Hi Carlos,
Putting the perl script in a file is a good idea -- some strange character
appears in your email in the pasted-in text (maybe where there is an initial
space or tab character in the original copied text?), and if a strange
character is pasted into the command shell I could imagine it could cause
trouble.
The original perl command uses -p, which has the effect of wrapping a 'while
(<>) { [your -e command]; print; }' loop around the command that follows the
-e. So your perl script file should look more like this:
#!/usr/bin/perl
while (<>) {
($c, $start, undef, $depth) = split;
if ($c ne $lastC || $start != $lastStart+1) {
print "fixedStep chrom=chr$c start=$start step=1 span=1\n";
}
print "$depth\n";
($lastC, $lastStart) = ($c, $start);
}
Hope that helps, and please write back to the list if it still fails.
Angie
----- "Hiram Clawson" <[email protected]> wrote:
> From: "Hiram Clawson" <[email protected]>
> To: "Carlos Javier Borroto" <[email protected]>
> Cc: [email protected]
> Sent: Thursday, February 24, 2011 10:32:59 AM GMT -08:00 US/Canada Pacific
> Subject: Re: [Genome] Problem with BAM coverage support through BEBTools /
> genomeCoverageBed
>
> Good Morning Carlos:
>
> Maybe your samtools pileup command is giving a different
> output than this script expects. I just tried this here:
>
> samtools pileup test.bam | perl -pe '
> ($c, $start, undef, $depth) = split;
> if ($c ne $lastC || $start != $lastStart+1) {
> print "fixedStep chrom=$c start=$start step=1 span=1\n";
> }
> $_ = "$depth\n";
> ($lastC, $lastStart) = ($c, $start);'
>
> and it works just fine. The output of the samtools pileup looks
> like:
>
> chr10 65700 N 1 ^!T I
> chr10 65701 N 1 A I
> chr10 65702 N 1 T I
> chr10 65703 N 1 C I
> chr10 65704 N 1 A I
> chr10 65705 N 1 A I
> chr10 65706 N 1 G I
> chr10 65707 N 1 A I
> chr10 65708 N 1 C I
> chr10 65709 N 1 C I
>
> My samtools says its version is:
>
> > Program: samtools (Tools for alignments in the SAM format)
> > Version: 0.1.12a (r862)
>
> --Hiram
>
> > On Thu, Feb 24, 2011 at 1:05 PM, Carlos Javier Borroto
> >> On Thu, Feb 24, 2011 at 12:21 PM, Hiram Clawson wrote:
> >>> Good Morning Carlos:
> >>>
> >>> Here is an alternative procedure to create a coverage graph
> >>> for a bam file:
> >>>
> >>>
> https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html
> >>>
> >> I tried this, but is failing on Ubuntu Lucid:
> >> samtools pileup mybam.sorted.bam     | perl -pe '($c,
> $start,
> >> undef, $depth) = split; \
> >> Â Â Â Â Â Â Â Â Â Â if ($c ne $lastC || $start !=
> $lastStart+1) { \
> >> Â Â Â Â Â Â Â Â Â Â Â print "fixedStep chrom=chr$c
> start=$start step=1
> >> span=1\n"; \
> >> Â Â Â Â Â Â Â Â Â Â } \
> >> Â Â Â Â Â Â Â Â Â Â $_ = "$depth\n"; \
> >> Â Â Â Â Â Â Â Â Â Â ($lastC, $lastStart) = ($c, $start);'
> >> syntax error at -e line 2, near "if"
> >> syntax error at -e line 6, near ";}"
> >>
> >> My perl skills aren't that good, I even tried to move it to a file
> and
> >> I got rid of the syntax error, but the script only prints the
> first
> >> line. This is the file I created.
> >> pileupToWiggle.pl:
> >>
> >> #!/usr/bin/perl
> >>
> >> ($c, $start, undef, $depth) = split;
> >> if ($c ne $lastC || $start != $lastStart+1) {
> >> Â print "fixedStep chrom=chr$c start=$start step=1 span=1\n";
> >> }
> >> $_ = "$depth\n";
> >> ($lastC, $lastStart) = ($c, $start);
> >>
> >> And I tried to use it like this:
> >> $ samtools pileup mybam.sorted.bam | pileupToWiggle.pl
> >> fixedStep chrom=chr start= step=1 span=1
> >>
> >> Would be nice to get it to work, any further help?
> >>
> >>> For assistance with BEDTools, please consult the bedTools
> project:
> >>> http://code.google.com/p/bedtools/
> >>>
> >> I thought the problem could had been in the way I was declaring my
> >> track, that there was an option to get it to display the data in
> the
> >> way I wanted, but you are right, I should have gone to BEBTools
> >> project website.
> >>
> >>> Can you intersect your graph with 'NOT gap' in the table browser
> >>> to display the graph in areas that are not gap ?
> >>>
> >> This I did not understand, I'm very new to the Genome Browser.
> >>
> >>> --Hiram
> >> Thanks for your comments,
> >> --
> >> Carlos Javier Borroto
> >> Baltimore, MD
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
