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Commit bf296c8c authored by nkindlon's avatar nkindlon
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Added unit test to intersect for gff files.

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chr2L . UTR 41 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
chr2L . CDS 71 130 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
chr2L . intron 131 170 0 + . ID=mRNA:xs2:intron:131-170;Parent=mRNA:xs2;
chr2L . CDS 171 200 0 + . ID=mRNA:xs2:CDS:171-200;Parent=mRNA:xs2;
chr2L . UTR 201 220 0 + . ID=mRNA:xs2:UTR:201-220;Parent=mRNA:xs2;
chr2L . exon 41 130 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
chr2L . exon 171 220 0 + . ID=mRNA:xs2:exon:171-220;Parent=mRNA:xs2;
chr2L . mRNA 41 220 0 + . ID=mRNA:xs2;Parent=g2;
chr2L . CDS 161 230 0 - . ID=tRNA:t2:CDS:161-230;Parent=tRNA:t2;
chr2L . exon 161 230 0 - . ID=tRNA:t2:exon:161-230;Parent=tRNA:t2;
chr2L . tRNA 161 230 0 - . ID=tRNA:t2;Parent=t2;
chr2L . gene 41 220 0 + . ID=g2;
chr2L 50 100
......@@ -650,7 +650,19 @@ check obs exp
rm obs exp
###########################################################
# Test that gff files work correctly
############################################################
echo " intersect.new.t55...\c"
echo \
"chr2L . UTR 50 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
chr2L . CDS 71 100 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
chr2L . exon 50 100 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
chr2L . mRNA 50 100 0 + . ID=mRNA:xs2;Parent=g2;
chr2L . gene 50 100 0 + . ID=g2;" > exp
$BT intersect -a gdc.gff -b gdc_one.bed > obs
check obs exp
rm obs exp
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