Cameron
Deleted
Apr 25, 2001, 2:43 PM
Post #1 of 1
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Regex confusion
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I have two reports (BLAST), generated by the same program(blastn), for two different databases(na_EST.dros, and newArmU.dros).
Visually, I can see no formatting difference between the two reports generated by blastn.
I have a piece of code i use to parse these reports . . .
It works brilliantly for one of the reports, and breaks after the header information is gathered from the other.
I have done my usuall debugging print staements, and all of the data is getting through to my parsing subroutine intact, and looks exactly like i think it should.
I tried using Boulder::Blast to parse the reports, and still get nothing for the one file, and wonderful data for the other report.
I tried using a different server set-up and maintained by a different staff from myself, and was able to reproduce the problem.
All file transferes were done in ASCII mode, and were transfered from a
sun ultra10 workstation running solaris7 to a Macintosh Ibook running debian linux 2.2.
Perl on the iBook is 5.6.0 built from source.
Perl on the sun machine is perl 5.6.1, build from source.
Niether machine will parse the reports from the armU database.
I hope, I am just tired, and missing something really easy,
Any ideas ?
Cameron
-------------------------------------------
report excerpt from EST database
>RE18439.5prime
Length = 596
Score = 71.9 bits (36), Expect = 6e-12
Identities = 48/52 (92%)
Strand = Plus / Minus
Excerpt from ArmU database report
>fasta_output_Scaffold_1939
Length = 1687
Score = 32.2 bits (16), Expect = 1.3
Identities = 16/16 (100%)
Strand = Plus / Minus
-----------------------------
Code segment where program goes worng
# Newlines(\n) have been replaced with whitespace from $_, which holds the records shown above
print "in the subroutine, and \$_is\n$_";
my $length = $1 if /Length\s=\s(\d+)/;
rmy ($score,$bits)=($1,$2) if /(\d+\.?\d*)\sbits\s\((\d+)\)/;
#prints
i am in th sub, and $_ is
fasta_output_Scaffold_3645 Length = 361578 30.2 bits (15), Expect = 4.9 Identities = 15/15 (100%) Strand = Plus / Plus3
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