| Previous changeset 2:f99d7825a501 (2019-02-05) Next changeset 4:0f710191a66d (2019-10-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526 |
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modified:
gffcompare.xml test-data/gffcompare_in1.gtf test-data/gffcompare_in2.gtf test-data/gffcompare_in3.gtf test-data/gffcompare_out1-1.tmap test-data/gffcompare_out1-2.tmap 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_table_conf.xml.sample |
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added:
test-data/fasta_indexes.loc test-data/gene_sets.loc test-data/gffcompare_out2-1.refmap test-data/gffcompare_out2-1.tmap test-data/gffcompare_out2-2.refmap test-data/gffcompare_out2-2.tmap test-data/gffcompare_out3.gtf test-data/gffcompare_out3.loci test-data/gffcompare_out3.stats test-data/gffcompare_out3.tracking test-data/sequence.fa tool-data/gene_sets.loc.sample tool_data_table_conf.xml.test |
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removed:
test-data/gffcompare_out1-1.refmap test-data/gffcompare_out1-2.refmap |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f gffcompare.xml --- a/gffcompare.xml Tue Feb 05 15:51:44 2019 -0500 +++ b/gffcompare.xml Mon May 27 13:54:15 2019 -0400 |
| [ |
| b'@@ -1,11 +1,15 @@\n-<tool id="gffcompare" name="GffCompare" version="0.10.6">\n+<tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@">\n <description>compare assembled transcripts to a reference annotation</description>\n- <requirements>\n- <requirement type="package" version="0.10.6">gffcompare</requirement>\n+ <macros>\n+ <token name="@GFFCOMPARE_VERSION@">0.11.2</token>\n+ </macros>\n+\t<requirements>\n+ <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement>\n </requirements>\n <version_command>gffcompare -v | awk \'{print $2}\'</version_command>\n <command detect_errors="aggressive"><![CDATA[\n #import re\n+\n #set escaped_element_identifiers = [re.sub(\'[^\\w\\-]\', \'_\', str(_.element_identifier)) for _ in $gffinputs]\n #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):\n ln -s \'$input\' \'$escaped_element_identifier\' &&\n@@ -18,15 +22,24 @@\n #end if\n #end if\n \n+#if $annotation.use_ref_annotation == "Yes":\n+ #if $annotation.ref_source.ref_source_sel == "history":\n+ ln -s \'$annotation.ref_source.reference_annotation\' ref_annotation &&\n+ #else\n+ ln -s \'$annotation.ref_source.index.fields.path\' ref_annotation &&\n+ #end if\n+#end if\n+\n gffcompare\n ## Use annotation reference?\n #if $annotation.use_ref_annotation == "Yes":\n- -r \'$annotation.reference_annotation\'\n+ -r ref_annotation\n $annotation.ignore_nonoverlapping_reference\n $annotation.ignore_nonoverlapping_transfrags\n- #if not $annotation.refmap_tmap:\n- -T\n- #end if\n+ $annotation.strict_match\n+#end if\n+#if $annotation.refmap_tmap == "":\n+ -T\n #end if\n \n ## Use sequence data?\n@@ -35,8 +48,10 @@\n #end if\n \n $discard_single_exon\n+$discard_duplicates\n -e $max_dist_exon\n -d $max_dist_group\n+$chr_stats\n -p \'$adv_output.p\'\n $adv_output.A\n $adv_output.C\n@@ -56,26 +71,46 @@\n <option value="Yes">Yes</option>\n </param>\n <when value="Yes">\n- <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />\n+ <conditional name="ref_source">\n+ <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param argument="-r" label="Using reference annotation" name="index" type="select">\n+ <options from_data_table="gene_sets">\n+ <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />\n+ </options>\n+ <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" />\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />\n+ </when>\n+ </conditional>\n <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" />\n <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'..b'uts="4">\n+ <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />\n+ <conditional name="annotation">\n+ <param name="use_ref_annotation" value="Yes" />\n+ <conditional name="ref_source">\n+ <param name="ref_source_sel" value="history"/>\n+ <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />\n+ </conditional>\n+ <param name="refmap_tmap" value="" />\n+ </conditional>\n+ <conditional name="seq_data">\n+ <param name="use_seq_data" value="No" />\n+ </conditional>\n+ <assert_command>\n+ <not_has_text text="-R " />\n+ <not_has_text text="-Q " />\n+ <has_text text="-T " />\n+ <not_has_text text="-M " />\n+ <not_has_text text="-N " />\n+ <has_text text="-e 100 " />\n+ <has_text text="-d 100 " />\n+ <has_text text="-p TCONS " />\n+ <not_has_text text="-C " />\n+ <not_has_text text="-A " />\n+ <not_has_text text="-X " />\n+ <not_has_text text="-K " />\n+ </assert_command>\n+ <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />\n+ <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />\n+ <output file="gffcompare_out2.tracking" name="transcripts_tracking" />\n+ <output file="gffcompare_out2.gtf" name="transcripts_combined" />\n+ </test>\n+\n <test expect_num_outputs="4">\n <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />\n- <param name="use_ref_annotation" value="Yes" />\n <conditional name="annotation">\n- <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />\n+ <param name="use_ref_annotation" value="Yes" />\n+ <conditional name="ref_source">\n+ <param name="ref_source_sel" value="history"/>\n+ <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />\n+ </conditional>\n <param name="ignore_nonoverlapping_reference" value="Yes" />\n <param name="ignore_nonoverlapping_transfrags" value="No" />\n <param name="refmap_tmap" value="" />\n@@ -166,10 +449,10 @@\n <param name="discard_single_exon" value="" />\n <param name="max_dist_exon" value="100" />\n <param name="max_dist_group" value="100" />\n- <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />\n- <output file="gffcompare_out2.loci" name="transcripts_loci" />\n- <output file="gffcompare_out2.tracking" name="transcripts_tracking" />\n- <output file="gffcompare_out2.gtf" name="transcripts_annotated" />\n+ <output file="gffcompare_out3.stats" name="transcripts_stats" lines_diff="6" />\n+ <output file="gffcompare_out3.loci" name="transcripts_loci" />\n+ <output file="gffcompare_out3.tracking" name="transcripts_tracking" />\n+ <output file="gffcompare_out3.gtf" name="transcripts_annotated" />\n </test>\n </tests>\n <help>\n@@ -182,6 +465,8 @@\n * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a\n annotation file (also in GTF/GFF3 format)\n \n+More information can be found here: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml.\n+\n The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"\n (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare\n are supported by GffCompare, while new features will likely be added to GffCompare in the future.\n' |
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| diff -r f99d7825a501 -r 2bb86e2c417f test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,30 @@ +#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: +# +test_buildid hg17 test_displayname ${__HERE__}/sequence.fa +#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 |
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| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gene_sets.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_sets.loc Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +#<unique_build_id> <dbkey> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +test_buildid hg17 test_displayname ${__HERE__}/gffcompare_in3.gtf + |
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| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_in1.gtf --- a/test-data/gffcompare_in1.gtf Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_in1.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,100 +1,11 @@\n-chr1\tCufflinks\ttranscript\t3111450\t3111490\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3111450\t3111490\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3111546\t3111576\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3111546\t3111576\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3200326\t3200352\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3200326\t3200352\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3200023\t3200191\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3201078\t3201481\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3201078\t3201481\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3201673\t3201699\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3201673\t3201699\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3204755\t3204833\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3204755\t3204833\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3212214\t3212292\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3212214\t3212292\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3213096\t3213192\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3213096\t3213192\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3212368\t3212439\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3212368\t3212439\t1000\t.\t.\tgene_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";\n-chr1\tCufflink'..b'71646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n-chr1\tCufflinks\ttranscript\t3391326\t3391352\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3391326\t3391352\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3435842\t3435880\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3435842\t3435880\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3447762\t3447788\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3447762\t3447788\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3450907\t3450965\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3450907\t3450965\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3451052\t3451109\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3451052\t3451109\t1000\t.\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t5\t10\t0.000000\t-\t.\tgene_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";\n+chr1\tCufflinks\texon\t2\t10\t0.000000\t-\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t15\t20\t0.000000\t-\t.\tgene_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";\n+chr1\tCufflinks\texon\t22\t30\t0.000000\t-\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t32\t37\t0.000000\t+\t.\tgene_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";\n+chr1\tCufflinks\texon\t32\t40\t0.000000\t+\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t42\t50\t0.000000\t+\t.\tgene_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";\n+chr1\tCufflinks\texon\t42\t50\t0.000000\t+\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t52\t60\t0.000000\t+\t.\tgene_id "CUFF.10"; transcript_id "CUFF.10.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t52\t60\t0.000000\t+\t.\tgene_id "CUFF.10"; transcript_id "CUFF.10.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+\n' |
