Mercurial > repos > iuc > gffcompare
changeset 0:3c97c841a443 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2017 16:02:07 -0400 |
| parents | |
| children | c80cdc2eac6d |
| files | gffcompare.xml test-data/gffcompare_in1.gtf test-data/gffcompare_in2.gtf test-data/gffcompare_in3.gtf test-data/gffcompare_in4.gtf test-data/gffcompare_in5.gtf test-data/gffcompare_out1.gtf test-data/gffcompare_out1.loci test-data/gffcompare_out1.stats test-data/gffcompare_out1.tracking test-data/gffcompare_out2.gtf test-data/gffcompare_out2.loci test-data/gffcompare_out2.stats test-data/gffcompare_out2.tracking tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 16 files changed, 2809 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gffcompare.xml Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,164 @@ +<tool id="gffcompare" name="GffCompare" version="0.9.8"> + <description>compare assembled transcripts to a reference annotation</description> + <requirements> + <requirement type="package" version="0.9.8">gffcompare</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error" /> + <regex match="Exception" /> + </stdio> + <version_command>gffcompare -v | awk '{print $2}'</version_command> + <command> + <![CDATA[ + #set $input_gtf = "' '".join(str($inputs).split(',')) + #if $seq_data.use_seq_data == "Yes": + #if $seq_data.seq_source.index_source == "history": + ln -s '$seq_data.seq_source.ref_file' ref_seq.fa && + #else: + ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && + #end if + #end if + gffcompare + ## Use annotation reference? + #if $annotation.use_ref_annotation == "Yes": + -r '$annotation.reference_annotation' $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags + #end if + + ## Use sequence data? + + #if $seq_data.use_seq_data == "Yes": + -s ref_seq.fa + #end if + + $discard_single_exon -e $max_dist_exon -d $max_dist_group $discard_intron_redundant_transfrags + + '$input_gtf' + ]]> + </command> + <inputs> + <param format="gtf" name="inputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> + <conditional name="annotation"> + <param label="Use Reference Annotation" name="use_ref_annotation" type="select"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" /> + <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" /> + <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" /> + </when> + <when value="No"> + </when> + </conditional> + <conditional name="seq_data"> + <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="No" /> + <when value="Yes"> + <conditional name="seq_source"> + <param label="Choose the source for the reference list" name="index_source" type="select"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param argument="-s" label="Using reference genome" name="index" type="select"> + <options from_data_table="fasta_indexes"> + <filter column="1" key="dbkey" ref="inputs" type="data_meta" /> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + <when value="history"> + <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" /> + </when> + </conditional> + </when> + </conditional> + <param argument="-M/-N" label="discard (ignore) single-exon transcripts" name="discard_single_exon" type="select"> + <option selected="True" value="">No</option> + <option value="-M">Discard single-exon transfrags and reference transcripts</option> + <option value="-N">Discard single-exon reference transcripts</option> + </param> + <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> + <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> + <param argument="-F" help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" truevalue="-F" falsevalue="" label="discard intron-redundant transfrags sharing 5'" name="discard_intron_redundant_transfrags" type="boolean" /> + </inputs> + <outputs> + <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" /> + <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" /> + <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tracking file" name="transcripts_tracking" /> + <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined"> + <filter>(use_seq_data == 'No')</filter> + </data> + <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated"> + <filter>(use_seq_data == 'Yes')</filter> + </data> + </outputs> + <tests> + <test> + <param ftype="gtf" name="inputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> + <param name="use_ref_annotation" value="Yes" /> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> + <param name="ignore_nonoverlapping_reference" value="Yes" /> + <param name="ignore_nonoverlapping_transfrags" value="No" /> + <param name="use_seq_data" value="No" /> + <param name="discard_single_exon" value="" /> + <param name="max_dist_exon" value="100" /> + <param name="max_dist_group" value="100" /> + <param name="discard_intron_redundant_transfrags" value="No" /> + <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" /> + <output file="gffcompare_out1.loci" name="transcripts_loci" /> + <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out1.gtf" name="transcripts_combined" /> + </test> + <test> + <param ftype="gtf" name="inputs" value="gffcompare_in4.gtf" /> + <param name="use_ref_annotation" value="Yes" /> + <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" /> + <param name="ignore_nonoverlapping_reference" value="Yes" /> + <param name="ignore_nonoverlapping_transfrags" value="No" /> + <param name="use_seq_data" value="No" /> + <param name="discard_single_exon" value="" /> + <param name="max_dist_exon" value="100" /> + <param name="max_dist_group" value="100" /> + <param name="discard_intron_redundant_transfrags" value="No" /> + <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" /> + <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" /> + <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> + <output file="gffcompare_out2.gtf" name="transcripts_annotated" /> + </test> + </tests> + <help> +<![CDATA[ +**GffCompare Overview** + +## GffCompare +* compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). +* collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) +* classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a +annotation file (also in GTF/GFF3 format) + +The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare" +(see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare +are supported by GffCompare, while new features will likely be added to GffCompare in the future. + +A notable difference from GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option), +gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the +same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per +their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus +be used as a simple way of annotating a set of transcripts. + +Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e. +contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into +their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed +and is simply ignored when given). + ]]> + </help> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in1.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,100 @@ +chr1 Cufflinks transcript 3111450 3111490 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks exon 3111450 3111490 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935"; +chr1 Cufflinks exon 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935"; +chr1 Cufflinks transcript 3200326 3200352 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3200326 3200352 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3200023 3200191 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053"; +chr1 Cufflinks exon 3200023 3200191 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053"; +chr1 Cufflinks transcript 3201078 3201481 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139"; +chr1 Cufflinks exon 3201078 3201481 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139"; +chr1 Cufflinks transcript 3201673 3201699 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3201673 3201699 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3204755 3204833 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3204755 3204833 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3212214 3212292 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3212214 3212292 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3213096 3213192 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701"; +chr1 Cufflinks exon 3213096 3213192 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701"; +chr1 Cufflinks transcript 3212368 3212439 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000"; +chr1 Cufflinks exon 3212368 3212439 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000"; +chr1 Cufflinks transcript 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +chr1 Cufflinks exon 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +chr1 Cufflinks transcript 3243348 3243401 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000"; +chr1 Cufflinks exon 3243348 3243401 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000"; +chr1 Cufflinks transcript 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +chr1 Cufflinks exon 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +chr1 Cufflinks transcript 3256975 3257011 1000 . . gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189"; +chr1 Cufflinks exon 3256975 3257011 1000 . . gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189"; +chr1 Cufflinks transcript 3189900 3190041 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070"; +chr1 Cufflinks exon 3189900 3190041 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070"; +chr1 Cufflinks transcript 3190273 3190303 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710"; +chr1 Cufflinks exon 3190273 3190303 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710"; +chr1 Cufflinks transcript 3190455 3190481 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000"; +chr1 Cufflinks exon 3190455 3190481 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000"; +chr1 Cufflinks transcript 3191539 3191669 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206"; +chr1 Cufflinks exon 3191539 3191669 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206"; +chr1 Cufflinks transcript 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +chr1 Cufflinks exon 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +chr1 Cufflinks transcript 3192442 3192494 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302"; +chr1 Cufflinks exon 3192442 3192494 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302"; +chr1 Cufflinks transcript 3192551 3192629 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3192551 3192629 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3192732 3192811 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000"; +chr1 Cufflinks exon 3192732 3192811 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000"; +chr1 Cufflinks transcript 3192941 3193042 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529"; +chr1 Cufflinks exon 3192941 3193042 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529"; +chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks transcript 3194303 3194329 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3194303 3194329 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3195084 3195110 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3195084 3195110 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3195451 3195477 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3195451 3195477 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3197090 3197116 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3197090 3197116 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3197247 3197273 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3197247 3197273 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3197347 3197373 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3197347 3197373 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3280687 3280741 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks exon 3280687 3280741 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks transcript 3290489 3290553 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769"; +chr1 Cufflinks exon 3290489 3290553 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769"; +chr1 Cufflinks transcript 3290940 3291023 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857"; +chr1 Cufflinks exon 3290940 3291023 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857"; +chr1 Cufflinks transcript 3291089 3291186 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020"; +chr1 Cufflinks exon 3291089 3291186 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020"; +chr1 Cufflinks transcript 3299610 3299664 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks exon 3299610 3299664 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks transcript 3300052 3300078 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3300052 3300078 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3319000 3319051 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462"; +chr1 Cufflinks exon 3319000 3319051 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462"; +chr1 Cufflinks transcript 3355888 3355914 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3355888 3355914 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3363215 3363278 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750"; +chr1 Cufflinks exon 3363215 3363278 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750"; +chr1 Cufflinks transcript 3363754 3363849 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750"; +chr1 Cufflinks exon 3363754 3363849 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750"; +chr1 Cufflinks transcript 3367136 3367162 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3367136 3367162 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3367334 3367382 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041"; +chr1 Cufflinks exon 3367334 3367382 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041"; +chr1 Cufflinks transcript 3377212 3377262 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824"; +chr1 Cufflinks exon 3377212 3377262 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824"; +chr1 Cufflinks transcript 3391326 3391352 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3391326 3391352 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3435842 3435880 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615"; +chr1 Cufflinks exon 3435842 3435880 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615"; +chr1 Cufflinks transcript 3447762 3447788 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000"; +chr1 Cufflinks exon 3447762 3447788 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000"; +chr1 Cufflinks transcript 3450907 3450965 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881"; +chr1 Cufflinks exon 3450907 3450965 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881"; +chr1 Cufflinks transcript 3451052 3451109 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034"; +chr1 Cufflinks exon 3451052 3451109 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in2.