Bioinformatics.org
[Regeneron]
[Repositive.io]
[OMICtools]
Not logged in
  • Log in
  • Bioinformatics.org
    Membership (39397+) Group hosting [?] Wiki
    Franklin Award
    Sponsorships

    Careers
    About bioinformatics
    Bioinformatics training
    Bioinformatics jobs

    Research
    All information groups
    Online databases Online analysis tools Online education tools More tools

    Development
    All software groups
    FTP repository
    SVN & CVS repositories [?]
    Mailing lists

    Forums
    News & Commentary
  • Submit
  • Archives
  • Subscribe

  • Jobs Forum
    (Career Center)
  • Submit
  • Archives
  • Subscribe
  • Scriptome: Biological Data Manipulation - Message forums

    Discussion forums: Help

    Expanded view | Monitor forum | Save place

    Message
    Contribute
    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



    Post a followup to this message:
    You have to be logged in to post a reply.
    Thread view
    Contribute
    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)
    Contribute
    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

     

    [G6GFindr]
    Copyright © 2017 · Scilico, LLC