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| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_in2.gtf --- a/test-data/gffcompare_in2.gtf Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_in2.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,100 +1,9 @@\n-chr1\tCufflinks\ttranscript\t3174766\t3174792\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3174766\t3174792\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3187402\t3187428\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3187402\t3187428\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3188522\t3188548\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3188522\t3188548\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3190859\t3191434\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3190859\t3191434\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3191513\t3192077\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3191513\t3192077\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3189811\t3190789\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3189811\t3190789\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3192251\t3192336\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3192251\t3192336\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3192650\t3192676\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3192650\t3192676\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3194707\t3194733\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3194707\t3194733\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3197426\t3197452\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3197426\t3197452\t1000\t.\t.\tgene_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";\n-chr1'..b'4.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";\n-chr1\tCufflinks\ttranscript\t3364872\t3364919\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3364872\t3364919\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3367211\t3367237\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3367211\t3367237\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3369581\t3369607\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3369581\t3369607\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3375002\t3375028\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3375002\t3375028\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3379889\t3379915\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3379889\t3379915\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\ttranscript\t3386740\t3386836\t1000\t.\t.\tgene_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";\n-chr1\tCufflinks\texon\t3386740\t3386836\t1000\t.\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t5\t10\t1000\t-\t.\tgene_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";\n+chr1\tCufflinks\texon\t2\t10\t1000\t-\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t15\t20\t1000\t+\t.\tgene_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";\n+chr1\tCufflinks\texon\t12\t20\t0.000000\t+\t.\tgene_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";\n+chr1\tCufflinks\ttranscript\t25\t30\t1000\t-\t.\tgene_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";\n+chr1\tCufflinks\texon\t22\t30\t0.000000\t-\t.\t 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";\n+chr1\tCufflinks\ttranscript\t42\t47\t1000\t+\t.\t 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";\n+chr1\tCufflinks\texon\t42\t47\t0.000000\t+\t.\tgene_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";\n+\n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_in3.gtf --- a/test-data/gffcompare_in3.gtf Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_in3.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,100 +1,10 @@\n-chr1\tmm9_refFlat\tstop_codon\t3206103\t3206105\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\tCDS\t3206106\t3207049\t0.000000\t-\t2\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\texon\t3204563\t3207049\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\tCDS\t3411783\t3411982\t0.000000\t-\t1\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\texon\t3411783\t3411982\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\tCDS\t3660633\t3661429\t0.000000\t-\t0\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\tstart_codon\t3661427\t3661429\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\texon\t3660633\t3661579\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n-chr1\tmm9_refFlat\tstop_codon\t4334681\t4334683\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\tCDS\t4334684\t4340172\t0.000000\t-\t2\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\texon\t4334224\t4340172\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\tCDS\t4341991\t4342162\t0.000000\t-\t0\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\texon\t4341991\t4342162\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\tCDS\t4342283\t4342906\t0.000000\t-\t0\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\tstart_codon\t4342904\t4342906\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\texon\t4342283\t4342918\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\texon\t4350281\t4350473\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n-chr1\tmm9_refFlat\tstop_codon\t4481797\t4481799\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\tCDS\t4481800\t4482749\t0.000000\t-\t2\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\texon\t4481009\t4482749\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\tCDS\t4483181\t4483487\t0.000000\t-\t0\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\tstart_codon\t4483485\t4483487\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\texon\t4483181\t4483547\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\texon\t4483853\t4483944\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\texon\t4485217\t4486023\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\texon\t4486372\t4486494\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n-chr1\tmm9_refFlat\tstop_codon\t4766545\t4766547\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tCDS\t4766548\t4766882\t0.000000\t-\t2\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\texon\t4763279\t4766882\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tCDS\t4767606\t4767729\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\texon\t4767606\t4767729\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tCDS\t4772649\t4772814\t0.000000\t-\t1\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\texon\t4772649\t4772814\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tCDS\t4774032\t4774186\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\texon\t4774032\t4774186\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tCDS\t4775654\t4775758\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tstart_codon\t4775756\t4775758\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\texon\t4775654\t4775807\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n-chr1\tmm9_refFlat\tstop_codon\t4764533\t4764535\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n-chr1\tmm9_refFlat\tCDS\t4764536\t4764597\t0.000000\t-\t2\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n-chr1\tmm9_refFlat\texon\t4763279\t4764597\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n-chr1\tmm9_refFlat\tCDS\t4767606\t4767729\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n-chr1\tmm9_refFlat\texon\t4767606\t'..b'2\t4827155\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\tCDS\t4829468\t4829569\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\texon\t4829468\t4829569\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\tCDS\t4831037\t4831213\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\texon\t4831037\t4831213\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\tCDS\t4835044\t4835094\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\tstop_codon\t4835095\t4835097\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\texon\t4835044\t4836816\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n-chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4857551\t4857613\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4868108\t4868213\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4868108\t4868213\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4876825\t4876912\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4876825\t4876912\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4879538\t4879683\t0.000000\t+\t1\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4879538\t4879683\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4880821\t4880877\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4880821\t4880877\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4881996\t4882150\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4881996\t4882150\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4883498\t4883644\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4883498\t4883644\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4885015\t4885086\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4885015\t4885086\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tCDS\t4886437\t4886442\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tstop_codon\t4886443\t4886445\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\texon\t4886437\t4887987\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n-chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n-chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n-chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n-chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\tCDS\t5\t10\t0.000000\t-\t0\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t2\t10\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t15\t20\t0.000000\t-\t0\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\texon\t12\t20\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tCDS\t25\t30\t0.000000\t-\t0\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t22\t30\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\tCDS\t32\t37\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t32\t40\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t42\t50\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t42\t50\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1-1.refmap --- a/test-data/gffcompare_out1-1.refmap Tue Feb 05 15:51:44 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -ref_gene_id ref_id class_code qry_id_list -Xkr4 Xkr4 c CUFF.13|CUFF.13.1 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1-1.tmap --- a/test-data/gffcompare_out1-1.tmap Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1-1.tmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,51 +1,7 @@ ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 1 20.607936 0.000000 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 1 27.255658 0.000000 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 1 31.293533 0.000000 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 1 9.999117 0.000000 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 1 17.776896 0.000000 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 1 31.293533 0.000000 2.000000 27 CUFF.11.1 - -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 1 10.695258 0.000000 0.683544 79 CUFF.13.1 3634 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 1 10.695258 0.000000 0.683544 79 CUFF.15.1 3634 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 1 8.710571 0.000000 0.556701 97 CUFF.17.1 3634 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 1 29.337687 0.000000 1.875000 72 CUFF.19.1 3634 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 1 13.851236 0.000000 0.885246 61 CUFF.21.1 3634 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 1 23.470150 0.000000 1.500000 54 CUFF.23.1 3634 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 1 14.567679 0.000000 0.931034 290 CUFF.25.1 3634 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 1 34.253732 0.000000 2.189189 37 CUFF.27.1 3634 -- - u CUFF.29 CUFF.29.1 1 107.103219 0.000000 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 1 122.650461 0.000000 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 1 109.527366 0.000000 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 1 96.747183 0.000000 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 1 104.085013 0.000000 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 1 23.912983 0.000000 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 1 10.695258 0.000000 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 1 10.561567 0.000000 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 1 20.708956 0.000000 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 1 20.607936 0.000000 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 1 15.646767 0.000000 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 1 31.293533 0.000000 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 1 31.293533 0.000000 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 1 31.293533 0.000000 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 1 15.646767 0.000000 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 1 15.646767 0.000000 1.000000 27 CUFF.59.1 - -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 1 45.263860 0.000000 2.892857 28 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 1 15.646767 0.000000 1.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 1 15.362280 0.000000 0.981818 55 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 1 12.998852 0.000000 0.830769 65 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 1 10.058636 0.000000 0.642857 84 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 1 8.621688 0.000000 0.551020 98 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 1 15.362280 0.000000 0.981818 55 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 1 31.293533 0.000000 2.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 1 16.248565 0.000000 1.038462 52 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 1 31.293533 0.000000 2.000000 27 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 1 13.201959 0.000000 0.843750 64 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 1 13.201959 0.000000 0.843750 96 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 1 31.293533 0.000000 2.000000 27 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 1 17.243375 0.000000 1.102041 49 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 1 16.567165 0.000000 1.058824 51 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 1 31.293533 0.000000 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 1 21.664754 0.000000 1.384615 39 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 1 46.940300 0.000000 3.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 1 21.481154 0.000000 1.372881 59 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 1 14.567679 0.000000 0.931034 58 CUFF.99.1 3634 +- - u CUFF.1 CUFF.1.1 1 20.607936 0.000000 1.317073 9 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 27.255658 0.000000 1.741935 6 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 1 31.293533 0.000000 2.000000 9 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 1 9.999117 0.000000 0.639053 9 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 1 17.776896 0.000000 1.136139 9 CUFF.9.1 - +- - u CUFF.10 CUFF.10.1 1 17.776896 0.000000 1.136139 9 CUFF.10.1 - |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1-2.refmap --- a/test-data/gffcompare_out1-2.refmap Tue Feb 05 15:51:44 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -ref_gene_id ref_id class_code qry_id_list |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1-2.tmap --- a/test-data/gffcompare_out1-2.tmap Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1-2.tmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,51 +1,5 @@ ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 1 35.211287 0.000000 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 1 35.211287 0.000000 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 1 21.226627 0.000000 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 1 29.709524 0.000000 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 1 34.072933 0.000000 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 1 32.531777 0.000000 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 1 16.582060 0.000000 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 1 35.211287 0.000000 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 1 35.211287 0.000000 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 1 35.211287 0.000000 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 1 35.211287 0.000000 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 1 16.205195 0.000000 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 1 35.211287 0.000000 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 1 29.709524 0.000000 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 1 13.581496 0.000000 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 1 22.635827 0.000000 1.285714 84 CUFF.31.1 - -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 1 23.767619 0.000000 1.350000 40 CUFF.33.1 3634 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 1 11.317914 0.000000 0.642857 84 CUFF.35.1 3634 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 1 11.500461 0.000000 0.653226 124 CUFF.37.1 3634 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 1 52.816931 0.000000 3.000000 27 CUFF.39.1 3634 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 1 43.213852 0.000000 2.454545 33 CUFF.41.1 3634 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 1 23.474191 0.000000 1.333333 81 CUFF.43.1 3634 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 1 20.667495 0.000000 1.173913 46 CUFF.45.1 3634 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 1 35.211287 0.000000 2.000000 27 CUFF.47.1 3634 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 1 35.211287 0.000000 2.000000 27 CUFF.49.1 3634 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 1 14.948188 0.000000 0.849057 477 CUFF.51.1 3634 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 1 52.816931 0.000000 3.000000 27 CUFF.53.1 3634 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 1 35.211287 0.000000 2.000000 27 CUFF.55.1 3634 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 1 35.211287 0.000000 2.000000 27 CUFF.57.1 3634 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 1 35.211287 0.000000 2.000000 27 CUFF.59.1 3634 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 1 13.204233 0.000000 0.750000 72 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 1 35.211287 0.000000 2.