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,100 @@ +chr1 Cufflinks transcript 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; +chr1 Cufflinks exon 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; +chr1 Cufflinks transcript 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; +chr1 Cufflinks exon 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; +chr1 Cufflinks transcript 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; +chr1 Cufflinks exon 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; +chr1 Cufflinks transcript 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; +chr1 Cufflinks exon 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; +chr1 Cufflinks transcript 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr1 Cufflinks exon 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr1 Cufflinks transcript 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; +chr1 Cufflinks exon 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; +chr1 Cufflinks transcript 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr1 Cufflinks exon 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr1 Cufflinks transcript 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; +chr1 Cufflinks exon 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; +chr1 Cufflinks transcript 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; +chr1 Cufflinks exon 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; +chr1 Cufflinks transcript 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr1 Cufflinks exon 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr1 Cufflinks transcript 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; +chr1 Cufflinks exon 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; +chr1 Cufflinks transcript 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; +chr1 Cufflinks exon 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; +chr1 Cufflinks transcript 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; +chr1 Cufflinks exon 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; +chr1 Cufflinks transcript 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; +chr1 Cufflinks exon 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; +chr1 Cufflinks transcript 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; +chr1 Cufflinks exon 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; +chr1 Cufflinks transcript 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; +chr1 Cufflinks exon 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; +chr1 Cufflinks transcript 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; +chr1 Cufflinks exon 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; +chr1 Cufflinks transcript 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; +chr1 Cufflinks exon 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; +chr1 Cufflinks transcript 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; +chr1 Cufflinks exon 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; +chr1 Cufflinks transcript 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; +chr1 Cufflinks exon 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; +chr1 Cufflinks transcript 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; +chr1 Cufflinks exon 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; +chr1 Cufflinks transcript 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr1 Cufflinks exon 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr1 Cufflinks transcript 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr1 Cufflinks exon 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr1 Cufflinks transcript 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; +chr1 Cufflinks exon 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; +chr1 Cufflinks transcript 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; +chr1 Cufflinks exon 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; +chr1 Cufflinks transcript 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; +chr1 Cufflinks exon 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; +chr1 Cufflinks transcript 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; +chr1 Cufflinks exon 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; +chr1 Cufflinks transcript 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; +chr1 Cufflinks exon 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; +chr1 Cufflinks transcript 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; +chr1 Cufflinks exon 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in3.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,100 @@ +chr1 mm9_refFlat stop_codon 3206103 3206105 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3206106 3207049 0.000000 - 2 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3204563 3207049 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3411783 3411982 0.000000 - 1 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3411783 3411982 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3660633 3661429 0.000000 - 0 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat start_codon 3661427 3661429 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3660633 3661579 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat stop_codon 4334681 4334683 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4334684 4340172 0.000000 - 2 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4334224 4340172 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4341991 4342162 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4341991 4342162 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4342283 4342906 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat start_codon 4342904 4342906 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4342283 4342918 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4350281 4350473 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat stop_codon 4481797 4481799 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat CDS 4481800 4482749 0.000000 - 2 gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4481009 4482749 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat CDS 4483181 4483487 0.000000 - 0 gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat start_codon 4483485 4483487 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4483181 4483547 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4483853 4483944 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4485217 4486023 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4486372 4486494 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat stop_codon 4766545 4766547 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4766548 4766882 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4766882 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat stop_codon 4764533 4764535 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4764536 4764597 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat start_codon 4797995 4797997 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4797995 4798063 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4797974 4798063 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4798536 4798567 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4798536 4798567 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4818665 4818730 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4818665 4818730 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4820349 4820396 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4820349 4820396 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4822392 4822462 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4822392 4822462 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4827082 4827155 0.000000 + 2 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4827082 4827155 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4829468 4829569 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4829468 4829569 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4831037 4831213 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4831037 4831213 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4835044 4835094 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat stop_codon 4835095 4835097 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4835044 4836816 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4857551 4857613 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4868108 4868213 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4868108 4868213 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4876825 4876912 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4876825 4876912 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4879538 4879683 0.000000 + 1 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4879538 4879683 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4880821 4880877 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4880821 4880877 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4881996 4882150 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4881996 4882150 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4883498 4883644 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4883498 4883644 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4885015 4885086 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4885015 4885086 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4886437 4886442 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat stop_codon 4886443 4886445 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4886437 4887987 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in4.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,208 @@ +# stringtie --merge -p 1 -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /galaxy-repl/main/files/019/441/dataset_19441936.dat /galaxy-repl/main/files/018/604/dataset_18604623.dat /galaxy-repl/main/files/018/604/dataset_18604626.dat /galaxy-repl/main/files/018/604/dataset_18604628.dat /galaxy-repl/main/files/018/604/dataset_18604631.dat +# StringTie version 1.2.3 +chr1 StringTie transcript 29485012 29485458 1000 - . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; +chr1 StringTie exon 29485012 29485458 1000 - . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; +chr1 StringTie transcript 86909344 86909692 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; +chr1 StringTie exon 86909344 86909692 1000 - . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; +chr1 StringTie transcript 160930303 160940234 1000 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; +chr1 StringTie exon 160930303 160930344 1000 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; +chr1 StringTie exon 160938112 160938232 1000 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "2"; +chr1 StringTie exon 160939995 160940234 1000 + . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "3"; +chr1 StringTie transcript 160940817 160967997 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; +chr1 StringTie exon 160940817 160940994 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1"; +chr1 StringTie exon 160942528 160942728 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "2"; +chr1 StringTie exon 160946534 160946666 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "3"; +chr1 StringTie exon 160948307 160948425 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "4"; +chr1 StringTie exon 160950222 160950334 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "5"; +chr1 StringTie exon 160950841 160951122 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "6"; +chr1 StringTie exon 160951615 160951829 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "7"; +chr1 StringTie exon 160954784 160955151 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "8"; +chr1 StringTie exon 160955815 160955979 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "9"; +chr1 StringTie exon 160959401 160959553 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "10"; +chr1 StringTie exon 160962271 160962484 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "11"; +chr1 StringTie exon 160963479 160963569 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "12"; +chr1 StringTie exon 160963708 160963840 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "13"; +chr1 StringTie exon 160964950 160965120 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "14"; +chr1 StringTie exon 160965673 160965788 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "15"; +chr1 StringTie exon 160967647 160967997 1000 + . gene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "16"; +chr1 StringTie transcript 160968644 160972020 1000 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; +chr1 StringTie exon 160968644 160972020 1000 + . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; +chr1 StringTie transcript 160972938 160974977 1000 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; +chr1 StringTie exon 160972938 160974977 1000 + . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; +chr1 StringTie transcript 161003085 161003516 1000 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; +chr1 StringTie exon 161003085 161003516 1000 + . