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#52 blast.p4m doesn't extract hit name and score

v1.6.0
open
nobody
Gap4 (50)
5
2005-10-18
2005-10-18
Torsten Seemann
No

Using Staden 1.6.0 and NCBI blast 2.2.10

The Staden parser expects a space after the ">" sign
for a hit name,
and no space before the "Score =" line. My blast
reports seem to have the OPPOSITE situation.

Here is a diff which fixed the problem for me:

--- /bio/sw/staden/lib/pregap4/modules/blast.p4m.orig
2005-10-18 15:07:00.000000000 +1000
+++ /bio/sw/staden/lib/pregap4/modules/blast.p4m
2005-10-18 15:08:26.000000000 +1000
@@ -135,9 +135,9 @@
catch {unset exp_file}
array set exp_file [read_exp_file $query]
}
- } elseif {[regsub {^> (.*)$} $line {\1} tmp]} {
+ } elseif {[regsub {^>(.*)$} $line {\1} tmp]} {
set match_name $tmp
- } elseif {[regsub {^(Score = .* Expect.*)}
$line {\1} tmp]} {
+ } elseif {[regsub {^ (Score = .* Expect.*)}
$line {\1} tmp]} {
set match_score $tmp
} elseif {[regsub {^Query:? ([0-9]*) .*
([0-9]*)$} $line {\1 \2} range]} {
set from [lindex $range 0]

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