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 1 31.170648 0.000000 1.770492 61 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 1 15.681351 0.000000 0.890700 197 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 1 18.799247 0.000000 1.067797 354 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 1 22.635827 0.000000 1.285714 42 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 1 35.211287 0.000000 2.000000 27 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 1 52.816931 0.000000 3.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 1 17.605644 0.000000 1.000000 27 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 1 13.390208 0.000000 0.760563 71 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 1 11.211141 0.000000 0.636792 212 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 1 21.126772 0.000000 1.200000 45 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 1 19.014095 0.000000 1.080000 100 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 1 24.170460 0.000000 1.372881 59 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 1 29.709524 0.000000 1.687500 48 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 1 35.211287 0.000000 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 1 35.211287 0.000000 2.000000 27 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 1 35.211287 0.000000 2.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 1 35.211287 0.000000 2.000000 27 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 1 19.602160 0.000000 1.113402 97 CUFF.99.1 3634 +- - u CUFF.1 CUFF.1.1 1 35.211287 0.000000 2.000000 9 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 35.211287 0.000000 2.000000 9 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 1 21.226627 0.000000 1.205672 9 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 1 29.709524 0.000000 1.687500 6 CUFF.7.1 - |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1.gtf --- a/test-data/gffcompare_out1.gtf Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,200 +1,16 @@\n-chr1\tCufflinks\ttranscript\t3204755\t3204833\t.\t-\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000001"; gene_name "Xkr4"; oId "CUFF.13.1"; cmp_ref "Xkr4"; class_code "c"; tss_id "TSS1";\n-chr1\tCufflinks\texon\t3204755\t3204833\t.\t-\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3111450\t3111490\t.\t.\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";\n-chr1\tCufflinks\texon\t3111450\t3111490\t.\t.\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3111546\t3111576\t.\t.\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";\n-chr1\tCufflinks\texon\t3111546\t3111576\t.\t.\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3174766\t3174792\t.\t.\t.\ttranscript_id "TCONS_00000051"; gene_id "XLOC_000004"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";\n-chr1\tCufflinks\texon\t3174766\t3174792\t.\t.\t.\ttranscript_id "TCONS_00000051"; gene_id "XLOC_000004"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3187402\t3187428\t.\t.\t.\ttranscript_id "TCONS_00000052"; gene_id "XLOC_000005"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";\n-chr1\tCufflinks\texon\t3187402\t3187428\t.\t.\t.\ttranscript_id "TCONS_00000052"; gene_id "XLOC_000005"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3188522\t3188548\t.\t.\t.\ttranscript_id "TCONS_00000053"; gene_id "XLOC_000006"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";\n-chr1\tCufflinks\texon\t3188522\t3188548\t.\t.\t.\ttranscript_id "TCONS_00000053"; gene_id "XLOC_000006"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3189811\t3190789\t.\t.\t.\ttranscript_id "TCONS_00000054"; gene_id "XLOC_000007"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";\n-chr1\tCufflinks\texon\t3189811\t3190789\t.\t.\t.\ttranscript_id "TCONS_00000054"; gene_id "XLOC_000007"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3189900\t3190041\t.\t.\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000007"; oId "CUFF.29.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS7";\n-chr1\tCufflinks\texon\t3189900\t3190041\t.\t.\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000007"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3190273\t3190303\t.\t.\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000007"; oId "CUFF.31.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS8";\n-chr1\tCufflinks\texon\t3190273\t3190303\t.\t.\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000007"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3190455\t3190481\t.\t.\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000007"; oId "CUFF.33.1"; contained_in "TCONS_00000054"; class_code "u"; tss_id "TSS9";\n-chr1\tCufflinks\texon\t3190455\t3190481\t.\t.\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000007"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3190859\t3191434\t.\t.\t.\ttranscript_id "TCONS_00000055"; gene_id "XLOC_000008"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";\n-chr1\tCufflinks\texon\t3190859\t3191434\t.\t.\t.\ttranscript_id "TCONS_00000055"; gene_id "XLOC_000008"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3191513\t3192077\t.\t.\t.\ttranscript_id "TCONS_00000056"; gene_id "XLOC_000009"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";\n-chr1\tCufflinks\texon\t3191513\t3192077\t.\t.\t.\ttranscript_id "TCONS_00000056"; gene_id "XLOC_000009"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3191539\t3191669\t.\t.\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000009"; oId "CUFF.35.1"; contained_in "TCONS_00000056"; class_code "u"; tss_id "TSS11";\n-chr1\tCufflinks\texon\t3191539\t3191669\t.\t.\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000009"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3191877\t3191945\t.\t.\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000009"; oId "CUFF.37.1"; contained_in "TCONS_00000056"; class_code "u"; tss_id "TSS12";\n-chr1\tCufflinks\texon\t3191877\t3191945\t.\t.\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000009"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3192251\t3192336\t.\t.\t.\ttranscr'..b'on_number "1";\n-chr1\tCufflinks\ttranscript\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000099"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n-chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000099"; gene_id "XLOC_000081"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000100"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n-chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000100"; gene_id "XLOC_000082"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3391326\t3391352\t.\t.\t.\ttranscript_id "TCONS_00000046"; gene_id "XLOC_000083"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS89";\n-chr1\tCufflinks\texon\t3391326\t3391352\t.\t.\t.\ttranscript_id "TCONS_00000046"; gene_id "XLOC_000083"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3435842\t3435880\t.\t.\t.\ttranscript_id "TCONS_00000047"; gene_id "XLOC_000084"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS90";\n-chr1\tCufflinks\texon\t3435842\t3435880\t.\t.\t.\ttranscript_id "TCONS_00000047"; gene_id "XLOC_000084"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3447762\t3447788\t.\t.\t.\ttranscript_id "TCONS_00000048"; gene_id "XLOC_000085"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS91";\n-chr1\tCufflinks\texon\t3447762\t3447788\t.\t.\t.\ttranscript_id "TCONS_00000048"; gene_id "XLOC_000085"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3450907\t3450965\t.\t.\t.\ttranscript_id "TCONS_00000049"; gene_id "XLOC_000086"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS92";\n-chr1\tCufflinks\texon\t3450907\t3450965\t.\t.\t.\ttranscript_id "TCONS_00000049"; gene_id "XLOC_000086"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3451052\t3451109\t.\t.\t.\ttranscript_id "TCONS_00000050"; gene_id "XLOC_000087"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS93";\n-chr1\tCufflinks\texon\t3451052\t3451109\t.\t.\t.\ttranscript_id "TCONS_00000050"; gene_id "XLOC_000087"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t12\t20\t.\t+\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000001"; oId "CUFF.3.1"; tss_id "TSS1";\n+chr1\tCufflinks\texon\t12\t20\t.\t+\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000001"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t32\t40\t.\t+\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000002"; oId "CUFF.7.1"; tss_id "TSS2";\n+chr1\tCufflinks\texon\t32\t40\t.\t+\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000002"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t42\t47\t.\t+\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000003"; oId "CUFF.7.1"; contained_in "TCONS_00000002"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t42\t47\t.\t+\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000003"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t42\t50\t.\t+\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000003"; oId "CUFF.9.1"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t42\t50\t.\t+\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000003"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t52\t60\t.\t+\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000004"; oId "CUFF.10.1"; tss_id "TSS4";\n+chr1\tCufflinks\texon\t52\t60\t.\t+\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000004"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t2\t10\t.\t-\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000005"; oId "CUFF.1.1"; tss_id "TSS5";\n+chr1\tCufflinks\texon\t2\t10\t.\t-\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000005"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t15\t20\t.\t-\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000006"; oId "CUFF.3.1"; tss_id "TSS6";\n+chr1\tCufflinks\texon\t15\t20\t.\t-\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000006"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t22\t30\t.\t-\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000007"; oId "CUFF.5.1"; tss_id "TSS7";\n+chr1\tCufflinks\texon\t22\t30\t.\t-\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000007"; exon_number "1";\n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1.loci --- a/test-data/gffcompare_out1.loci Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1.loci Mon May 27 13:54:15 2019 -0400 |