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; +chr1 StringTie transcript 161003658 161004769 1000 - . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; +chr1 StringTie exon 161003658 161004769 1000 - . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; +chr1 StringTie transcript 161005030 161005802 1000 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; +chr1 StringTie exon 161005030 161005802 1000 - . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; +chr1 StringTie transcript 161006151 161006466 1000 + . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; +chr1 StringTie exon 161006151 161006466 1000 + . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; +chr1 StringTie transcript 161007444 161007700 1000 - . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; +chr1 StringTie exon 161007444 161007700 1000 - . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; +chr1 StringTie transcript 161008375 161008625 1000 + . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; +chr1 StringTie exon 161008375 161008625 1000 + . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; +chr1 StringTie transcript 161009768 161010195 1000 + . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; +chr1 StringTie exon 161009768 161010195 1000 + . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; +chr1 StringTie transcript 161019713 161019962 1000 + . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; +chr1 StringTie exon 161019713 161019962 1000 + . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; +chr1 StringTie transcript 161032044 161032396 1000 - . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; +chr1 StringTie exon 161032044 161032396 1000 - . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; +chr1 StringTie transcript 161034351 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; +chr1 StringTie exon 161034351 161034719 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "11"; +chr1 StringTie transcript 161034584 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; +chr1 StringTie exon 161034584 161034719 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "6"; +chr1 StringTie exon 161037124 161037164 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "7"; +chr1 StringTie exon 161037288 161037315 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "8"; +chr1 StringTie exon 161037505 161037547 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "9"; +chr1 StringTie exon 161037995 161038037 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "10"; +chr1 StringTie exon 161038225 161038272 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "11"; +chr1 StringTie exon 161038457 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.2"; exon_number "12"; +chr1 StringTie transcript 161034642 161038338 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; +chr1 StringTie exon 161034642 161035194 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "6"; +chr1 StringTie exon 161037124 161037164 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "7"; +chr1 StringTie exon 161037288 161037315 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "8"; +chr1 StringTie exon 161037505 161037547 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "9"; +chr1 StringTie exon 161037995 161038037 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "10"; +chr1 StringTie exon 161038225 161038338 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.3"; exon_number "11"; +chr1 StringTie transcript 161035095 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; +chr1 StringTie exon 161035095 161035194 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.4"; exon_number "11"; +chr1 StringTie transcript 161035164 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; +chr1 StringTie exon 161035164 161035194 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "3"; +chr1 StringTie exon 161036208 161036579 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "4"; +chr1 StringTie exon 161036820 161036852 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "5"; +chr1 StringTie exon 161037124 161037164 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 1000 + . gene_id "MSTRG.16"; transcript_id "MSTRG.16.5"; exon_number "11"; +chr1 StringTie transcript 161041525 161050001 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; +chr1 StringTie exon 161041525 161041930 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; +chr1 StringTie exon 161043613 161043688 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "2"; +chr1 StringTie exon 161044959 161045069 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "3"; +chr1 StringTie exon 161045258 161045476 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "4"; +chr1 StringTie exon 161046777 161046929 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "5"; +chr1 StringTie exon 161049938 161050001 1000 - . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "6"; +chr1 StringTie transcript 161041562 161070639 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; +chr1 StringTie exon 161041562 161041930 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; +chr1 StringTie exon 161043613 161043688 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "2"; +chr1 StringTie exon 161044959 161045069 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "3"; +chr1 StringTie exon 161045258 161045476 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "4"; +chr1 StringTie exon 161046777 161046929 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "5"; +chr1 StringTie exon 161049938 161050000 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "6"; +chr1 StringTie exon 161051331 161051438 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "7"; +chr1 StringTie exon 161056461 161056530 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "8"; +chr1 StringTie exon 161057447 161057553 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "9"; +chr1 StringTie exon 161060045 161060091 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "10"; +chr1 StringTie exon 161060736 161060859 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "11"; +chr1 StringTie exon 161062782 161062877 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "12"; +chr1 StringTie exon 161063247 161063348 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "13"; +chr1 StringTie exon 161065225 161065291 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "14"; +chr1 StringTie exon 161069080 161069179 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "15"; +chr1 StringTie exon 161069993 161070639 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "16"; +chr1 StringTie transcript 161045151 161056533 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; +chr1 StringTie exon 161045151 161045476 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "1"; +chr1 StringTie exon 161046777 161046929 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "2"; +chr1 StringTie exon 161049938 161050000 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "3"; +chr1 StringTie exon 161051331 161051438 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "4"; +chr1 StringTie exon 161053941 161054120 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "5"; +chr1 StringTie exon 161056461 161056533 1000 + . gene_id "MSTRG.18"; transcript_id "MSTRG.18.2"; exon_number "6"; +chr1 StringTie transcript 161051330 161070504 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; +chr1 StringTie exon 161051330 161051438 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; +chr1 StringTie exon 161053941 161054120 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "2"; +chr1 StringTie exon 161056461 161056530 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "3"; +chr1 StringTie exon 161057447 161057553 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "4"; +chr1 StringTie exon 161060045 161060091 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "5"; +chr1 StringTie exon 161060736 161060859 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "6"; +chr1 StringTie exon 161062782 161062877 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "7"; +chr1 StringTie exon 161063247 161063348 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "8"; +chr1 StringTie exon 161065225 161065291 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "9"; +chr1 StringTie exon 161069080 161069179 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "10"; +chr1 StringTie exon 161069993 161070504 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "11"; +chr1 StringTie transcript 161051331 161070649 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; +chr1 StringTie exon 161051331 161051438 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "1"; +chr1 StringTie exon 161056461 161056530 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "2"; +chr1 StringTie exon 161057447 161057553 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "3"; +chr1 StringTie exon 161060045 161060091 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "4"; +chr1 StringTie exon 161060736 161060859 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "5"; +chr1 StringTie exon 161062782 161062877 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "6"; +chr1 StringTie exon 161063247 161063348 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "7"; +chr1 StringTie exon 161065225 161065291 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "8"; +chr1 StringTie exon 161069080 161069179 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "9"; +chr1 StringTie exon 161069993 161070649 1000 - . gene_id "MSTRG.19"; transcript_id "MSTRG.19.2"; exon_number "10"; +chr1 StringTie transcript 161070945 161078458 1000 + . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; +chr1 StringTie exon 161070945 161071356 1000 + . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; +chr1 StringTie exon 161074757 161074930 1000 + . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "2"; +chr1 StringTie exon 161078329 161078458 1000 + . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "3"; +chr1 StringTie transcript 161082956 161083421 1000 + . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; +chr1 StringTie exon 161082956 161083421 1000 + . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; +chr1 StringTie transcript 161084121 161084344 1000 + . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; +chr1 StringTie exon 161084121 161084344 1000 + . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; +chr1 StringTie transcript 161085014 161086329 1000 + . gene_id "MSTRG.23"; transcript_id "MSTRG.23.1"; +chr1 StringTie exon 161085014 161086329 1000 + . gene_id "MSTRG.23"; transcript_id "MSTRG.23.1"; exon_number "1"; +chr1 StringTie transcript 161088497 161088913 1000 + . gene_id "MSTRG.24"; transcript_id "MSTRG.24.1"; +chr1 StringTie exon 161088497 161088913 1000 + . gene_id "MSTRG.24"; transcript_id "MSTRG.24.1"; exon_number "1"; +chr1 StringTie transcript 161088915 161090275 1000 - . gene_id "MSTRG.25"; transcript_id "MSTRG.25.1"; +chr1 StringTie exon 161088915 161090275 1000 - . gene_id "MSTRG.25"; transcript_id "MSTRG.25.1"; exon_number "1"; +chr1 StringTie transcript 161089415 161131512 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; +chr1 StringTie exon 161089415 161090511 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "1"; +chr1 StringTie exon 161093681 161093787 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "2"; +chr1 StringTie exon 161095529 161095737 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "3"; +chr1 StringTie exon 161098263 161098396 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "4"; +chr1 StringTie exon 161099142 161099285 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "5"; +chr1 StringTie exon 161101451 161101634 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "6"; +chr1 StringTie exon 161102979 161103094 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "7"; +chr1 StringTie exon 161105401 161105495 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "8"; +chr1 StringTie exon 161106707 161106865 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "9"; +chr1 StringTie exon 161109222 161109795 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "10"; +chr1 StringTie exon 161130389 161130452 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "11"; +chr1 StringTie exon 161131363 161131512 1000 + . gene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "12"; +chr1 StringTie transcript 161090412 161131492 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; +chr1 StringTie exon 161090412 161090511 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "1"; +chr1 StringTie exon 161093681 161093787 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "2"; +chr1 StringTie exon 161095529 161095737 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "3"; +chr1 StringTie exon 161098263 161098396 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "4"; +chr1 StringTie exon 161099142 161099285 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "5"; +chr1 StringTie exon 161101451 161101634 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "6"; +chr1 StringTie exon 161102979 161103094 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "7"; +chr1 StringTie exon 161105401 161105495 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "8"; +chr1 StringTie exon 161106707 161106865 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "9"; +chr1 StringTie exon 161109222 161109795 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "10"; +chr1 StringTie exon 161130389 161130452 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "11"; +chr1 StringTie exon 161131363 161131492 1000 - . gene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "12"; +chr1 StringTie transcript 161123665 161123877 1000 + . gene_id "MSTRG.28"; transcript_id "MSTRG.28.1"; +chr1 StringTie exon 161123665 161123877 1000 + . gene_id "MSTRG.28"; transcript_id "MSTRG.28.1"; exon_number "1"; +chr1 StringTie transcript 192074156 192074378 1000 - . gene_id "MSTRG.29"; transcript_id "MSTRG.29.1"; +chr1 StringTie exon 192074156 192074378 1000 - . gene_id "MSTRG.29"; transcript_id "MSTRG.29.1"; exon_number "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in5.