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    Scriptome: Biological Data Manipulation - Message forums
    Discussion forums: Help

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    Submitted by Amir Karger; posted on Monday, November 21, 2005
    Andrew wrote: > Hi Amir, Hi. I'm sorry I didn't get back to you sooner. I could have sworn I'm "monitoring" this forum, but I didn't get any notification that this posting was made. Hm. > [snip...] a one-liner to count A, T, G, C from a fasta sequence. > perl -ne "BEGIN {%cnt}" -e "@nt= /^>/ || split //, $_; foreach (@nt) { $cnt{a}++ if /[Aa]/; $cnt{t}++ if /[Tt]/; $cnt{g}++ if /[Gg]/; $cnt{c}++ if /[Cc]/; } END { print "a$cnt{a}\tt$cnt{t}\tg$cnt{g}\tc$cnt{c}"; }" 1. Thanks! I'll put it on the list of possible things to include. 2. I think when you type backslash-t, the forum doesn't print the backslash. What a bummer! 3. I think I would do it a bit differently. Something like (untested!): perl -ne 'BEGIN {%cnt=()} if (! /^>/) {while (/([actg])/ig) {$cnt{lc $1}++}} END {print ...} > Also, are you looking for a developer to help your project? I'm definitely interested in getting help. (That goes for anyone else reading this, too!) Please email me (My email's at the bottom of http://cgr.harvard.edu/cbg/scriptome/UNIX/) so we can discuss this further. -Amir Karger



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    Submitted by Andrew Leung; posted on Friday, November 04, 2005
    Hi Amir, This is my first contribution. Please review and consider inclusion. It is a one-liner to count A, T, G, C from a fasta sequence. perl -ne "BEGIN {%cnt}" -e "@nt= /^>/ || split //, $_; foreach ( @nt) { $cnt{a}++ if /[Aa]/; $cnt{t}++ if /[Tt]/; $cnt{g}++ if /[Gg]/; $cnt{c}++ if /[Cc]/; } END { print \"a$cnt{a}\tt$cnt{t}\tg$cnt{g}\tc$cnt{c}\"; }" Also, are you looking for a developer to help your project? If yes, would you please let me join and please advise what I can help? Andrew (Hong Kong)
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    Submitted by Amir Karger; posted on Monday, November 21, 2005
    Andrew wrote: > Hi Amir, Hi. I'm sorry I didn't get back to you sooner. I could have sworn I'm "monitoring" this forum, but I didn't get any notification that this posting was made. Hm. > [snip...] a one-liner to count A, T, G, C from a fasta sequence. > perl -ne "BEGIN {%cnt}" -e "@nt= /^>/ || split //, $_; foreach (@nt) { $cnt{a}++ if /[Aa]/; $cnt{t}++ if /[Tt]/; $cnt{g}++ if /[Gg]/; $cnt{c}++ if /[Cc]/; } END { print "a$cnt{a}\tt$cnt{t}\tg$cnt{g}\tc$cnt{c}"; }" 1. Thanks! I'll put it on the list of possible things to include. 2. I think when you type backslash-t, the forum doesn't print the backslash. What a bummer! 3. I think I would do it a bit differently. Something like (untested!): perl -ne 'BEGIN {%cnt=()} if (! /^>/) {while (/([actg])/ig) {$cnt{lc $1}++}} END {print ...} > Also, are you looking for a developer to help your project? I'm definitely interested in getting help. (That goes for anyone else reading this, too!) Please email me (My email's at the bottom of http://cgr.harvard.edu/cbg/scriptome/UNIX/) so we can discuss this further. -Amir Karger

     
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