /^>/{sub(">","");p=$0;next}{a[p]}+= <<< 
    extra }
awk: bailing out at source line 1

Please Let me know what might have occurred.

LA

---------- Post updated at 11:12 AM ---------- Previous update was at 11:01 AM ----------

Thanks Image vgersh99,

It didn't give any error message but I think its not giving me what I needed.

Code:
awk '/^>/ {if(n) print n,l;n=substr($0,2);next} {l+=length}END{print n,l}' sample1.txt 
AB_1 208
AB_2 544
AB_3 709

Obviously AB_3 have less number of sequences than AB_2
# 5  
Old 07-02-2010
sorry......
Code:
nawk '/^>/ {if(n) print n,l;n=substr($0,2);l=0;next} {l+=length}END{print n,l}'

# 6  
Old 07-02-2010
Thanks this work.

It would be nice If I could get the output in a tab delimited format

LA
# 7  
Old 07-02-2010
Quote:
Originally Posted by Lucky Ali
Thanks this work.

It would be nice If I could get the output in a tab delimited format

LA
Code:
nawk '/^>/ {if(n) print n,l;n=substr($0,2);l=0;next} {l+=length}END{print n,l}' OFS='\t' myFile

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