| [ |
| @@ -1,87 +1,7 @@ -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 - +XLOC_000001 chr1[+]12-20 - - CUFF.3.1 +XLOC_000002 chr1[+]32-40 - CUFF.7.1 - +XLOC_000003 chr1[+]42-50 - CUFF.9.1 CUFF.7.1 +XLOC_000004 chr1[+]52-60 - CUFF.10.1 - +XLOC_000005 chr1[-]2-10 - CUFF.1.1 CUFF.1.1 +XLOC_000006 chr1[-]15-20 - CUFF.3.1 - +XLOC_000007 chr1[-]22-30 - - CUFF.5.1 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1.stats --- a/test-data/gffcompare_out1.stats Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1.stats Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,35 +1,15 @@ -# gffcompare v0.10.6 | Command line was: -#gffcompare -r /tmp/tmp7AvPf0/files/000/dataset_3.dat -R -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf +# gffcompare v0.11.2 | Command line was: +#gffcompare -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf # #= Summary for dataset: gffcompare_in1_gtf -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# Query mRNAs : 5 in 5 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: gffcompare_in2_gtf -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# Query mRNAs : 4 in 4 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 + Total union super-loci across all input datasets: 7 (0 multi-transcript, ~1.1 transcripts per locus) -100 out of 100 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant) +8 out of 8 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant) |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out1.tracking --- a/test-data/gffcompare_out1.tracking Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out1.tracking Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,100 +1,8 @@\n-TCONS_00000001\tXLOC_000001\tXkr4|Xkr4\tc\tq1:CUFF.13|CUFF.13.1|1|10.695258|0.000000|0.683544|79\t-\n-TCONS_00000002\tXLOC_000002\t-\tu\tq1:CUFF.1|CUFF.1.1|1|20.607936|0.000000|1.317073|41\t-\n-TCONS_00000003\tXLOC_000003\t-\tu\tq1:CUFF.3|CUFF.3.1|1|27.255658|0.000000|1.741935|31\t-\n-TCONS_00000004\tXLOC_000007\t-\tu\tq1:CUFF.29|CUFF.29.1|1|107.103219|0.000000|6.845070|142\t-\n-TCONS_00000005\tXLOC_000007\t-\tu\tq1:CUFF.31|CUFF.31.1|1|122.650461|0.000000|7.838710|31\t-\n-TCONS_00000006\tXLOC_000007\t-\tu\tq1:CUFF.33|CUFF.33.1|1|109.527366|0.000000|7.000000|27\t-\n-TCONS_00000007\tXLOC_000009\t-\tu\tq1:CUFF.35|CUFF.35.1|1|96.747183|0.000000|6.183206|131\t-\n-TCONS_00000008\tXLOC_000009\t-\tu\tq1:CUFF.37|CUFF.37.1|1|104.085013|0.000000|6.652174|69\t-\n-TCONS_00000009\tXLOC_000011\t-\tu\tq1:CUFF.39|CUFF.39.1|1|23.912983|0.000000|1.528302|53\t-\n-TCONS_00000010\tXLOC_000012\t-\tu\tq1:CUFF.41|CUFF.41.1|1|10.695258|0.000000|0.683544|79\t-\n-TCONS_00000011\tXLOC_000014\t-\tu\tq1:CUFF.43|CUFF.43.1|1|10.561567|0.000000|0.675000|80\t-\n-TCONS_00000012\tXLOC_000015\t-\tu\tq1:CUFF.45|CUFF.45.1|1|20.708956|0.000000|1.323529|102\t-\n-TCONS_00000013\tXLOC_000016\t-\tu\tq1:CUFF.47|CUFF.47.1|1|20.607936|0.000000|1.317073|41\t-\n-TCONS_00000014\tXLOC_000017\t-\tu\tq1:CUFF.49|CUFF.49.1|1|15.646767|0.000000|1.000000|27\t-\n-TCONS_00000015\tXLOC_000019\t-\tu\tq1:CUFF.51|CUFF.51.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000016\tXLOC_000020\t-\tu\tq1:CUFF.53|CUFF.53.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000017\tXLOC_000021\t-\tu\tq1:CUFF.55|CUFF.55.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000018\tXLOC_000022\t-\tu\tq1:CUFF.57|CUFF.57.1|1|15.646767|0.000000|1.000000|27\t-\n-TCONS_00000019\tXLOC_000023\t-\tu\tq1:CUFF.59|CUFF.59.1|1|15.646767|0.000000|1.000000|27\t-\n-TCONS_00000020\tXLOC_000025\t-\tu\tq1:CUFF.7|CUFF.7.1|1|9.999117|0.000000|0.639053|169\t-\n-TCONS_00000021\tXLOC_000026\t-\tu\tq1:CUFF.5|CUFF.5.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000022\tXLOC_000029\t-\tu\tq1:CUFF.9|CUFF.9.1|1|17.776896|0.000000|1.136139|404\t-\n-TCONS_00000023\tXLOC_000031\t-\tu\tq1:CUFF.11|CUFF.11.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000024\tXLOC_000034\tXkr4|Xkr4\ti\tq1:CUFF.15|CUFF.15.1|1|10.695258|0.000000|0.683544|79\t-\n-TCONS_00000025\tXLOC_000035\tXkr4|Xkr4\ti\tq1:CUFF.19|CUFF.19.1|1|29.337687|0.000000|1.875000|72\t-\n-TCONS_00000026\tXLOC_000037\tXkr4|Xkr4\ti\tq1:CUFF.17|CUFF.17.1|1|8.710571|0.000000|0.556701|97\t-\n-TCONS_00000027\tXLOC_000040\tXkr4|Xkr4\ti\tq1:CUFF.25|CUFF.25.1|1|14.567679|0.000000|0.931034|290\t-\n-TCONS_00000028\tXLOC_000042\tXkr4|Xkr4\ti\tq1:CUFF.21|CUFF.21.1|1|13.851236|0.000000|0.885246|61\t-\n-TCONS_00000029\tXLOC_000044\tXkr4|Xkr4\ti\tq1:CUFF.23|CUFF.23.1|1|23.470150|0.000000|1.500000|54\t-\n-TCONS_00000030\tXLOC_000046\tXkr4|Xkr4\ti\tq1:CUFF.27|CUFF.27.1|1|34.253732|0.000000|2.189189|37\t-\n-TCONS_00000031\tXLOC_000048\tXkr4|Xkr4\ti\tq1:CUFF.61|CUFF.61.1|1|45.263860|0.000000|2.892857|28\t-\n-TCONS_00000032\tXLOC_000049\tXkr4|Xkr4\ti\tq1:CUFF.63|CUFF.63.1|1|15.646767|0.000000|1.000000|27\t-\n-TCONS_00000033\tXLOC_000052\tXkr4|Xkr4\ti\tq1:CUFF.65|CUFF.65.1|1|15.362280|0.000000|0.981818|55\t-\n-TCONS_00000034\tXLOC_000057\tXkr4|Xkr4\ti\tq1:CUFF.67|CUFF.67.1|1|12.998852|0.000000|0.830769|65\t-\n-TCONS_00000035\tXLOC_000059\tXkr4|Xkr4\ti\tq1:CUFF.69|CUFF.69.1|1|10.058636|0.000000|0.642857|84\t-\n-TCONS_00000036\tXLOC_000059\tXkr4|Xkr4\ti\tq1:CUFF.71|CUFF.71.1|1|8.621688|0.000000|0.551020|98\t-\n-TCONS_00000037\tXLOC_000060\tXkr4|Xkr4\ti\tq1:CUFF.73|CUFF.73.1|1|15.362280|0.000000|0.981818|55\t-\n-TCONS_00000038\tXLOC_000062\tXkr4|Xkr4\ti\tq1:CUFF.75|CUFF.75.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000039\tXLOC_000065\tXkr4|Xkr4\ti\tq1:CUFF.77|CUFF.77.1|1|16.248565|0.000000|1.038462|52\t-\n-TCONS_00000040\tXLOC_000068\tXkr4|Xkr4\ti\tq1:CUFF.79|CUFF.79.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000041\tXLOC_000071\tXkr4|Xkr4\ti\tq1:CUFF.81|CUFF.81.1|1|13.201959|0.000000|0.843750|64\t-\n-TCONS_00000042\tXLOC_000073\tXkr4|Xkr4\ti\tq1:CUFF.83|CUFF.83.1|1|13.201959|0.000000|0.843750|96\t-\n-TCONS_00000043\tXLOC_000075\tXkr4|Xkr4\ti\tq1:CUFF.85|CUFF.85.1|1|31.293533|0.000000|2.000000|27\t-\n-TCONS_00000044\tXLOC_000077\tXkr4'..b'TCONS_00000067\tXLOC_000033\tXkr4|Xkr4\ti\t-\tq2:CUFF.33|CUFF.33.1|1|23.767619|0.000000|1.350000|40\n-TCONS_00000068\tXLOC_000036\tXkr4|Xkr4\ti\t-\tq2:CUFF.35|CUFF.35.1|1|11.317914|0.000000|0.642857|84\n-TCONS_00000069\tXLOC_000037\tXkr4|Xkr4\ti\t-\tq2:CUFF.37|CUFF.37.1|1|11.500461|0.000000|0.653226|124\n-TCONS_00000070\tXLOC_000038\tXkr4|Xkr4\ti\t-\tq2:CUFF.39|CUFF.39.1|1|52.816931|0.000000|3.000000|27\n-TCONS_00000071\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|1|43.213852|0.000000|2.454545|33\n-TCONS_00000072\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|1|23.474191|0.000000|1.333333|81\n-TCONS_00000073\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|1|20.667495|0.000000|1.173913|46\n-TCONS_00000074\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000075\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000076\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|1|14.948188|0.000000|0.849057|477\n-TCONS_00000077\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|1|52.816931|0.000000|3.000000|27\n-TCONS_00000078\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000079\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000080\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000081\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|1|13.204233|0.000000|0.750000|72\n-TCONS_00000082\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000083\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|1|31.170648|0.000000|1.770492|61\n-TCONS_00000084\tXLOC_000059\tXkr4|Xkr4\ti\t-\tq2:CUFF.69|CUFF.69.1|1|18.799247|0.000000|1.067797|354\n-TCONS_00000085\tXLOC_000060\tXkr4|Xkr4\ti\t-\tq2:CUFF.67|CUFF.67.1|1|15.681351|0.000000|0.890700|197\n-TCONS_00000086\tXLOC_000061\tXkr4|Xkr4\ti\t-\tq2:CUFF.71|CUFF.71.1|1|22.635827|0.000000|1.285714|42\n-TCONS_00000087\tXLOC_000063\tXkr4|Xkr4\ti\t-\tq2:CUFF.73|CUFF.73.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000088\tXLOC_000064\tXkr4|Xkr4\ti\t-\tq2:CUFF.75|CUFF.75.1|1|52.816931|0.000000|3.000000|27\n-TCONS_00000089\tXLOC_000066\tXkr4|Xkr4\ti\t-\tq2:CUFF.77|CUFF.77.1|1|17.605644|0.000000|1.000000|27\n-TCONS_00000090\tXLOC_000067\tXkr4|Xkr4\ti\t-\tq2:CUFF.79|CUFF.79.1|1|13.390208|0.000000|0.760563|71\n-TCONS_00000091\tXLOC_000068\tXkr4|Xkr4\ti\t-\tq2:CUFF.81|CUFF.81.1|1|11.211141|0.000000|0.636792|212\n-TCONS_00000092\tXLOC_000069\tXkr4|Xkr4\ti\t-\tq2:CUFF.83|CUFF.83.1|1|21.126772|0.000000|1.200000|45\n-TCONS_00000093\tXLOC_000070\tXkr4|Xkr4\ti\t-\tq2:CUFF.85|CUFF.85.1|1|19.014095|0.000000|1.080000|100\n-TCONS_00000094\tXLOC_000072\tXkr4|Xkr4\ti\t-\tq2:CUFF.87|CUFF.87.1|1|24.170460|0.000000|1.372881|59\n-TCONS_00000095\tXLOC_000074\tXkr4|Xkr4\ti\t-\tq2:CUFF.89|CUFF.89.1|1|29.709524|0.000000|1.687500|48\n-TCONS_00000096\tXLOC_000076\tXkr4|Xkr4\ti\t-\tq2:CUFF.91|CUFF.91.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000097\tXLOC_000078\tXkr4|Xkr4\ti\t-\tq2:CUFF.93|CUFF.93.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000098\tXLOC_000079\tXkr4|Xkr4\ti\t-\tq2:CUFF.95|CUFF.95.