a1d34750a532bea424b58b6c27f9732b3c95ea73 hiram Thu Sep 30 12:06:55 2021 -0700 fix broken command syntax no redmine diff --git src/hg/utils/automation/asmHubAssembly.pl src/hg/utils/automation/asmHubAssembly.pl index 0b3c011..7134730 100755 --- src/hg/utils/automation/asmHubAssembly.pl +++ src/hg/utils/automation/asmHubAssembly.pl @@ -80,33 +80,33 @@ blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks.</p> <p> This assembly has $partCount component parts, with the following principal types of parts: <ul> _EOF_ ; open (GL, "zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 != \"N\" && \$5 != \"U\"' | awk '{print \$5}' | sort | uniq -c | sort -n|") or die "can not read $asmId.agp.gz"; while (my $line = <GL>) { chomp $line; $line =~ s/^\s+//; my ($count, $type) = split('\s+', $line); my $singleMessage = ""; if ((1 == $count) && (("F" eq $type) || ("O" eq $type))) { - my $chr = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\" | cut -f1'`; + my $chr = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\"' | cut -f1`; chomp $chr; - my $frag = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\" | cut -f6'`; + my $frag = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\"' | cut -f6`; chomp $frag; $singleMessage = sprintf("(%s/%s)", $chr, $frag); } if (exists ($goldTypes{$type}) ) { if (length($singleMessage)) { printf "<li>%s - one %s %s</li>\n", $type, $goldTypes{$type}, $singleMessage; } else { printf "<li>%s - %s (count: %s)</li>\n", $type, $goldTypes{$type}, &AsmHub::commify($count); } } else { printf STDERR "'%s'\n", $line; die "asmHubAssembly.pl: missing AGP contig type definition: $type"; } } close (GL);