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,1395 @@ +chr1 mm10_knownGene CDS 160930303 160930344 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160930303 160930344 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160930303 160930344 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160930303 160930344 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160938112 160938232 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160938112 160938232 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160938112 160938232 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160938112 160938232 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160939995 160940234 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160939995 160940234 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160939995 160940234 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160939995 160940234 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160940819 160940994 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160940819 160940994 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160940819 160940994 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160940819 160940994 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160942528 160942728 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160942528 160942728 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; 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transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160950222 160950334 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160950222 160950334 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160950222 160950334 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160950222 160950334 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160950841 160951122 0.000000 + 1 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160950841 160951122 0.000000 + 1 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160950841 160951122 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160950841 160951122 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160951615 160951829 0.000000 + 1 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160951615 160951829 0.000000 + 1 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160951615 160951829 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160951615 160951829 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160954784 160955151 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160954784 160955151 0.000000 + 2 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160954784 160955151 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160954784 160955151 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160955815 160955979 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160955815 160955979 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160955815 160955979 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160955815 160955979 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160959401 160959553 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160959401 160959553 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160959401 160959553 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160959401 160959553 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160962271 160962484 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene CDS 160962271 160962484 0.000000 + 0 gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160962271 160962484 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; +chr1 mm10_knownGene exon 160962271 160962484 0.000000 + . gene_id "uc007del.2"; transcript_id "uc007del.2"; 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+chr1 mm10_knownGene exon 161131363 161131479 0.000000 - . gene_id "uc007dfi.1"; transcript_id "uc007dfi.1"; +chr1 mm10_knownGene exon 161131363 161131479 0.000000 - . gene_id "uc007dfi.1"; transcript_id "uc007dfi.1"; +chr1 mm10_knownGene exon 161131363 161131479 0.000000 - . gene_id "uc007dfi.1"; transcript_id "uc007dfi.1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,196 @@ +chr1 Cufflinks transcript 3204755 3204833 . - . transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; gene_name "Xkr4"; oId "CUFF.13.1"; cmp_ref "Xkr4"; class_code "c"; tss_id "TSS1"; +chr1 Cufflinks exon 3204755 3204833 . - . transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "1"; +chr1 Cufflinks transcript 3111450 3111490 . . . transcript_id "TCONS_00000002"; gene_id "XLOC_000002"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2"; +chr1 Cufflinks exon 3111450 3111490 . . . transcript_id "TCONS_00000002"; gene_id "XLOC_000002"; exon_number "1"; +chr1 Cufflinks transcript 3111546 3111576 . . . transcript_id "TCONS_00000003"; gene_id "XLOC_000003"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3"; +chr1 Cufflinks exon 3111546 3111576 . . . transcript_id "TCONS_00000003"; gene_id "XLOC_000003"; exon_number "1"; +chr1 Cufflinks transcript 3174766 3174792 . . . transcript_id "TCONS_00000051"; gene_id "XLOC_000004"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4"; +chr1 Cufflinks exon 3174766 3174792 . . . transcript_id "TCONS_00000051"; gene_id "XLOC_000004"; exon_number "1"; +chr1 Cufflinks transcript 3187402 3187428 . . . transcript_id "TCONS_00000052"; gene_id "XLOC_000005"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5"; +chr1 Cufflinks exon 3187402 3187428 . . . transcript_id "TCONS_00000052"; gene_id "XLOC_000005"; exon_number "1"; +chr1 Cufflinks transcript 3188522 3188548 . . . transcript_id "TCONS_00000053"; gene_id "XLOC_000006"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6"; +chr1 Cufflinks exon 3188522 3188548 . . . transcript_id "TCONS_00000053"; gene_id "XLOC_000006"; exon_number "1"; +chr1 Cufflinks transcript 3189811 3190789 . . . transcript_id "TCONS_00000054"; gene_id "XLOC_000007"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7"; +chr1 Cufflinks exon 3189811 3190789 . . . transcript_id "TCONS_00000054"; gene_id "XLOC_000007"; exon_number "1"; +chr1 Cufflinks transcript 3189900 3190041 . . . transcript_id "TCONS_00000004"; gene_id "XLOC_000007"; oId "CUFF.29.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS7"; +chr1 Cufflinks exon 3189900 3190041 . . . transcript_id "TCONS_00000004"; gene_id "XLOC_000007"; exon_number "1"; +chr1 Cufflinks transcript 3190273 3190303 . . . transcript_id "TCONS_00000005"; gene_id "XLOC_000007"; oId "CUFF.31.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS8"; +chr1 Cufflinks exon 3190273 3190303 . . . transcript_id "TCONS_00000005"; gene_id "XLOC_000007"; exon_number "1"; +chr1 Cufflinks transcript 3190455 3190481 . . . transcript_id "TCONS_00000006"; gene_id "XLOC_000007"; oId "CUFF.33.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS9"; +chr1 Cufflinks exon 3190455 3190481 . . . transcript_id "TCONS_00000006"; gene_id "XLOC_000007"; exon_number "1"; +chr1 Cufflinks transcript 3190859 3191434 . . . transcript_id "TCONS_00000055"; gene_id "XLOC_000008"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10"; +chr1 Cufflinks exon 3190859 3191434 . . . transcript_id "TCONS_00000055"; gene_id "XLOC_000008"; exon_number "1"; +chr1 Cufflinks transcript 3191513 3192077 . . . transcript_id "TCONS_00000056"; gene_id "XLOC_000009"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11"; +chr1 Cufflinks exon 3191513 3192077 . . . transcript_id "TCONS_00000056"; gene_id "XLOC_000009"; exon_number "1"; +chr1 Cufflinks transcript 3191539 3191669 . . . transcript_id "TCONS_00000007"; gene_id "XLOC_000009"; oId "CUFF.35.1"; contained_in "TCONS_00000056"; class_code "u"; tss_id "TSS11"; +chr1 Cufflinks exon 3191539 3191669 . . . transcript_id "TCONS_00000007"; gene_id "XLOC_000009"; exon_number "1"; +chr1 Cufflinks transcript 3191877 3191945 . . . transcript_id "TCONS_00000008"; gene_id "XLOC_000009"; oId "CUFF.37.1"; contained_in "TCONS_00000056"; class_code "u"; tss_id "TSS12"; +chr1 Cufflinks exon 3191877 3191945 . . . transcript_id "TCONS_00000008"; gene_id "XLOC_000009"; exon_number "1"; +chr1 Cufflinks transcript 3192251 3192336 . . . transcript_id "TCONS_00000057"; gene_id "XLOC_000010"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13"; +chr1 Cufflinks exon 3192251 3192336 . . . transcript_id "TCONS_00000057"; gene_id "XLOC_000010"; exon_number "1"; +chr1 Cufflinks transcript 3192442 3192494 . . . transcript_id "TCONS_00000009"; gene_id "XLOC_000011"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14"; +chr1 Cufflinks exon 3192442 3192494 . . . transcript_id "TCONS_00000009"; gene_id "XLOC_000011"; exon_number "1"; +chr1 Cufflinks transcript 3192551 3192629 . . . transcript_id "TCONS_00000010"; gene_id "XLOC_000012"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15"; +chr1 Cufflinks exon 3192551 3192629 . . . transcript_id "TCONS_00000010"; gene_id "XLOC_000012"; exon_number "1"; +chr1 Cufflinks transcript 3192650 3192676 . . . transcript_id "TCONS_00000058"; gene_id "XLOC_000013"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16"; +chr1 Cufflinks exon 3192650 3192676 . . . transcript_id "TCONS_00000058"; gene_id "XLOC_000013"; exon_number "1"; +chr1 Cufflinks transcript 3192732 3192811 . . . transcript_id "TCONS_00000011"; gene_id "XLOC_000014"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17"; +chr1 Cufflinks exon 3192732 3192811 . . . transcript_id "TCONS_00000011"; gene_id "XLOC_000014"; exon_number "1"; +chr1 Cufflinks transcript 3192941 3193042 . . . transcript_id "TCONS_00000012"; gene_id "XLOC_000015"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18"; +chr1 Cufflinks exon 3192941 3193042 . . . transcript_id "TCONS_00000012"; gene_id "XLOC_000015"; exon_number "1"; +chr1 Cufflinks transcript 3194186 3194226 . . . transcript_id "TCONS_00000013"; gene_id "XLOC_000016"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19"; +chr1 Cufflinks exon 3194186 3194226 . . . transcript_id "TCONS_00000013"; gene_id "XLOC_000016"; exon_number "1"; +chr1 Cufflinks transcript 3194303 3194329 . . . transcript_id "TCONS_00000014"; gene_id "XLOC_000017"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20"; +chr1 Cufflinks exon 3194303 3194329 . . . transcript_id "TCONS_00000014"; gene_id "XLOC_000017"; exon_number "1"; +chr1 Cufflinks transcript 3194707 3194733 . . . transcript_id "TCONS_00000059"; gene_id "XLOC_000018"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21"; +chr1 Cufflinks exon 3194707 3194733 . . . transcript_id "TCONS_00000059"; gene_id "XLOC_000018"; exon_number "1"; +chr1 Cufflinks transcript 3195084 3195110 . . . transcript_id "TCONS_00000015"; gene_id "XLOC_000019"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22"; +chr1 Cufflinks exon 3195084 3195110 . . . transcript_id "TCONS_00000015"; gene_id "XLOC_000019"; exon_number "1"; +chr1 Cufflinks transcript 3195451 3195477 . . . transcript_id "TCONS_00000016"; gene_id "XLOC_000020"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23"; +chr1 Cufflinks exon 3195451 3195477 . . . transcript_id "TCONS_00000016"; gene_id "XLOC_000020"; exon_number "1"; +chr1 Cufflinks transcript 3197090 3197116 . . . transcript_id "TCONS_00000017"; gene_id "XLOC_000021"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24"; +chr1 Cufflinks exon 3197090 3197116 . . . transcript_id "TCONS_00000017"; gene_id "XLOC_000021"; exon_number "1"; +chr1 Cufflinks transcript 3197247 3197273 . . . transcript_id "TCONS_00000018"; gene_id "XLOC_000022"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25"; +chr1 Cufflinks exon 3197247 3197273 . . . transcript_id "TCONS_00000018"; gene_id "XLOC_000022"; exon_number "1"; +chr1 Cufflinks transcript 3197347 3197373 . . . transcript_id "TCONS_00000019"; gene_id "XLOC_000023"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26"; +chr1 Cufflinks exon 3197347 3197373 . . . transcript_id "TCONS_00000019"; gene_id "XLOC_000023"; exon_number "1"; +chr1 Cufflinks transcript 3197426 3197452 . . . transcript_id "TCONS_00000060"; gene_id "XLOC_000024"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27"; +chr1 Cufflinks exon 3197426 3197452 . . . transcript_id "TCONS_00000060"; gene_id "XLOC_000024"; exon_number "1"; +chr1 Cufflinks transcript 3200023 3200191 . . . transcript_id "TCONS_00000020"; gene_id "XLOC_000025"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28"; +chr1 Cufflinks exon 3200023 3200191 . . . transcript_id "TCONS_00000020"; gene_id "XLOC_000025"; exon_number "1"; +chr1 Cufflinks transcript 3200326 3200352 . . . transcript_id "TCONS_00000021"; gene_id "XLOC_000026"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29"; +chr1 Cufflinks exon 3200326 3200352 . . . transcript_id "TCONS_00000021"; gene_id "XLOC_000026"; exon_number "1"; +chr1 Cufflinks transcript 3200431 3200457 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000027"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; +chr1 Cufflinks exon 3200431 3200457 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000027"; exon_number "1"; +chr1 Cufflinks transcript 3201008 3201039 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000028"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; +chr1 Cufflinks exon 3201008 3201039 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000028"; exon_number "1"; +chr1 Cufflinks transcript 3201078 3201481 . . . transcript_id "TCONS_00000022"; gene_id "XLOC_000029"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32"; +chr1 Cufflinks exon 3201078 3201481 . . . transcript_id "TCONS_00000022"; gene_id "XLOC_000029"; exon_number "1"; +chr1 Cufflinks transcript 3201597 3201666 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000030"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; +chr1 Cufflinks exon 3201597 3201666 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000030"; exon_number "1"; +chr1 Cufflinks transcript 3201673 3201699 . . . transcript_id "TCONS_00000023"; gene_id "XLOC_000031"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34"; +chr1 Cufflinks exon 3201673 3201699 . . . transcript_id "TCONS_00000023"; gene_id "XLOC_000031"; exon_number "1"; +chr1 Cufflinks transcript 3201726 3201809 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000032"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; +chr1 Cufflinks exon 3201726 3201809 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000032"; exon_number "1"; +chr1 Cufflinks transcript 3211522 3211561 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000033"; gene_name "Xkr4"; oId "CUFF.33.