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000099\tXLOC_000081\tXkr4|Xkr4\ti\t-\tq2:CUFF.97|CUFF.97.1|1|35.211287|0.000000|2.000000|27\n-TCONS_00000100\tXLOC_000082\tXkr4|Xkr4\ti\t-\tq2:CUFF.99|CUFF.99.1|1|19.602160|0.000000|1.113402|97\n+TCONS_00000001\tXLOC_000002\t-\tu\tq1:CUFF.7|CUFF.7.1|1|9.999117|0.000000|0.639053|9\t-\n+TCONS_00000002\tXLOC_000003\t-\tu\tq1:CUFF.9|CUFF.9.1|1|17.776896|0.000000|1.136139|9\t-\n+TCONS_00000003\tXLOC_000004\t-\tu\tq1:CUFF.10|CUFF.10.1|1|17.776896|0.000000|1.136139|9\t-\n+TCONS_00000004\tXLOC_000005\t-\tu\tq1:CUFF.1|CUFF.1.1|1|20.607936|0.000000|1.317073|9\tq2:CUFF.1|CUFF.1.1|1|35.211287|0.000000|2.000000|9\n+TCONS_00000005\tXLOC_000006\t-\tu\tq1:CUFF.3|CUFF.3.1|1|27.255658|0.000000|1.741935|6\t-\n+TCONS_00000006\tXLOC_000001\t-\tu\t-\tq2:CUFF.3|CUFF.3.1|1|35.211287|0.000000|2.000000|9\n+TCONS_00000007\tXLOC_000003\t-\tu\t-\tq2:CUFF.7|CUFF.7.1|1|29.709524|0.000000|1.687500|6\n+TCONS_00000008\tXLOC_000007\t-\tu\t-\tq2:CUFF.5|CUFF.5.1|1|21.226627|0.000000|1.205672|9\n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2-1.refmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2-1.refmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code qry_id_list +Lypla1 Lypla1 c CUFF.7|CUFF.7.1 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2-1.tmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2-1.tmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 1 20.607936 0.000000 1.317073 9 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 27.255658 0.000000 1.741935 6 CUFF.3.1 - +Lypla1 Lypla1 c CUFF.7 CUFF.7.1 1 9.999117 0.000000 0.639053 9 CUFF.7.1 19 +Lypla1 Lypla1 c CUFF.9 CUFF.9.1 1 17.776896 0.000000 1.136139 9 CUFF.9.1 19 +Lypla1 Lypla1 p CUFF.10 CUFF.10.1 1 17.776896 0.000000 1.136139 9 CUFF.10.1 19 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2-2.refmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2-2.refmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code qry_id_list +Lypla1 Lypla1 c CUFF.7|CUFF.7.1 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2-2.tmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2-2.tmap Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 1 35.211287 0.000000 2.000000 9 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 35.211287 0.000000 2.000000 9 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 1 21.226627 0.000000 1.205672 9 CUFF.5.1 - +Lypla1 Lypla1 c CUFF.7 CUFF.7.1 1 29.709524 0.000000 1.687500 6 CUFF.7.1 19 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2.gtf --- a/test-data/gffcompare_out2.gtf Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out2.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -1,206 +1,16 @@\n-chr1\tStringTie\ttranscript\t160930303\t160940234\t.\t+\t.\ttranscript_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";\n-chr1\tStringTie\texon\t160930303\t160930344\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1";\n-chr1\tStringTie\texon\t160938112\t160938232\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "2";\n-chr1\tStringTie\texon\t160939995\t160940234\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "3";\n-chr1\tStringTie\ttranscript\t160940817\t160967997\t.\t+\t.\ttranscript_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";\n-chr1\tStringTie\texon\t160940817\t160940994\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "1";\n-chr1\tStringTie\texon\t160942528\t160942728\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "2";\n-chr1\tStringTie\texon\t160946534\t160946666\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "3";\n-chr1\tStringTie\texon\t160948307\t160948425\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "4";\n-chr1\tStringTie\texon\t160950222\t160950334\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "5";\n-chr1\tStringTie\texon\t160950841\t160951122\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "6";\n-chr1\tStringTie\texon\t160951615\t160951829\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "7";\n-chr1\tStringTie\texon\t160954784\t160955151\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "8";\n-chr1\tStringTie\texon\t160955815\t160955979\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "9";\n-chr1\tStringTie\texon\t160959401\t160959553\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "10";\n-chr1\tStringTie\texon\t160962271\t160962484\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "11";\n-chr1\tStringTie\texon\t160963479\t160963569\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "12";\n-chr1\tStringTie\texon\t160963708\t160963840\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "13";\n-chr1\tStringTie\texon\t160964950\t160965120\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "14";\n-chr1\tStringTie\texon\t160965673\t160965788\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "15";\n-chr1\tStringTie\texon\t160967647\t160967997\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "16";\n-chr1\tStringTie\ttranscript\t160968644\t160972020\t.\t+\t.\ttranscript_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";\n-chr1\tStringTie\texon\t160968644\t160972020\t.\t+\t.\ttranscript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1";\n-chr1\tStringTie\ttranscript\t160972938\t160974977\t.\t+\t.\ttranscript_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";\n-chr1\tStringTie\texon\t160972938\t160974977\t.\t+\t.\ttranscript_id "MSTRG.6.1"; gene_id "MSTRG.6"; exon_number "1";\n-chr1\tStringTie\ttranscript\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS5";\n-chr1\tStringTie\texon\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; exon_number "1";\n-chr1\tStringTie\ttranscript\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS6";\n-chr1\tStringTie\texon\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; exon_number "1";\n-chr1\tStringTie\ttranscript\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS7";\n-chr1\tStringTie\texon\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; exon_number "1";\n-chr1\tStringTie\ttranscript\t161009768\t161010195\t.\t+\t.\ttranscript_id "MSTRG.13.1"; gene_id "M'..b' gene_id "MSTRG.25"; exon_number "1";\n-chr1\tStringTie\ttranscript\t161090412\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "="; tss_id "TSS32";\n-chr1\tStringTie\texon\t161090412\t161090511\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "1";\n-chr1\tStringTie\texon\t161093681\t161093787\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "2";\n-chr1\tStringTie\texon\t161095529\t161095737\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "3";\n-chr1\tStringTie\texon\t161098263\t161098396\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "4";\n-chr1\tStringTie\texon\t161099142\t161099285\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "5";\n-chr1\tStringTie\texon\t161101451\t161101634\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "6";\n-chr1\tStringTie\texon\t161102979\t161103094\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "7";\n-chr1\tStringTie\texon\t161105401\t161105495\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "8";\n-chr1\tStringTie\texon\t161106707\t161106865\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "9";\n-chr1\tStringTie\texon\t161109222\t161109795\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "10";\n-chr1\tStringTie\texon\t161130389\t161130452\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "11";\n-chr1\tStringTie\texon\t161131363\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "12";\n-chr1\tStringTie\ttranscript\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; xloc "XLOC_000021"; class_code "u"; tss_id "TSS33";\n-chr1\tStringTie\texon\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t12\t20\t.\t+\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000001"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS1";\n+chr1\tCufflinks\texon\t12\t20\t.\t+\t.\ttranscript_id "TCONS_00000006"; gene_id "XLOC_000001"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t32\t40\t.\t+\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000002"; gene_name "Lypla1"; oId "CUFF.7.1"; cmp_ref "Lypla1"; class_code "c"; tss_id "TSS2";\n+chr1\tCufflinks\texon\t32\t40\t.\t+\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000002"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t42\t47\t.\t+\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000002"; gene_name "Lypla1"; oId "CUFF.7.1"; contained_in "TCONS_00000002"; cmp_ref "Lypla1"; class_code "c"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t42\t47\t.\t+\t.\ttranscript_id "TCONS_00000007"; gene_id "XLOC_000002"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t42\t50\t.\t+\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; gene_name "Lypla1"; oId "CUFF.9.1"; cmp_ref "Lypla1"; class_code "c"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t42\t50\t.\t+\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t52\t60\t.\t+\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; gene_name "Lypla1"; oId "CUFF.10.1"; cmp_ref "Lypla1"; class_code "p"; tss_id "TSS4";\n+chr1\tCufflinks\texon\t52\t60\t.\t+\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t2\t10\t.\t-\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000004"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS5";\n+chr1\tCufflinks\texon\t2\t10\t.\t-\t.\ttranscript_id "TCONS_00000004"; gene_id "XLOC_000004"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t15\t20\t.\t-\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000005"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS6";\n+chr1\tCufflinks\texon\t15\t20\t.\t-\t.\ttranscript_id "TCONS_00000005"; gene_id "XLOC_000005"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t22\t30\t.\t-\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000006"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS7";\n+chr1\tCufflinks\texon\t22\t30\t.\t-\t.\ttranscript_id "TCONS_00000008"; gene_id "XLOC_000006"; exon_number "1";\n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2.loci --- a/test-data/gffcompare_out2.loci Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out2.loci Mon May 27 13:54:15 2019 -0400 |
| [ |
| @@ -1,21 +1,6 @@ -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 +XLOC_000001 chr1[+]12-20 - - CUFF.3.1 +XLOC_000002 chr1[+]32-50 Lypla1|Lypla1 CUFF.7.1,CUFF.9.1 CUFF.7.1 +XLOC_000003 chr1[+]52-60 - CUFF.10.1 - +XLOC_000004 chr1[-]2-10 - CUFF.1.1 CUFF.1.1 +XLOC_000005 chr1[-]15-20 - CUFF.3.1 - +XLOC_000006 chr1[-]22-30 - - CUFF.5.1 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2.stats --- a/test-data/gffcompare_out2.stats Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out2.stats Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,30 +1,47 @@ -# gffcompare v0.10.6 | Command line was: -#gffcompare -r /tmp/tmp7AvPf0/files/000/dataset_13.dat -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf +# gffcompare v0.11.2 | Command line was: +#gffcompare -r ref_annotation -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf # -#= Summary for dataset: gffcompare_in4_gtf -# 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 +#= Summary for dataset: gffcompare_in1_gtf +# Query mRNAs : 5 in 5 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (0 multi-exon) +# Super-loci w/ reference transcripts: 1 #-----------------| Sensitivity | Precision | - Base level: 72.6 | 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 | + Base level: 94.7 | 42.9 | + Exon level: 100.0 | 40.0 | + Transcript level: 0.0 | 0.0 | + Locus level: 0.0 | 0.0 | + + Matching intron chains: 0 + Matching transcripts: 0 + Matching loci: 0 + + Missed exons: 0/1 ( 0.0%) + Novel exons: 3/5 ( 60.0%) + Missed loci: 0/1 ( 0.0%) + Novel loci: 3/5 ( 60.0%) - Matching intron chains: 2 - Matching transcripts: 2 - Matching loci: 2 +#= Summary for dataset: gffcompare_in2_gtf +# Query mRNAs : 4 in 4 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (0 multi-exon) +# Super-loci w/ reference transcripts: 1 +#-----------------| Sensitivity | Precision | + Base level: 31.6 | 18.2 | + Exon level: 100.0 | 25.0 | + Transcript level: 0.0 | 0.0 | + Locus level: 0.0 | 0.0 | - 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%) + Matching intron chains: 0 + Matching transcripts: 0 + Matching loci: 0 - Total union super-loci across all input datasets: 21 -35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) + Missed exons: 0/1 ( 0.0%) + Novel exons: 3/4 ( 75.0%) + Missed loci: 0/1 ( 0.0%) + Novel loci: 3/4 ( 75.0%) + + Total union super-loci across all input datasets: 6 + (0 multi-transcript, ~1.3 transcripts per locus) +8 out of 8 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant) |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out2.tracking --- a/test-data/gffcompare_out2.tracking Tue Feb 05 15:51:44 2019 -0500 +++ b/test-data/gffcompare_out2.tracking Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,35 +1,8 @@ -TCONS_00000001 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.3|MSTRG.3.1|3|0.000000|0.000000|0.000000|403 -TCONS_00000002 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.4|MSTRG.4.1|16|0.000000|0.000000|0.000000|3003 -TCONS_00000003 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.5|MSTRG.5.1|1|0.000000|0.000000|0.000000|3377 -TCONS_00000004 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.6|MSTRG.6.1|1|0.000000|0.000000|0.000000|2040 -TCONS_00000005 XLOC_000002 - u q1:MSTRG.7|MSTRG.7.1|1|0.000000|0.000000|0.000000|432 -TCONS_00000006 XLOC_000003 - u q1:MSTRG.10|MSTRG.10.1|1|0.000000|0.000000|0.000000|316 -TCONS_00000007 XLOC_000004 - u q1:MSTRG.12|MSTRG.12.1|1|0.000000|0.000000|0.000000|251 -TCONS_00000008 XLOC_000005 - u q1:MSTRG.13|MSTRG.13.1|1|0.000000|0.000000|0.000000|428 -TCONS_00000009 XLOC_000006 uc007der.1|uc007der.1 x q1:MSTRG.14|MSTRG.14.1|1|0.000000|0.000000|0.000000|250 -TCONS_00000010 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.1|11|0.000000|0.000000|0.000000|800 -TCONS_00000011 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.2|12|0.000000|0.000000|0.000000|608 -TCONS_00000012 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.3|11|0.000000|0.000000|0.000000|1008 -TCONS_00000013 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.4|11|0.000000|0.000000|0.000000|531 -TCONS_00000014 XLOC_000007 uc007dev.1|uc007dev.1 = q1:MSTRG.16|MSTRG.16.5|11|0.000000|0.000000|0.000000|807 -TCONS_00000015 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.1|16|0.000000|0.000000|0.000000|2459 -TCONS_00000016 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.2|6|0.000000|0.000000|0.000000|903 -TCONS_00000017 XLOC_000009 uc007dfd.3|uc007dfd.3 c q1:MSTRG.20|MSTRG.20.1|3|0.000000|0.000000|0.000000|716 -TCONS_00000018 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.21|MSTRG.21.1|1|0.000000|0.000000|0.000000|466 -TCONS_00000019 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.22|MSTRG.22.1|1|0.000000|0.000000|0.000000|224 -TCONS_00000020 XLOC_000009 uc056yep.1|uc056yep.1 c q1:MSTRG.23|MSTRG.23.1|1|0.000000|0.000000|0.000000|1316 -TCONS_00000021 XLOC_000010 uc007dff.1|uc007dff.1 x q1:MSTRG.24|MSTRG.24.1|1|0.000000|0.000000|0.000000|417 -TCONS_00000022 XLOC_000011 uc007dff.1|uc007dff.1 s q1:MSTRG.26|MSTRG.26.1|12|0.000000|0.000000|0.000000|3033 -TCONS_00000023 XLOC_000012 uc007dff.1|uc007dff.1 i q1:MSTRG.28|MSTRG.28.1|1|0.000000|0.000000|0.000000|213 -TCONS_00000024 XLOC_000013 - u q1:MSTRG.1|MSTRG.1.1|1|0.000000|0.000000|0.000000|447 -TCONS_00000025 XLOC_000014 - u q1:MSTRG.2|MSTRG.2.1|1|0.000000|0.000000|0.000000|349 -TCONS_00000026 XLOC_000015 - u q1:MSTRG.8|MSTRG.8.1|1|0.000000|0.000000|0.000000|1112 -TCONS_00000027 XLOC_000016 - u q1:MSTRG.9|MSTRG.9.1|1|0.000000|0.000000|0.000000|773 -TCONS_00000028 XLOC_000017 - u q1:MSTRG.11|MSTRG.11.1|1|0.000000|0.000000|0.000000|257 -TCONS_00000029 XLOC_000018 uc007des.1|uc007des.1 c q1:MSTRG.15|MSTRG.15.1|1|0.000000|0.000000|0.000000|353 -TCONS_00000030 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.17|MSTRG.17.1|6|0.000000|0.000000|0.000000|1029 -TCONS_00000031 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.19|MSTRG.19.1|11|0.000000|0.000000|0.000000|1514 -TCONS_00000032 XLOC_000019 uc007dey.2|uc007dey.2 j q1:MSTRG.19|MSTRG.19.2|10|0.000000|0.000000|0.000000|1478 -TCONS_00000033 XLOC_000020 uc007dff.1|uc007dff.1 c q1:MSTRG.25|MSTRG.25.1|1|0.000000|0.000000|0.000000|1361 -TCONS_00000034 XLOC_000020 uc007dff.1|uc007dff.1 = q1:MSTRG.27|MSTRG.27.1|12|0.000000|0.000000|0.000000|2016 -TCONS_00000035 XLOC_000021 - u q1:MSTRG.29|MSTRG.29.1|1|0.000000|0.000000|0.000000|223 +TCONS_00000001 XLOC_000002 Lypla1|Lypla1 c q1:CUFF.7|CUFF.7.1|1|9.999117|0.000000|0.639053|9 - +TCONS_00000002 XLOC_000002 Lypla1|Lypla1 c q1:CUFF.9|CUFF.9.1|1|17.776896|0.000000|1.136139|9 - +TCONS_00000003 XLOC_000003 Lypla1|Lypla1 p q1:CUFF.10|CUFF.10.1|1|17.776896|0.000000|1.136139|9 - +TCONS_00000004 XLOC_000004 - u q1:CUFF.1|CUFF.1.1|1|20.607936|0.000000|1.317073|9 q2:CUFF.1|CUFF.1.1|1|35.211287|0.000000|2.000000|9 +TCONS_00000005 XLOC_000005 - u q1:CUFF.3|CUFF.3.1|1|27.255658|0.000000|1.741935|6 - +TCONS_00000006 XLOC_000001 - u - q2:CUFF.3|CUFF.3.1|1|35.211287|0.000000|2.000000|9 +TCONS_00000007 XLOC_000002 Lypla1|Lypla1 c - q2:CUFF.7|CUFF.7.1|1|29.709524|0.000000|1.687500|6 +TCONS_00000008 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|1|21.226627|0.000000|1.205672|9 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out3.gtf Mon May 27 13:54:15 2019 -0400 |
| b |
| b'@@ -0,0 +1,206 @@\n+chr1\tStringTie\ttranscript\t160930303\t160940234\t.\t+\t.\ttranscript_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";\n+chr1\tStringTie\texon\t160930303\t160930344\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1";\n+chr1\tStringTie\texon\t160938112\t160938232\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "2";\n+chr1\tStringTie\texon\t160939995\t160940234\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "3";\n+chr1\tStringTie\ttranscript\t160940817\t160967997\t.\t+\t.\ttranscript_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";\n+chr1\tStringTie\texon\t160940817\t160940994\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "1";\n+chr1\tStringTie\texon\t160942528\t160942728\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "2";\n+chr1\tStringTie\texon\t160946534\t160946666\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "3";\n+chr1\tStringTie\texon\t160948307\t160948425\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "4";\n+chr1\tStringTie\texon\t160950222\t160950334\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "5";\n+chr1\tStringTie\texon\t160950841\t160951122\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "6";\n+chr1\tStringTie\texon\t160951615\t160951829\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "7";\n+chr1\tStringTie\texon\t160954784\t160955151\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "8";\n+chr1\tStringTie\texon\t160955815\t160955979\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "9";\n+chr1\tStringTie\texon\t160959401\t160959553\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "10";\n+chr1\tStringTie\texon\t160962271\t160962484\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "11";\n+chr1\tStringTie\texon\t160963479\t160963569\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "12";\n+chr1\tStringTie\texon\t160963708\t160963840\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "13";\n+chr1\tStringTie\texon\t160964950\t160965120\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "14";\n+chr1\tStringTie\texon\t160965673\t160965788\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "15";\n+chr1\tStringTie\texon\t160967647\t160967997\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "16";\n+chr1\tStringTie\ttranscript\t160968644\t160972020\t.\t+\t.\ttranscript_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";\n+chr1\tStringTie\texon\t160968644\t160972020\t.\t+\t.\ttranscript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1";\n+chr1\tStringTie\ttranscript\t160972938\t160974977\t.\t+\t.\ttranscript_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";\n+chr1\tStringTie\texon\t160972938\t160974977\t.\t+\t.\ttranscript_id "MSTRG.6.1"; gene_id "MSTRG.6"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS5";\n+chr1\tStringTie\texon\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS6";\n+chr1\tStringTie\texon\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS7";\n+chr1\tStringTie\texon\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161009768\t161010195\t.