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Author: Aaron M. Ucko <ucko@debian.org>
Last-Update: Mon, 19 Oct 2020 16:14:20 -0400
Forwarded: https://github.com/paulstothard/cgview_comparison_tool/issues/5
Description: Address BLAST usage errors as of BLAST+ 2.10.
Supply the legacy blastall command's -Q and -D flags only in BLAST
variants that involve translating queries and subjects respectively.
(tblastx notably translates both.)
NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the
supplied $format_type value (7 or 9) results in the warning
Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output
Actually substituting -max_target_seqs would require bypassing the
legacy blastall wrapper, which isn't entirely straightforward in this
instance due to the need to convert a variable format string to modern
options. (Also, this script technically only knows the path to
blastall, though that shouldn't be a concern in practice on Debian.)
--- a/lib/scripts/local_blast_client/local_blast_client.pl
+++ b/lib/scripts/local_blast_client/local_blast_client.pl
@@ -198,7 +198,16 @@ while ( my $sequenceEntry = <SEQFILE> )
#-b can be used to specify the number of hits to return when using -m 9. Each hit may consist of one or more HSPs.
#-b and -v must be set to specify the number of hits to return when using -m 7. Each hit may consist of one or more HSPs.
my $blast_command
- = "$settings{BLAST_PATH} -p $settings{PROGRAM} -d $settings{DATABASE} -e $settings{EXPECT} -i $filename -b $settings{HITLIST_SIZE} -v $settings{HITLIST_SIZE} -m $format_type -Q $settings{QUERY_GENETIC_CODE} -D $settings{DATABASE_GENETIC_CODE} -W $settings{WORD_SIZE} -F $settings{FILTER}";
+ = "$settings{BLAST_PATH} -p $settings{PROGRAM} -d $settings{DATABASE} -e $settings{EXPECT} -i $filename -b $settings{HITLIST_SIZE} -v $settings{HITLIST_SIZE} -m $format_type -W $settings{WORD_SIZE} -F $settings{FILTER}";
+ if ($settings{ALIGN_TYPE} eq 'TRANSLATED') {
+ if ($settings{INPUTTYPE} eq 'DNA') {
+ $blast_command .= "-Q $settings{QUERY_GENETIC_CODE}";
+ }
+ # Not elsif; tblastx notably accepts both.
+ if ($settings{ENTREZ_DB} eq 'nucleotide') {
+ $blast_command .= "-D $settings{DATABASE_GENETIC_CODE}";
+ }
+ }
print
"Performing BLAST search for sequence number $seqCount ($sequenceTitle).\n";
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