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS36"; +chr1 Cufflinks exon 3211522 3211561 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000033"; exon_number "1"; +chr1 Cufflinks transcript 3212214 3212292 . . . transcript_id "TCONS_00000024"; gene_id "XLOC_000034"; gene_name "Xkr4"; oId "CUFF.15.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS37"; +chr1 Cufflinks exon 3212214 3212292 . . . transcript_id "TCONS_00000024"; gene_id "XLOC_000034"; exon_number "1"; +chr1 Cufflinks transcript 3212368 3212439 . . . transcript_id "TCONS_00000025"; gene_id "XLOC_000035"; gene_name "Xkr4"; oId "CUFF.19.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS38"; +chr1 Cufflinks exon 3212368 3212439 . . . transcript_id "TCONS_00000025"; gene_id "XLOC_000035"; exon_number "1"; +chr1 Cufflinks transcript 3212718 3212801 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000036"; gene_name "Xkr4"; oId "CUFF.35.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS39"; +chr1 Cufflinks exon 3212718 3212801 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000036"; exon_number "1"; +chr1 Cufflinks transcript 3213096 3213192 . . . transcript_id "TCONS_00000026"; gene_id "XLOC_000037"; gene_name "Xkr4"; oId "CUFF.17.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS40"; +chr1 Cufflinks exon 3213096 3213192 . . . transcript_id "TCONS_00000026"; gene_id "XLOC_000037"; exon_number "1"; +chr1 Cufflinks transcript 3213119 3213242 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000037"; gene_name "Xkr4"; oId "CUFF.37.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS40"; +chr1 Cufflinks exon 3213119 3213242 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000037"; exon_number "1"; +chr1 Cufflinks transcript 3240607 3240633 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000038"; gene_name "Xkr4"; oId "CUFF.39.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS41"; +chr1 Cufflinks exon 3240607 3240633 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000038"; exon_number "1"; +chr1 Cufflinks transcript 3242480 3242512 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000039"; gene_name "Xkr4"; oId "CUFF.41.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS42"; +chr1 Cufflinks exon 3242480 3242512 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000039"; exon_number "1"; +chr1 Cufflinks transcript 3242634 3242923 . . . transcript_id "TCONS_00000027"; gene_id "XLOC_000040"; gene_name "Xkr4"; oId "CUFF.25.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS43"; +chr1 Cufflinks exon 3242634 3242923 . . . transcript_id "TCONS_00000027"; gene_id "XLOC_000040"; exon_number "1"; +chr1 Cufflinks transcript 3242925 3243005 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000041"; gene_name "Xkr4"; oId "CUFF.43.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS44"; +chr1 Cufflinks exon 3242925 3243005 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000041"; exon_number "1"; +chr1 Cufflinks transcript 3243019 3243079 . . . transcript_id "TCONS_00000028"; gene_id "XLOC_000042"; gene_name "Xkr4"; oId "CUFF.21.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS45"; +chr1 Cufflinks exon 3243019 3243079 . . . transcript_id "TCONS_00000028"; gene_id "XLOC_000042"; exon_number "1"; +chr1 Cufflinks transcript 3243109 3243154 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000043"; gene_name "Xkr4"; oId "CUFF.45.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS46"; +chr1 Cufflinks exon 3243109 3243154 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000043"; exon_number "1"; +chr1 Cufflinks transcript 3243348 3243401 . . . transcript_id "TCONS_00000029"; gene_id "XLOC_000044"; gene_name "Xkr4"; oId "CUFF.23.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS47"; +chr1 Cufflinks exon 3243348 3243401 . . . transcript_id "TCONS_00000029"; gene_id "XLOC_000044"; exon_number "1"; +chr1 Cufflinks transcript 3254080 3254106 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000045"; gene_name "Xkr4"; oId "CUFF.47.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS48"; +chr1 Cufflinks exon 3254080 3254106 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000045"; exon_number "1"; +chr1 Cufflinks transcript 3256975 3257011 . . . transcript_id "TCONS_00000030"; gene_id "XLOC_000046"; gene_name "Xkr4"; oId "CUFF.27.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS49"; +chr1 Cufflinks exon 3256975 3257011 . . . transcript_id "TCONS_00000030"; gene_id "XLOC_000046"; exon_number "1"; +chr1 Cufflinks transcript 3277156 3277182 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000047"; gene_name "Xkr4"; oId "CUFF.49.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS50"; +chr1 Cufflinks exon 3277156 3277182 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000047"; exon_number "1"; +chr1 Cufflinks transcript 3277191 3277218 . . . transcript_id "TCONS_00000031"; gene_id "XLOC_000048"; gene_name "Xkr4"; oId "CUFF.61.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS51"; +chr1 Cufflinks exon 3277191 3277218 . . . transcript_id "TCONS_00000031"; gene_id "XLOC_000048"; exon_number "1"; +chr1 Cufflinks transcript 3277914 3278390 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.51.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS52"; +chr1 Cufflinks exon 3277914 3278390 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000049"; exon_number "1"; +chr1 Cufflinks transcript 3278237 3278263 . . . transcript_id "TCONS_00000032"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.63.1"; contained_in "TCONS_00000074"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS53"; +chr1 Cufflinks exon 3278237 3278263 . . . transcript_id "TCONS_00000032"; gene_id "XLOC_000049"; exon_number "1"; +chr1 Cufflinks transcript 3280118 3280144 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000050"; gene_name "Xkr4"; oId "CUFF.53.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS54"; +chr1 Cufflinks exon 3280118 3280144 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000050"; exon_number "1"; +chr1 Cufflinks transcript 3280499 3280525 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000051"; gene_name "Xkr4"; oId "CUFF.55.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS55"; +chr1 Cufflinks exon 3280499 3280525 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000051"; exon_number "1"; +chr1 Cufflinks transcript 3280687 3280741 . . . transcript_id "TCONS_00000033"; gene_id "XLOC_000052"; gene_name "Xkr4"; oId "CUFF.65.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS56"; +chr1 Cufflinks exon 3280687 3280741 . . . transcript_id "TCONS_00000033"; gene_id "XLOC_000052"; exon_number "1"; +chr1 Cufflinks transcript 3282505 3282531 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000053"; gene_name "Xkr4"; oId "CUFF.57.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS57"; +chr1 Cufflinks exon 3282505 3282531 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000053"; exon_number "1"; +chr1 Cufflinks transcript 3282651 3282677 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000054"; gene_name "Xkr4"; oId "CUFF.59.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS58"; +chr1 Cufflinks exon 3282651 3282677 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000054"; exon_number "1"; +chr1 Cufflinks transcript 3282761 3282832 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000055"; gene_name "Xkr4"; oId "CUFF.61.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS59"; +chr1 Cufflinks exon 3282761 3282832 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000055"; exon_number "1"; +chr1 Cufflinks transcript 3284967 3284993 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000056"; gene_name "Xkr4"; oId "CUFF.63.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS60"; +chr1 Cufflinks exon 3284967 3284993 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000056"; exon_number "1"; +chr1 Cufflinks transcript 3290489 3290553 . . . transcript_id "TCONS_00000034"; gene_id "XLOC_000057"; gene_name "Xkr4"; oId "CUFF.67.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS61"; +chr1 Cufflinks exon 3290489 3290553 . . . transcript_id "TCONS_00000034"; gene_id "XLOC_000057"; exon_number "1"; +chr1 Cufflinks transcript 3290799 3290859 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000058"; gene_name "Xkr4"; oId "CUFF.65.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS62"; +chr1 Cufflinks exon 3290799 3290859 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000058"; exon_number "1"; +chr1 Cufflinks transcript 3290920 3291273 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; +chr1 Cufflinks exon 3290920 3291273 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000059"; exon_number "1"; +chr1 Cufflinks transcript 3290940 3291023 . . . transcript_id "TCONS_00000035"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; contained_in "TCONS_00000082"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; +chr1 Cufflinks exon 3290940 3291023 . . . transcript_id "TCONS_00000035"; gene_id "XLOC_000059"; exon_number "1"; +chr1 Cufflinks transcript 3291089 3291186 . . . transcript_id "TCONS_00000036"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.71.1"; contained_in "TCONS_00000082"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS64"; +chr1 Cufflinks exon 3291089 3291186 . . . transcript_id "TCONS_00000036"; gene_id "XLOC_000059"; exon_number "1"; +chr1 Cufflinks transcript 3299444 3299640 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000060"; gene_name "Xkr4"; oId "CUFF.67.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS65"; +chr1 Cufflinks exon 3299444 3299640 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000060"; exon_number "1"; +chr1 Cufflinks transcript 3299610 3299664 . . . transcript_id "TCONS_00000037"; gene_id "XLOC_000060"; gene_name "Xkr4"; oId "CUFF.73.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS66"; +chr1 Cufflinks exon 3299610 3299664 . . . transcript_id "TCONS_00000037"; gene_id "XLOC_000060"; exon_number "1"; +chr1 Cufflinks transcript 3299692 3299733 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000061"; gene_name "Xkr4"; oId "CUFF.71.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS67"; +chr1 Cufflinks exon 3299692 3299733 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000061"; exon_number "1"; +chr1 Cufflinks transcript 3300052 3300078 . . . transcript_id "TCONS_00000038"; gene_id "XLOC_000062"; gene_name "Xkr4"; oId "CUFF.75.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS68"; +chr1 Cufflinks exon 3300052 3300078 . . . transcript_id "TCONS_00000038"; gene_id "XLOC_000062"; exon_number "1"; +chr1 Cufflinks transcript 3307749 3307775 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000063"; gene_name "Xkr4"; oId "CUFF.73.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS69"; +chr1 Cufflinks exon 3307749 3307775 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000063"; exon_number "1"; +chr1 Cufflinks transcript 3318621 3318647 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000064"; gene_name "Xkr4"; oId "CUFF.75.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS70"; +chr1 Cufflinks exon 3318621 3318647 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000064"; exon_number "1"; +chr1 Cufflinks transcript 3319000 3319051 . . . transcript_id "TCONS_00000039"; gene_id "XLOC_000065"; gene_name "Xkr4"; oId "CUFF.77.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS71"; +chr1 Cufflinks exon 3319000 3319051 . . . transcript_id "TCONS_00000039"; gene_id "XLOC_000065"; exon_number "1"; +chr1 Cufflinks transcript 3330528 3330554 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000066"; gene_name "Xkr4"; oId "CUFF.77.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS72"; +chr1 Cufflinks exon 3330528 3330554 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000066"; exon_number "1"; +chr1 Cufflinks transcript 3351241 3351311 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000067"; gene_name "Xkr4"; oId "CUFF.79.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS73"; +chr1 Cufflinks exon 3351241 3351311 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000067"; exon_number "1"; +chr1 Cufflinks transcript 3355888 3355914 . . . transcript_id "TCONS_00000040"; gene_id "XLOC_000068"; gene_name "Xkr4"; oId "CUFF.79.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS74"; +chr1 Cufflinks exon 3355888 3355914 . . . transcript_id "TCONS_00000040"; gene_id "XLOC_000068"; exon_number "1"; +chr1 Cufflinks transcript 3355908 3356119 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000068"; gene_name "Xkr4"; oId "CUFF.81.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS74"; +chr1 Cufflinks exon 3355908 3356119 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000068"; exon_number "1"; +chr1 Cufflinks transcript 3356181 3356225 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000069"; gene_name "Xkr4"; oId "CUFF.83.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS75"; +chr1 Cufflinks exon 3356181 3356225 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000069"; exon_number "1"; +chr1 Cufflinks transcript 3363077 3363176 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000070"; gene_name "Xkr4"; oId "CUFF.85.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS76"; +chr1 Cufflinks exon 3363077 3363176 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000070"; exon_number "1"; +chr1 Cufflinks transcript 3363215 3363278 . . . transcript_id "TCONS_00000041"; gene_id "XLOC_000071"; gene_name "Xkr4"; oId "CUFF.81.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS77"; +chr1 Cufflinks exon 3363215 3363278 . . . transcript_id "TCONS_00000041"; gene_id "XLOC_000071"; exon_number "1"; +chr1 Cufflinks transcript 3363388 3363446 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000072"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS78"; +chr1 Cufflinks exon 3363388 3363446 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000072"; exon_number "1"; +chr1 Cufflinks transcript 3363754 3363849 . . . transcript_id "TCONS_00000042"; gene_id "XLOC_000073"; gene_name "Xkr4"; oId "CUFF.83.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS79"; +chr1 Cufflinks exon 3363754 3363849 . . . transcript_id "TCONS_00000042"; gene_id "XLOC_000073"; exon_number "1"; +chr1 Cufflinks transcript 3364872 3364919 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000074"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS80"; +chr1 Cufflinks exon 3364872 3364919 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000074"; exon_number "1"; +chr1 Cufflinks transcript 3367136 3367162 . . . transcript_id "TCONS_00000043"; gene_id "XLOC_000075"; gene_name "Xkr4"; oId "CUFF.85.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS81"; +chr1 Cufflinks exon 3367136 3367162 . . . transcript_id "TCONS_00000043"; gene_id "XLOC_000075"; exon_number "1"; +chr1 Cufflinks transcript 3367211 3367237 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000076"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS82"; +chr1 Cufflinks exon 3367211 3367237 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000076"; exon_number "1"; +chr1 Cufflinks transcript 3367334 3367382 . . . transcript_id "TCONS_00000044"; gene_id "XLOC_000077"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS83"; +chr1 Cufflinks exon 3367334 3367382 . . . transcript_id "TCONS_00000044"; gene_id "XLOC_000077"; exon_number "1"; +chr1 Cufflinks transcript 3369581 3369607 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000078"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS84"; +chr1 Cufflinks exon 3369581 3369607 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000078"; exon_number "1"; +chr1 Cufflinks transcript 3375002 3375028 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000079"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS85"; +chr1 Cufflinks exon 3375002 3375028 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000079"; exon_number "1"; +chr1 Cufflinks transcript 3377212 3377262 . . . transcript_id "TCONS_00000045"; gene_id "XLOC_000080"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS86"; +chr1 Cufflinks exon 3377212 3377262 . . . transcript_id "TCONS_00000045"; gene_id "XLOC_000080"; exon_number "1"; +chr1 Cufflinks transcript 3379889 3379915 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87"; +chr1 Cufflinks exon 3379889 3379915 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000081"; exon_number "1"; +chr1 Cufflinks transcript 3386740 3386836 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88"; +chr1 Cufflinks exon 3386740 3386836 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000082"; exon_number "1"; +chr1 Cufflinks transcript 3391326 3391352 . . . transcript_id "TCONS_00000046"; gene_id "XLOC_000083"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS89"; +chr1 Cufflinks exon 3391326 3391352 . . . transcript_id "TCONS_00000046"; gene_id "XLOC_000083"; exon_number "1"; +chr1 Cufflinks transcript 3435842 3435880 . . . transcript_id "TCONS_00000047"; gene_id "XLOC_000084"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS90"; +chr1 Cufflinks exon 3435842 3435880 . . . transcript_id "TCONS_00000047"; gene_id "XLOC_000084"; exon_number "1"; +chr1 Cufflinks transcript 3447762 3447788 . . . transcript_id "TCONS_00000048"; gene_id "XLOC_000085"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS91"; +chr1 Cufflinks exon 3447762 3447788 . . . transcript_id "TCONS_00000048"; gene_id "XLOC_000085"; exon_number "1"; +chr1 Cufflinks transcript 3450907 3450965 . . . transcript_id "TCONS_00000049"; gene_id "XLOC_000086"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS92"; +chr1 Cufflinks exon 3450907 3450965 . . . transcript_id "TCONS_00000049"; gene_id "XLOC_000086"; exon_number "1"; +chr1 Cufflinks transcript 3451052 3451109 . . . transcript_id "TCONS_00000050"; gene_id "XLOC_000087"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS93"; +chr1 Cufflinks exon 3451052 3451109 . . . transcript_id "TCONS_00000050"; gene_id "XLOC_000087"; exon_number "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.loci Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,87 @@ +XLOC_000001 chr1[-]3204563-3661579 Xkr4|Xkr4 CUFF.13.1 - +XLOC_000002 chr1[.]3111450-3111490 - CUFF.1.1 - +XLOC_000003 chr1[.]3111546-3111576 - CUFF.3.1 - +XLOC_000004 chr1[.]3174766-3174792 - - CUFF.1.1 +XLOC_000005 chr1[.]3187402-3187428 - - CUFF.3.1 +XLOC_000006 chr1[.]3188522-3188548 - - CUFF.5.1 +XLOC_000007 chr1[.]3189811-3190789 - CUFF.29.1,CUFF.31.1,CUFF.33.1 CUFF.11.1 +XLOC_000008 chr1[.]3190859-3191434 - - CUFF.7.1 +XLOC_000009 chr1[.]3191513-3192077 - CUFF.35.1,CUFF.37.1 CUFF.9.1 +XLOC_000010 chr1[.]3192251-3192336 - - CUFF.13.1 +XLOC_000011 chr1[.]3192442-3192494 - CUFF.39.1 - +XLOC_000012 chr1[.]3192551-3192629 - CUFF.41.1 - +XLOC_000013 chr1[.]3192650-3192676 - - CUFF.15.1 +XLOC_000014 chr1[.]3192732-3192811 - CUFF.43.1 - +XLOC_000015 chr1[.]3192941-3193042 - CUFF.45.1 - +XLOC_000016 chr1[.]3194186-3194226 - CUFF.47.1 - +XLOC_000017 chr1[.]3194303-3194329 - CUFF.49.1 - +XLOC_000018 chr1[.]3194707-3194733 - - CUFF.17.1 +XLOC_000019 chr1[.]3195084-3195110 - CUFF.51.1 - +XLOC_000020 chr1[.]3195451-3195477 - CUFF.53.1 - +XLOC_000021 chr1[.]3197090-3197116 - CUFF.55.1 - +XLOC_000022 chr1[.]3197247-3197273 - CUFF.57.1 - +XLOC_000023 chr1[.]3197347-3197373 - CUFF.59.1 - +XLOC_000024 chr1[.]3197426-3197452 - - CUFF.19.1 +XLOC_000025 chr1[.]3200023-3200191 - CUFF.7.1 CUFF.23.1 +XLOC_000026 chr1[.]3200326-3200352 - CUFF.5.1 - +XLOC_000027 chr1[.]3200431-3200457 - - CUFF.21.1 +XLOC_000028 chr1[.]3201008-3201039 - - CUFF.26.1 +XLOC_000029 chr1[.]3201078-3201481 - CUFF.9.1 CUFF.25.1 +XLOC_000030 chr1[.]3201597-3201666 - - CUFF.29.1 +XLOC_000031 chr1[.]3201673-3201699 - CUFF.11.1 - +XLOC_000032 chr1[.]3201726-3201809 - - CUFF.31.1 +XLOC_000033 chr1[.]3211522-3211561 - - CUFF.33.1 +XLOC_000034 chr1[.]3212214-3212292 - CUFF.15.1 - +XLOC_000035 chr1[.]3212368-3212439 - CUFF.19.1 - +XLOC_000036 chr1[.]3212718-3212801 - - CUFF.35.1 +XLOC_000037 chr1[.]3213096-3213242 - CUFF.17.1 CUFF.37.1 +XLOC_000038 chr1[.]3240607-3240633 - - CUFF.39.1 +XLOC_000039 chr1[.]3242480-3242512 - - CUFF.41.1 +XLOC_000040 chr1[.]3242634-3242923 - CUFF.25.1 - +XLOC_000041 chr1[.]3242925-3243005 - - CUFF.43.1 +XLOC_000042 chr1[.]3243019-3243079 - CUFF.21.1 - +XLOC_000043 chr1[.]3243109-3243154 - - CUFF.45.1 +XLOC_000044 chr1[.]3243348-3243401 - CUFF.23.1 - +XLOC_000045 chr1[.]3254080-3254106 - - CUFF.47.1 +XLOC_000046 chr1[.]3256975-3257011 - CUFF.27.1 - +XLOC_000047 chr1[.]3277156-3277182 - - CUFF.49.1 +XLOC_000048 chr1[.]3277191-3277218 - CUFF.61.1 - +XLOC_000049 chr1[.]3277914-3278390 - CUFF.63.1 CUFF.51.1 +XLOC_000050 chr1[.]3280118-3280144 - - CUFF.53.1 +XLOC_000051 chr1[.]3280499-3280525 - - CUFF.55.1 +XLOC_000052 chr1[.]3280687-3280741 - CUFF.65.1 - +XLOC_000053 chr1[.]3282505-3282531 - - CUFF.57.1 +XLOC_000054 chr1[.]3282651-3282677 - - CUFF.59.1 +XLOC_000055 chr1[.]3282761-3282832 - - CUFF.61.1 +XLOC_000056 chr1[.]3284967-3284993 - - CUFF.63.1 +XLOC_000057 chr1[.]3290489-3290553 - CUFF.67.1 - +XLOC_000058 chr1[.]3290799-3290859 - - CUFF.65.1 +XLOC_000059 chr1[.]3290920-3291273 - CUFF.69.1,CUFF.71.1 CUFF.69.1 +XLOC_000060 chr1[.]3299444-3299664 - CUFF.73.1 CUFF.67.1 +XLOC_000061 chr1[.]3299692-3299733 - - CUFF.71.1 +XLOC_000062 chr1[.]3300052-3300078 - CUFF.75.1 - +XLOC_000063 chr1[.]3307749-3307775 - - CUFF.73.1 +XLOC_000064 chr1[.]3318621-3318647 - - CUFF.75.1 +XLOC_000065 chr1[.]3319000-3319051 - CUFF.77.1 - +XLOC_000066 chr1[.]3330528-3330554 - - CUFF.77.1 +XLOC_000067 chr1[.]3351241-3351311 - - CUFF.79.1 +XLOC_000068 chr1[.]3355888-3356119 - CUFF.79.1 CUFF.81.1 +XLOC_000069 chr1[.]3356181-3356225 - - CUFF.83.1 +XLOC_000070 chr1[.]3363077-3363176 - - CUFF.85.1 +XLOC_000071 chr1[.]3363215-3363278 - CUFF.81.1 - +XLOC_000072 chr1[.]3363388-3363446 - - CUFF.87.1 +XLOC_000073 chr1[.]3363754-3363849 - CUFF.83.1 - +XLOC_000074 chr1[.]3364872-3364919 - - CUFF.89.1 +XLOC_000075 chr1[.]3367136-3367162 - CUFF.85.1 - +XLOC_000076 chr1[.]3367211-3367237 - - CUFF.91.1 +XLOC_000077 chr1[.]3367334-3367382 - CUFF.87.1 - +XLOC_000078 chr1[.]3369581-3369607 - - CUFF.93.1 +XLOC_000079 chr1[.]3375002-3375028 - - CUFF.95.1 +XLOC_000080 chr1[.]3377212-3377262 - CUFF.89.1 - +XLOC_000081 chr1[.]3379889-3379915 - - CUFF.97.1 +XLOC_000082 chr1[.]3386740-3386836 - - CUFF.99.1 +XLOC_000083 chr1[.]3391326-3391352 - CUFF.91.1 - +XLOC_000084 chr1[.]3435842-3435880 - CUFF.93.1 - +XLOC_000085 chr1[.]3447762-3447788 - CUFF.95.1 - +XLOC_000086 chr1[.]3450907-3450965 - CUFF.97.1 - +XLOC_000087 chr1[.]3451052-3451109 - CUFF.99.1 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.stats Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,34 @@ +# gffcompare v0.9.8 | Command line was: +#gffcompare -r /tmp/tmp9HJ0Pt/files/000/dataset_364.dat -R -e 100 -d 100 /tmp/tmp9HJ0Pt/files/000/dataset_362.dat /tmp/tmp9HJ0Pt/files/000/dataset_363.dat +# + +#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_362.dat +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Super-loci w/ reference transcripts: 1 +#-----------------| Sensitivity | Precision | + Base level: 2.2 | 2.3 | + Exon level: 0.0 | 0.0 | + Intron level: 0.0 | -nan | +Intron chain level: 0.0 | -nan | + Transcript level: 0.0 | 0.0 | + Locus level: 0.0 | 0.0 | + + Matching intron chains: 0 + Matching transcripts: 0 + Matching loci: 0 + + Missed exons: 2/3 ( 66.7%) + Novel exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Novel loci: 49/50 ( 98.0%) + +#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_363.dat +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + + Total union super-loci across all input datasets: 87 + (0 multi-transcript, ~1.1 transcripts per locus)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.tracking Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,98 @@ +TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - +TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - +TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - +TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - +TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - +TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - +TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - +TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - +TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - +TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - +TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - +TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000020 XLOC_000025 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169 q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88 +TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404 q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27 +TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - +TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - +TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - +TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - +TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - +TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - +TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - +TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - +TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - +TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - +TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - +TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - +TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - +TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - +TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - +TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - +TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - +TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - +TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - +TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - +TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - +TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- +TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- +TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- +TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- +TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- +TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000061 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000062 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- +TCONS_00000063 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- +TCONS_00000064 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- +TCONS_00000065 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- +TCONS_00000066 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- +TCONS_00000067 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- +TCONS_00000068 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000069 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- +TCONS_00000070 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- +TCONS_00000071 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- +TCONS_00000072 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000073 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000074 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- +TCONS_00000075 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000076 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000077 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000078 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000079 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- +TCONS_00000080 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000081 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- +TCONS_00000082 