\t+\t.\ttranscript_id "MSTRG.13.1"; gene_id "MS'..b'\tStringTie\texon\t161062782\t161062877\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "7";\n+chr1\tStringTie\texon\t161063247\t161063348\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "8";\n+chr1\tStringTie\texon\t161065225\t161065291\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "9";\n+chr1\tStringTie\texon\t161069080\t161069179\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "10";\n+chr1\tStringTie\texon\t161069993\t161070504\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "11";\n+chr1\tStringTie\ttranscript\t161051331\t161070649\t.\t-\t.\ttranscript_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";\n+chr1\tStringTie\texon\t161051331\t161051438\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "1";\n+chr1\tStringTie\texon\t161056461\t161056530\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "2";\n+chr1\tStringTie\texon\t161057447\t161057553\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "3";\n+chr1\tStringTie\texon\t161060045\t161060091\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "4";\n+chr1\tStringTie\texon\t161060736\t161060859\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "5";\n+chr1\tStringTie\texon\t161062782\t161062877\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "6";\n+chr1\tStringTie\texon\t161063247\t161063348\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "7";\n+chr1\tStringTie\texon\t161065225\t161065291\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "8";\n+chr1\tStringTie\texon\t161069080\t161069179\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "9";\n+chr1\tStringTie\texon\t161069993\t161070649\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "10";\n+chr1\tStringTie\ttranscript\t161088915\t161090275\t.\t-\t.\ttranscript_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";\n+chr1\tStringTie\texon\t161088915\t161090275\t.\t-\t.\ttranscript_id "MSTRG.25.1"; gene_id "MSTRG.25"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161090412\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "="; tss_id "TSS32";\n+chr1\tStringTie\texon\t161090412\t161090511\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "1";\n+chr1\tStringTie\texon\t161093681\t161093787\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "2";\n+chr1\tStringTie\texon\t161095529\t161095737\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "3";\n+chr1\tStringTie\texon\t161098263\t161098396\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "4";\n+chr1\tStringTie\texon\t161099142\t161099285\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "5";\n+chr1\tStringTie\texon\t161101451\t161101634\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "6";\n+chr1\tStringTie\texon\t161102979\t161103094\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "7";\n+chr1\tStringTie\texon\t161105401\t161105495\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "8";\n+chr1\tStringTie\texon\t161106707\t161106865\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "9";\n+chr1\tStringTie\texon\t161109222\t161109795\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "10";\n+chr1\tStringTie\texon\t161130389\t161130452\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "11";\n+chr1\tStringTie\texon\t161131363\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "12";\n+chr1\tStringTie\ttranscript\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; xloc "XLOC_000021"; class_code "u"; tss_id "TSS33";\n+chr1\tStringTie\texon\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; exon_number "1";\n' |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out3.loci --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out3.loci Mon May 27 13:54:15 2019 -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 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out3.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out3.stats Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,30 @@ +# gffcompare v0.10.6 | Command line was: +#gffcompare -r ref_annotation -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf +# + +#= Summary for dataset: gffcompare_in4_gtf +# 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: 72.6 | 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 +35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/gffcompare_out3.tracking --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out3.tracking Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,35 @@ +TCONS_00000001 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.3|MSTRG.3.1|3|0.000000|0.000000|0.000000|403 +TCONS_00000002 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.4|MSTRG.4.1|16|0.000000|0.000000|0.000000|3003 +TCONS_00000003 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.5|MSTRG.5.1|1|0.000000|0.000000|0.000000|3377 +TCONS_00000004 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.6|MSTRG.6.1|1|0.000000|0.000000|0.000000|2040 +TCONS_00000005 XLOC_000002 - u q1:MSTRG.7|MSTRG.7.1|1|0.000000|0.000000|0.000000|432 +TCONS_00000006 XLOC_000003 - u q1:MSTRG.10|MSTRG.10.1|1|0.000000|0.000000|0.000000|316 +TCONS_00000007 XLOC_000004 - u q1:MSTRG.12|MSTRG.12.1|1|0.000000|0.000000|0.000000|251 +TCONS_00000008 XLOC_000005 - u q1:MSTRG.13|MSTRG.13.1|1|0.000000|0.000000|0.000000|428 +TCONS_00000009 XLOC_000006 uc007der.1|uc007der.1 x q1:MSTRG.14|MSTRG.14.1|1|0.000000|0.000000|0.000000|250 +TCONS_00000010 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.1|11|0.000000|0.000000|0.000000|800 +TCONS_00000011 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.2|12|0.000000|0.000000|0.000000|608 +TCONS_00000012 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.3|11|0.000000|0.000000|0.000000|1008 +TCONS_00000013 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.4|11|0.000000|0.000000|0.000000|531 +TCONS_00000014 XLOC_000007 uc007dev.1|uc007dev.1 = q1:MSTRG.16|MSTRG.16.5|11|0.000000|0.000000|0.000000|807 +TCONS_00000015 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.1|16|0.000000|0.000000|0.000000|2459 +TCONS_00000016 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.2|6|0.000000|0.000000|0.000000|903 +TCONS_00000017 XLOC_000009 uc007dfd.3|uc007dfd.3 c q1:MSTRG.20|MSTRG.20.1|3|0.000000|0.000000|0.000000|716 +TCONS_00000018 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.21|MSTRG.21.1|1|0.000000|0.000000|0.000000|466 +TCONS_00000019 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.22|MSTRG.22.1|1|0.000000|0.000000|0.000000|224 +TCONS_00000020 XLOC_000009 uc056yep.1|uc056yep.1 c q1:MSTRG.23|MSTRG.23.1|1|0.000000|0.000000|0.000000|1316 +TCONS_00000021 XLOC_000010 uc007dff.1|uc007dff.1 x q1:MSTRG.24|MSTRG.24.1|1|0.000000|0.000000|0.000000|417 +TCONS_00000022 XLOC_000011 uc007dff.1|uc007dff.1 s q1:MSTRG.26|MSTRG.26.1|12|0.000000|0.000000|0.000000|3033 +TCONS_00000023 XLOC_000012 uc007dff.1|uc007dff.1 i q1:MSTRG.28|MSTRG.28.1|1|0.000000|0.000000|0.000000|213 +TCONS_00000024 XLOC_000013 - u q1:MSTRG.1|MSTRG.1.1|1|0.000000|0.000000|0.000000|447 +TCONS_00000025 XLOC_000014 - u q1:MSTRG.2|MSTRG.2.1|1|0.000000|0.000000|0.000000|349 +TCONS_00000026 XLOC_000015 - u q1:MSTRG.8|MSTRG.8.1|1|0.000000|0.000000|0.000000|1112 +TCONS_00000027 XLOC_000016 - u q1:MSTRG.9|MSTRG.9.1|1|0.000000|0.000000|0.000000|773 +TCONS_00000028 XLOC_000017 - u q1:MSTRG.11|MSTRG.11.1|1|0.000000|0.000000|0.000000|257 +TCONS_00000029 XLOC_000018 uc007des.1|uc007des.1 c q1:MSTRG.15|MSTRG.15.1|1|0.000000|0.000000|0.000000|353 +TCONS_00000030 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.17|MSTRG.17.1|6|0.000000|0.000000|0.000000|1029 +TCONS_00000031 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.19|MSTRG.19.1|11|0.000000|0.000000|0.000000|1514 +TCONS_00000032 XLOC_000019 uc007dey.2|uc007dey.2 j q1:MSTRG.19|MSTRG.19.2|10|0.000000|0.000000|0.000000|1478 +TCONS_00000033 XLOC_000020 uc007dff.1|uc007dff.1 c q1:MSTRG.25|MSTRG.25.1|1|0.000000|0.000000|0.000000|1361 +TCONS_00000034 XLOC_000020 uc007dff.1|uc007dff.1 = q1:MSTRG.27|MSTRG.27.1|12|0.000000|0.000000|0.000000|2016 +TCONS_00000035 XLOC_000021 - u q1:MSTRG.29|MSTRG.29.1|1|0.000000|0.000000|0.000000|223 |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f test-data/sequence.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.fa Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>chr1 +AGACACGACCTGCTCGGGTGAGCATCCTTAATTCGAGACAATGTCTAATCAATTGCCACGTATTCAGCTGCCGAACGTAGTGGGCACCACGAGTTTGGTT |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f tool-data/gene_sets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# This is a sample file that enables tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +#<unique_build_id> <dbkey> <display_name> <path> +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +#Homo_sapiens.GRCh37.74 hg19 GRCh37 (hg19) annotation from Ensembl, release 74 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf +#Homo_sapiens.NCBI36.54 hg18 hg18 annotation from Ensembl, release 54 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Feb 05 15:51:44 2019 -0500 +++ b/tool_data_table_conf.xml.sample Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -1,4 +1,9 @@ <tables> + <!-- Location of all GFF/GTF files --> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_sets.loc" /> + </table> <!-- Location of SAMTools indexed FASTA files --> <table name="fasta_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> |
| b |
| diff -r f99d7825a501 -r 2bb86e2c417f tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon May 27 13:54:15 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +<tables> + <!-- Location of all GFF/GTF files --> + <table name="gene_sets" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/gene_sets.loc" /> + </table> + <!-- Location of SAMTools indexed FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |