Thanks, but I forgot to mention in the beginning that i need to make this
modification only ONCE in my file- the ">" character comes up every few
lines, but I only want the title "ALIGNMENTS" in the beginning..i.e, it
shd not replace all the ">"s in my file..
?
sorry about that!
-thanks,
nandita
On Wed, 21 Aug 2002, Sudarshan Raghavan wrote:
> On Tue, 20 Aug 2002, Nandita wrote:
>
> > Thanks for your message, this is how it looks:
> >
> > beginning of file :
> >
> > Reading High Probability Sequences producing High-scoring Segment Pairs:
> > Frame Score P(N)N
> >
> > EMBL:B88446 CpG0200B CpIOWAgDNA1 Cryptosporidium parv... +3 75 0.391
> > EMBL:AQ935741 CpG2625B CpIOWAgDNA1 Cryptosporidium pa... +1 74 0.631
> > EMBL:AQ855708 CpG1711B CpIOWAgDNA1 Cryptosporidium pa... -1 71 0.891
> > EMBL:AQ935455 CpG2480A CpIOWAgDNA1 Cryptosporidium pa... +2 69 0.971
> > EMBL:AQ450103 500008A04.x1 CpIOWAM13mp18gDNA1 Cryptos... -1 69 0.981
> > EMBL:AQ254466 CpG0842A CpIOWAgDNA1 Cryptosporidium pa... +2 68 0.991
> > EMBL:AQ935528 CpG2517B CpIOWAgDNA1 Cryptosporidium pa... -2 67 0.9981
> > EMBL:AQ854869 CpG2093B CpIOWAgDNA1 Cryptosporidium pa... +2 67 0.9981
> > EMBL:AQ450236 500009E03.x1 CpIOWAM13mp18gDNA1 Cryptos... -1 65 0.99991
> > EMBL:AQ003639 CpG0296A CpIOWAgDNA1 Cryptosporidium pa... +2 5 0.999901
> >
> > "ALIGNMENTS:"
> >
> > >EMBL:B88446 CpG0200B CpIOWAgDNA1 Cryptosporidium parvum genomic, genomic
> > survey sequence.
> > Length = 508
>EMBL AQ935528 Cp....
above is the word "ALIGNMENTS:" which is not present and which i'd like
to
> > add in each file. i figure i'd have to write out a reg exp- something like
> > "newline followed by ">" ...but am not able to get a good start..-and dont
> > know how to go abt the actual task- figured it had to do with "printing
> > to" a variable in which i stored the file value...
> > am chewing on it..
>
> You don't have to check for the newline just a if (/^>/) would do
> This assumes that the files to be modified are given in the command line
> If you are getting it some place else, empty @ARGV and add these files to
> @ARGV.
>
> #!/usr/local/bin/perl -w
> use strict;
>
> $^I = '~'; # perldoc perlvar, inplace edit and creates a backup filename~
> while (<>) {
> print "ALIGNMENT:\n" if (/^>/);
> print;
> }
>
> The same can also be done as an oneliner
> perl -i~ -pe 'print "ALIGNMENTS:\n" if (/^>/);' *.txt
>
> Note: This will create a backup of all the files it processes, for e.g.
> if the file names1.txt the original file will be backed up as names1.txt~,
> the same as above.
>
> perldoc perlrun and read through the sections that explains these flags.
> You can replace the *.txt with the list of files that you want modified.
>
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