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- +TCONS_00000083 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- +TCONS_00000084 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- +TCONS_00000085 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000086 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000087 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- +TCONS_00000088 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- +TCONS_00000089 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- +TCONS_00000090 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- +TCONS_00000091 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- +TCONS_00000092 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- +TCONS_00000093 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- +TCONS_00000094 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000095 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000096 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000097 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000098 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.gtf Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,206 @@ +chr1 StringTie transcript 160930303 160940234 . + . transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS1"; +chr1 StringTie exon 160930303 160930344 . + . transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1"; +chr1 StringTie exon 160938112 160938232 . + . transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "2"; +chr1 StringTie exon 160939995 160940234 . + . transcript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "3"; +chr1 StringTie transcript 160940817 160967997 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS2"; +chr1 StringTie exon 160940817 160940994 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "1"; +chr1 StringTie exon 160942528 160942728 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "2"; +chr1 StringTie exon 160946534 160946666 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "3"; +chr1 StringTie exon 160948307 160948425 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "4"; +chr1 StringTie exon 160950222 160950334 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "5"; +chr1 StringTie exon 160950841 160951122 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "6"; +chr1 StringTie exon 160951615 160951829 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "7"; +chr1 StringTie exon 160954784 160955151 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "8"; +chr1 StringTie exon 160955815 160955979 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "9"; +chr1 StringTie exon 160959401 160959553 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "10"; +chr1 StringTie exon 160962271 160962484 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "11"; +chr1 StringTie exon 160963479 160963569 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "12"; +chr1 StringTie exon 160963708 160963840 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "13"; +chr1 StringTie exon 160964950 160965120 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "14"; +chr1 StringTie exon 160965673 160965788 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "15"; +chr1 StringTie exon 160967647 160967997 . + . transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "16"; +chr1 StringTie transcript 160968644 160972020 . + . transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS3"; +chr1 StringTie exon 160968644 160972020 . + . transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1"; +chr1 StringTie transcript 160972938 160974977 . + . transcript_id "MSTRG.6.1"; gene_id "MSTRG.6"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS4"; +chr1 StringTie exon 160972938 160974977 . + . transcript_id "MSTRG.6.1"; gene_id "MSTRG.6"; exon_number "1"; +chr1 StringTie transcript 161003085 161003516 . + . transcript_id "MSTRG.7.1"; gene_id "MSTRG.7"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS5"; +chr1 StringTie exon 161003085 161003516 . + . transcript_id "MSTRG.7.1"; gene_id "MSTRG.7"; exon_number "1"; +chr1 StringTie transcript 161006151 161006466 . + . transcript_id "MSTRG.10.1"; gene_id "MSTRG.10"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS6"; +chr1 StringTie exon 161006151 161006466 . + . transcript_id "MSTRG.10.1"; gene_id "MSTRG.10"; exon_number "1"; +chr1 StringTie transcript 161008375 161008625 . + . transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS7"; +chr1 StringTie exon 161008375 161008625 . + . transcript_id "MSTRG.12.1"; gene_id "MSTRG.12"; exon_number "1"; +chr1 StringTie transcript 161009768 161010195 . + . transcript_id "MSTRG.13.1"; gene_id "MSTRG.13"; xloc "XLOC_000005"; class_code "u"; tss_id "TSS8"; +chr1 StringTie exon 161009768 161010195 . + . transcript_id "MSTRG.13.1"; gene_id "MSTRG.13"; exon_number "1"; +chr1 StringTie transcript 161019713 161019962 . + . transcript_id "MSTRG.14.1"; gene_id "MSTRG.14"; gene_name "uc007der.1"; xloc "XLOC_000006"; cmp_ref "uc007der.1"; class_code "x"; tss_id "TSS9"; +chr1 StringTie exon 161019713 161019962 . + . transcript_id "MSTRG.14.1"; gene_id "MSTRG.14"; exon_number "1"; +chr1 StringTie transcript 161034351 161038539 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS10"; +chr1 StringTie exon 161034351 161034719 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 . + . transcript_id "MSTRG.16.1"; gene_id "MSTRG.16"; exon_number "11"; +chr1 StringTie transcript 161034584 161038539 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS11"; +chr1 StringTie exon 161034584 161034719 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "6"; +chr1 StringTie exon 161037124 161037164 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "7"; +chr1 StringTie exon 161037288 161037315 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "8"; +chr1 StringTie exon 161037505 161037547 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "9"; +chr1 StringTie exon 161037995 161038037 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "10"; +chr1 StringTie exon 161038225 161038272 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "11"; +chr1 StringTie exon 161038457 161038539 . + . transcript_id "MSTRG.16.2"; gene_id "MSTRG.16"; exon_number "12"; +chr1 StringTie transcript 161034642 161038338 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS11"; +chr1 StringTie exon 161034642 161035194 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "6"; +chr1 StringTie exon 161037124 161037164 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "7"; +chr1 StringTie exon 161037288 161037315 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "8"; +chr1 StringTie exon 161037505 161037547 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "9"; +chr1 StringTie exon 161037995 161038037 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "10"; +chr1 StringTie exon 161038225 161038338 . + . transcript_id "MSTRG.16.3"; gene_id "MSTRG.16"; exon_number "11"; +chr1 StringTie transcript 161035095 161038539 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "j"; tss_id "TSS12"; +chr1 StringTie exon 161035095 161035194 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "3"; +chr1 StringTie exon 161036208 161036244 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "4"; +chr1 StringTie exon 161036549 161036579 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "5"; +chr1 StringTie exon 161036820 161036852 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 . + . transcript_id "MSTRG.16.4"; gene_id "MSTRG.16"; exon_number "11"; +chr1 StringTie transcript 161035164 161038539 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; gene_name "uc007dev.1"; xloc "XLOC_000007"; cmp_ref "uc007dev.1"; class_code "="; tss_id "TSS12"; +chr1 StringTie exon 161035164 161035194 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "1"; +chr1 StringTie exon 161035752 161035804 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "2"; +chr1 StringTie exon 161035983 161036014 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "3"; +chr1 StringTie exon 161036208 161036579 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "4"; +chr1 StringTie exon 161036820 161036852 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "5"; +chr1 StringTie exon 161037124 161037164 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "6"; +chr1 StringTie exon 161037288 161037315 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "7"; +chr1 StringTie exon 161037505 161037547 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "8"; +chr1 StringTie exon 161037995 161038037 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "9"; +chr1 StringTie exon 161038225 161038272 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "10"; +chr1 StringTie exon 161038457 161038539 . + . transcript_id "MSTRG.16.5"; gene_id "MSTRG.16"; exon_number "11"; +chr1 StringTie transcript 161041562 161070639 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; gene_name "uc007dey.2"; xloc "XLOC_000008"; cmp_ref "uc007dey.2"; class_code "s"; tss_id "TSS13"; +chr1 StringTie exon 161041562 161041930 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "1"; +chr1 StringTie exon 161043613 161043688 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "2"; +chr1 StringTie exon 161044959 161045069 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "3"; +chr1 StringTie exon 161045258 161045476 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "4"; +chr1 StringTie exon 161046777 161046929 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "5"; +chr1 StringTie exon 161049938 161050000 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "6"; +chr1 StringTie exon 161051331 161051438 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "7"; +chr1 StringTie exon 161056461 161056530 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "8"; +chr1 StringTie exon 161057447 161057553 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "9"; +chr1 StringTie exon 161060045 161060091 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "10"; +chr1 StringTie exon 161060736 161060859 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "11"; +chr1 StringTie exon 161062782 161062877 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "12"; +chr1 StringTie exon 161063247 161063348 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "13"; +chr1 StringTie exon 161065225 161065291 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "14"; +chr1 StringTie exon 161069080 161069179 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "15"; +chr1 StringTie exon 161069993 161070639 . + . transcript_id "MSTRG.18.1"; gene_id "MSTRG.18"; exon_number "16"; +chr1 StringTie transcript 161045151 161056533 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; gene_name "uc007dey.2"; xloc "XLOC_000008"; cmp_ref "uc007dey.2"; class_code "s"; tss_id "TSS14"; +chr1 StringTie exon 161045151 161045476 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "1"; +chr1 StringTie exon 161046777 161046929 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "2"; +chr1 StringTie exon 161049938 161050000 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "3"; +chr1 StringTie exon 161051331 161051438 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "4"; +chr1 StringTie exon 161053941 161054120 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "5"; +chr1 StringTie exon 161056461 161056533 . + . transcript_id "MSTRG.18.2"; gene_id "MSTRG.18"; exon_number "6"; +chr1 StringTie transcript 161070945 161078458 . + . transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; gene_name "uc007dfd.3"; xloc "XLOC_000009"; cmp_ref "uc007dfd.3"; class_code "c"; tss_id "TSS15"; +chr1 StringTie exon 161070945 161071356 . + . transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "1"; +chr1 StringTie exon 161074757 161074930 . + . transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "2"; +chr1 StringTie exon 161078329 161078458 . + . transcript_id "MSTRG.20.1"; gene_id "MSTRG.20"; exon_number "3"; +chr1 StringTie transcript 161082956 161083421 . + . transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS16"; +chr1 StringTie exon 161082956 161083421 . + . transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; exon_number "1"; +chr1 StringTie transcript 161084121 161084344 . + . transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS17"; +chr1 StringTie exon 161084121 161084344 . + . transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; exon_number "1"; +chr1 StringTie transcript 161085014 161086329 . + . transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS18"; +chr1 StringTie exon 161085014 161086329 . + . transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; exon_number "1"; +chr1 StringTie transcript 161088497 161088913 . + . transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; gene_name "uc007dff.1"; xloc "XLOC_000010"; cmp_ref "uc007dff.1"; class_code "x"; tss_id "TSS19"; +chr1 StringTie exon 161088497 161088913 . + . transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; exon_number "1"; +chr1 StringTie transcript 161089415 161131512 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; gene_name "uc007dff.1"; xloc "XLOC_000011"; cmp_ref "uc007dff.1"; class_code "s"; tss_id "TSS20"; +chr1 StringTie exon 161089415 161090511 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "1"; +chr1 StringTie exon 161093681 161093787 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "2"; +chr1 StringTie exon 161095529 161095737 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "3"; +chr1 StringTie exon 161098263 161098396 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "4"; +chr1 StringTie exon 161099142 161099285 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "5"; +chr1 StringTie exon 161101451 161101634 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "6"; +chr1 StringTie exon 161102979 161103094 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "7"; +chr1 StringTie exon 161105401 161105495 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "8"; +chr1 StringTie exon 161106707 161106865 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "9"; +chr1 StringTie exon 161109222 161109795 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "10"; +chr1 StringTie exon 161130389 161130452 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "11"; +chr1 StringTie exon 161131363 161131512 . + . transcript_id "MSTRG.26.1"; gene_id "MSTRG.26"; exon_number "12"; +chr1 StringTie transcript 161123665 161123877 . + . transcript_id "MSTRG.28.1"; gene_id "MSTRG.28"; gene_name "uc007dff.1"; xloc "XLOC_000012"; cmp_ref "uc007dff.1"; class_code "i"; tss_id "TSS21"; +chr1 StringTie exon 161123665 161123877 . + . transcript_id "MSTRG.28.1"; gene_id "MSTRG.28"; exon_number "1"; +chr1 StringTie transcript 29485012 29485458 . - . transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; xloc "XLOC_000013"; class_code "u"; tss_id "TSS22"; +chr1 StringTie exon 29485012 29485458 . - . transcript_id "MSTRG.1.1"; gene_id "MSTRG.1"; exon_number "1"; +chr1 StringTie transcript 86909344 86909692 . - . transcript_id "MSTRG.2.1"; gene_id "MSTRG.2"; xloc "XLOC_000014"; class_code "u"; tss_id "TSS23"; +chr1 StringTie exon 86909344 86909692 . - . transcript_id "MSTRG.2.1"; gene_id "MSTRG.2"; exon_number "1"; +chr1 StringTie transcript 161003658 161004769 . - . transcript_id "MSTRG.8.1"; gene_id "MSTRG.8"; xloc "XLOC_000015"; class_code "u"; tss_id "TSS24"; +chr1 StringTie exon 161003658 161004769 . - . transcript_id "MSTRG.8.1"; gene_id "MSTRG.8"; exon_number "1"; +chr1 StringTie transcript 161005030 161005802 . - . transcript_id "MSTRG.9.1"; gene_id "MSTRG.9"; xloc "XLOC_000016"; class_code "u"; tss_id "TSS25"; +chr1 StringTie exon 161005030 161005802 . - . transcript_id "MSTRG.9.1"; gene_id "MSTRG.9"; exon_number "1"; +chr1 StringTie transcript 161007444 161007700 . - . transcript_id "MSTRG.11.1"; gene_id "MSTRG.11"; xloc "XLOC_000017"; class_code "u"; tss_id "TSS26"; +chr1 StringTie exon 161007444 161007700 . - . transcript_id "MSTRG.11.1"; gene_id "MSTRG.11"; exon_number "1"; +chr1 StringTie transcript 161032044 161032396 . - . transcript_id "MSTRG.15.1"; gene_id "MSTRG.15"; gene_name "uc007des.1"; xloc "XLOC_000018"; cmp_ref "uc007des.1"; class_code "c"; tss_id "TSS27"; +chr1 StringTie exon 161032044 161032396 . - . transcript_id "MSTRG.15.1"; gene_id "MSTRG.15"; exon_number "1"; +chr1 StringTie transcript 161041525 161050001 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "c"; tss_id "TSS28"; +chr1 StringTie exon 161041525 161041930 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "1"; +chr1 StringTie exon 161043613 161043688 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "2"; +chr1 StringTie exon 161044959 161045069 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "3"; +chr1 StringTie exon 161045258 161045476 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "4"; +chr1 StringTie exon 161046777 161046929 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "5"; +chr1 StringTie exon 161049938 161050001 . - . transcript_id "MSTRG.17.1"; gene_id "MSTRG.17"; exon_number "6"; +chr1 StringTie transcript 161051330 161070504 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "c"; tss_id "TSS29"; +chr1 StringTie exon 161051330 161051438 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "1"; +chr1 StringTie exon 161053941 161054120 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "2"; +chr1 StringTie exon 161056461 161056530 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "3"; +chr1 StringTie exon 161057447 161057553 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "4"; +chr1 StringTie exon 161060045 161060091 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "5"; +chr1 StringTie exon 161060736 161060859 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "6"; +chr1 StringTie exon 161062782 161062877 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "7"; +chr1 StringTie exon 161063247 161063348 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "8"; +chr1 StringTie exon 161065225 161065291 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "9"; +chr1 StringTie exon 161069080 161069179 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "10"; +chr1 StringTie exon 161069993 161070504 . - . transcript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "11"; +chr1 StringTie transcript 161051331 161070649 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "j"; tss_id "TSS30"; +chr1 StringTie exon 161051331 161051438 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "1"; +chr1 StringTie exon 161056461 161056530 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "2"; +chr1 StringTie exon 161057447 161057553 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "3"; +chr1 StringTie exon 161060045 161060091 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "4"; +chr1 StringTie exon 161060736 161060859 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "5"; +chr1 StringTie exon 161062782 161062877 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "6"; +chr1 StringTie exon 161063247 161063348 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "7"; +chr1 StringTie exon 161065225 161065291 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "8"; +chr1 StringTie exon 161069080 161069179 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "9"; +chr1 StringTie exon 161069993 161070649 . - . transcript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "10"; +chr1 StringTie transcript 161088915 161090275 . - . transcript_id "MSTRG.25.1"; gene_id "MSTRG.25"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "c"; tss_id "TSS31"; +chr1 StringTie exon 161088915 161090275 . - . transcript_id "MSTRG.25.1"; gene_id "MSTRG.25"; exon_number "1"; +chr1 StringTie transcript 161090412 161131492 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "="; tss_id "TSS32"; +chr1 StringTie exon 161090412 161090511 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "1"; +chr1 StringTie exon 161093681 161093787 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "2"; +chr1 StringTie exon 161095529 161095737 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "3"; +chr1 StringTie exon 161098263 161098396 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "4"; +chr1 StringTie exon 161099142 161099285 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "5"; +chr1 StringTie exon 161101451 161101634 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "6"; +chr1 StringTie exon 161102979 161103094 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "7"; +chr1 StringTie exon 161105401 161105495 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "8"; +chr1 StringTie exon 161106707 161106865 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "9"; +chr1 StringTie exon 161109222 161109795 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "10"; +chr1 StringTie exon 161130389 161130452 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "11"; +chr1 StringTie exon 161131363 161131492 . - . transcript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "12"; +chr1 StringTie transcript 192074156 192074378 . - . transcript_id "MSTRG.29.1"; gene_id "MSTRG.29"; xloc "XLOC_000021"; class_code "u"; tss_id "TSS33"; +chr1 StringTie exon 192074156 192074378 . - . transcript_id "MSTRG.29.1"; gene_id "MSTRG.29"; exon_number "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.loci Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,21 @@ +XLOC_000001 chr1[+]160930303-160974977 uc007del.2|uc007del.2 MSTRG.4.1,MSTRG.5.1,MSTRG.6.1,MSTRG.3.1 +XLOC_000002 chr1[+]161003085-161003516 - MSTRG.7.1 +XLOC_000003 chr1[+]161006151-161006466 - MSTRG.10.1 +XLOC_000004 chr1[+]161008375-161008625 - MSTRG.12.1 +XLOC_000005 chr1[+]161009768-161010195 - MSTRG.13.1 +XLOC_000006 chr1[+]161019713-161019962 - MSTRG.14.1 +XLOC_000007 chr1[+]161034351-161038539 uc007det.1|uc007det.1,uc007deu.1|uc007deu.1,uc007dev.1|uc007dev.1,uc007dew.1|uc007dew.1,uc011wun.1|uc011wun.1,uc007dex.1|uc007dex.1 MSTRG.16.1,MSTRG.16.2,MSTRG.16.3,MSTRG.16.4,MSTRG.16.5 +XLOC_000008 chr1[+]161041562-161070639 - MSTRG.18.1,MSTRG.18.2 +XLOC_000009 chr1[+]161070945-161086329 uc007dfe.4|uc007dfe.4,uc007dfc.3|uc007dfc.3,uc007dfd.3|uc007dfd.3,uc056yep.1|uc056yep.1 MSTRG.20.1,MSTRG.21.1,MSTRG.22.1,MSTRG.23.1 +XLOC_000010 chr1[+]161088497-161088913 - MSTRG.24.1 +XLOC_000011 chr1[+]161089415-161131512 - MSTRG.26.1 +XLOC_000012 chr1[+]161123665-161123877 - MSTRG.28.1 +XLOC_000013 chr1[-]29485012-29485458 - MSTRG.1.1 +XLOC_000014 chr1[-]86909344-86909692 - MSTRG.2.1 +XLOC_000015 chr1[-]161003658-161004769 - MSTRG.8.1 +XLOC_000016 chr1[-]161005030-161005802 - MSTRG.9.1 +XLOC_000017 chr1[-]161007444-161007700 - MSTRG.11.1 +XLOC_000018 chr1[-]161019713-161034848 uc007der.1|uc007der.1,uc007des.1|uc007des.1 MSTRG.15.1 +XLOC_000019 chr1[-]161041525-161070649 uc007dey.2|uc007dey.2,uc007dez.2|uc007dez.2 MSTRG.17.1,MSTRG.19.1,MSTRG.19.2 +XLOC_000020 chr1[-]161088497-161131492 uc007dff.1|uc007dff.1,uc007dfg.1|uc007dfg.1,uc007dfh.1|uc007dfh.1,uc007dfi.1|uc007dfi.1 MSTRG.25.1,MSTRG.27.1 +XLOC_000021 chr1[-]192074156-192074378 - MSTRG.29.1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.stats Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,29 @@ +# gffcompare v0.9.8 | Command line was: +#gffcompare -r /tmp/tmp6wAQh6/files/000/dataset_668.dat -R -e 100 -d 100 /tmp/tmp6wAQh6/files/000/dataset_667.dat +# + +#= Summary for dataset: /tmp/tmp6wAQh6/files/000/dataset_667.dat +# Query mRNAs : 35 in 29 loci (15 multi-exon transcripts) +# (3 multi-transcript loci, ~1.2 transcripts per locus) +# Reference mRNAs : 20 in 7 loci (19 multi-exon) +# Super-loci w/ reference transcripts: 6 +#-----------------| Sensitivity | Precision | + Base level: 74.7 | 60.7 | + Exon level: 80.0 | 55.7 | + Intron level: 81.2 | 64.4 | +Intron chain level: 10.5 | 13.3 | + Transcript level: 10.0 | 5.7 | + Locus level: 28.6 | 6.9 | + + Matching intron chains: 2 + Matching transcripts: 2 + Matching loci: 2 + + Missed exons: 3/85 ( 3.5%) + Novel exons: 46/122 ( 37.7%) + Missed introns: 11/69 ( 15.9%) + Novel introns: 28/87 ( 32.2%) + Missed loci: 0/7 ( 0.0%) + Novel loci: 15/29 ( 51.7%) + + Total union super-loci across all input datasets: 21
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.tracking Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,35 @@ +TCONS_00000001 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.3|MSTRG.3.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000002 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.4|MSTRG.4.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000003 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.5|MSTRG.5.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000004 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.6|MSTRG.6.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000005 XLOC_000002 - u q1:MSTRG.7|MSTRG.7.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000006 XLOC_000003 - u q1:MSTRG.10|MSTRG.10.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000007 XLOC_000004 - u q1:MSTRG.12|MSTRG.12.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000008 XLOC_000005 - u q1:MSTRG.13|MSTRG.13.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000009 XLOC_000006 uc007der.1|uc007der.1 x q1:MSTRG.14|MSTRG.14.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000010 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000011 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.2|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000012 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.3|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000013 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.4|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000014 XLOC_000007 uc007dev.1|uc007dev.1 = q1:MSTRG.16|MSTRG.16.5|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000015 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000016 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.2|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000017 XLOC_000009 uc007dfd.3|uc007dfd.3 c q1:MSTRG.20|MSTRG.20.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000018 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.21|MSTRG.21.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000019 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.22|MSTRG.22.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000020 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.23|MSTRG.23.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000021 XLOC_000010 uc007dff.1|uc007dff.1 x q1:MSTRG.24|MSTRG.24.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000022 XLOC_000011 uc007dff.1|uc007dff.1 s q1:MSTRG.26|MSTRG.26.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000023 XLOC_000012 uc007dff.1|uc007dff.1 i q1:MSTRG.28|MSTRG.28.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000024 XLOC_000013 - u q1:MSTRG.1|MSTRG.1.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000025 XLOC_000014 - u q1:MSTRG.2|MSTRG.2.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000026 XLOC_000015 - u q1:MSTRG.8|MSTRG.8.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000027 XLOC_000016 - u q1:MSTRG.9|MSTRG.9.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000028 XLOC_000017 - u q1:MSTRG.11|MSTRG.11.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000029 XLOC_000018 uc007des.1|uc007des.1 c q1:MSTRG.15|MSTRG.15.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000030 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.17|MSTRG.17.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000031 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.19|MSTRG.19.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000032 XLOC_000019 uc007dey.2|uc007dey.2 j q1:MSTRG.19|MSTRG.19.2|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000033 XLOC_000020 uc007dff.1|uc007dff.1 c q1:MSTRG.25|MSTRG.25.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000034 XLOC_000020 uc007dff.1|uc007dff.1 = q1:MSTRG.27|MSTRG.27.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000035 XLOC_000021 - u q1:MSTRG.29|MSTRG.29.1|100|0.000000|0.000000|0.000000|0.000000|-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Apr 07 16:02:07 2017 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexed FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables>