| Previous changeset 4:0f710191a66d (2019-10-17) Next changeset 6:3c5e024a18cf (2024-10-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8 |
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modified:
gffcompare.xml test-data/gffcompare_out1.gtf test-data/gffcompare_out1.stats 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_out2.gtf test-data/gffcompare_out2.loci test-data/gffcompare_out2.stats test-data/gffcompare_out2.tracking test-data/gffcompare_out3.gtf test-data/gffcompare_out3.loci test-data/gffcompare_out3.stats test-data/gffcompare_out3.tracking |
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added:
macros.xml |
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| diff -r 0f710191a66d -r f99dd58de04f gffcompare.xml --- a/gffcompare.xml Thu Oct 17 03:01:26 2019 -0400 +++ b/gffcompare.xml Fri Feb 03 10:57:30 2023 +0000 |
| [ |
| b'@@ -1,81 +1,84 @@\n-<tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@">\n+<tool id="gffcompare" name="GffCompare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n <description>compare assembled transcripts to a reference annotation</description>\n <macros>\n- <token name="@GFFCOMPARE_VERSION@">0.11.2</token>\n+ <import>macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement>\n- </requirements>\n+ <xrefs>\n+ <xref type="bio.tools">gffcompare</xref>\n+ </xrefs>\n+ <expand macro="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-#end for\n-#if $seq_data.use_seq_data == "Yes":\n- #if $seq_data.seq_source.index_source == "history":\n- ln -s \'$seq_data.seq_source.ref_file\' ref_seq.fa &&\n- #else:\n- ln -s \'${seq_data.seq_source.index.fields.path}\' ref_seq.fa &&\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+ #import re\n \n-gffcompare\n-## Use annotation reference?\n-#if $annotation.use_ref_annotation == "Yes":\n- -r ref_annotation\n- $annotation.ignore_nonoverlapping_reference\n- $annotation.ignore_nonoverlapping_transfrags\n- $annotation.strict_match\n-#end if\n-#if $annotation.refmap_tmap == "":\n- -T\n-#end if\n-\n-## Use sequence data?\n-#if $seq_data.use_seq_data == "Yes":\n- -s ref_seq.fa\n-#end if\n-\n-$discard_single_exon\n-$discard_duplicates\n-$no_merge\n--e $max_dist_exon\n--d $max_dist_group\n-$chr_stats\n--p \'$adv_output.p\'\n-$adv_output.A\n-$adv_output.C\n-$adv_output.X\n-$adv_output.K\n-\n-#for $escaped_element_identifier in $escaped_element_identifiers:\n- \'$escaped_element_identifier\'\n-#end for\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+ #end for\n+ #if $conditional_annotation.selector == "yes":\n+ #if $conditional_annotation.ref_source.selector == "history":\n+ ln -s \'$conditional_annotation.ref_source.reference_annotation\' reference_annotation &&\n+ #else:\n+ ln -s \'${conditional_annotation.ref_source.index.fields.path}\' reference_annotation &&\n+ #end if\n+ #end if\n+ #if $seq_data.selector == "Yes":\n+ #if $seq_data.seq_source.index_source == "history":\n+ ln -s \'$seq_data.seq_source.ref_genome\' ref_seq.fa &&\n+ samtools faidx ref_seq.fa &&\n+ #else:\n+ ln -s \'${seq_data.seq_source.index.fields.path}\' ref_seq.fa &&\n+ #end if\n+ #end if\n+ gffcompare -V\n+ #if $conditional_annotation.selector == "yes":\n+ -r reference_annotation\n+ $conditional_annotation.R\n+ $conditional_annotation.Q\n+ $conditional_annotation.conditional_strict.selector\n+ #if $conditional_annotation.conditional_strict.selector == \'--strict-match\'\n+ -e $conditional_annotation.conditional_strict.e\n+ #end if \n+ $conditional_annotation.discard_single_exon\n+ $conditional_annotation.conditional_duplication.selector\n+ #if $conditional_annotation.co'..b'e each intron of the predicted transcript is checked against any introns of the reference transcripts in the same region and if there is one with the same exact start-end coordinates, it is counted as a TP.\n+* **Intron chain level**: At this level we count as a TP any query transcript for which all of its introns can be found, with the same exact intron coordinates as in a reference transcript that has the same number of introns. Matching all the introns at this level implies that all the internal exons also match, but this might not be true for the external boundaries of the terminal exons.\n+* **Transcript level**: Note that intron chain level values are calculated only by looking at multi-exon transcripts, so it completely ignores the single-exon transcripts, which can be quite numerous in a RNA-Seq experiment (possibly due to a lot of transcriptional and alignment noise). The transcript level considers single-exons as well. A TP at this level is defined as a full exon chain match between the predicted transcript and a reference transcript, where all internal exons match and the outer boundaries of the terminal query exons can only slightly differ from the reference exons (with at most 100 bases by default). Also GffCompare considers single-exon transcripts as matching an overlapping single-exon reference transcript if there is a significant overlap between the two (more than 80% of the longer transcript by default).\n+* **Locus level**: At this level GffCompare considers that an observed locus, defined as a cluster of exon-overlapping transcripts, matches a similarly built reference locus if at least one predicted transcript has a transcript level match with a reference transcript in the corresponding reference locus.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Tracking transcripts**\n \n-Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e.\n-contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into\n-their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed\n-and is simply ignored when given).\n+GffCompare can also be used to track all transcripts that are structurally equivalent among the different input files. GffCompare considers transcripts matching (or structurally equivalent) if all \n+their introns are identical. Note that matching transcripts are allowed to differ on the length of the first and last exons, since these lengths can usually vary across samples for the same biological transcript.\n+\n+A list of all matching transcripts is reported in a file called *tracking file* in which each row represents a transcript. The first column in this file represents a unique id assigned to that transcripts. \n+The second file represents the super-locus that contains that transcript. If a reference annotation is provided, the 3 rd and 4 th columns contain the reference annotation transcript that was found to be \n+closest to the transcript and the classification code that specifies the relationship between these two transcripts, respectively. The rest of the columns show the corresponding \n+transcript from each input file in order.\n+\n+**RefMap and TMAP files**\n+\n+In order to quickly see which reference transcripts match which transcripts from a sample file, two other files, called *RefMap* and *TMAP* are also created for each query. The RefMap file is a tab-delimited file \n+that has a row for each reference transcript that either fully or partially matches a transcript from the given input file. Conversely, the TMAP file has a row for each input transcript, while the columns in this \n+file describe the most closely matching reference transcript for that transcript.\n+\n ]]>\n </help>\n- <citations>\n- <citation type="doi">10.1038/nbt.1621</citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 0f710191a66d -r f99dd58de04f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -0,0 +1,15 @@ +<macros> + <token name="@TOOL_VERSION@">0.12.6</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">gffcompare</requirement> + <requirement type="package" version="1.16.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out1.gtf --- a/test-data/gffcompare_out1.gtf Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out1.gtf Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,16 +1,16 @@ -chr1 Cufflinks transcript 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; oId "CUFF.3.1"; tss_id "TSS1"; +chr1 Cufflinks transcript 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; oId "CUFF.3.1"; tss_id "TSS1"; num_samples "1"; chr1 Cufflinks exon 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; exon_number "1"; -chr1 Cufflinks transcript 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; oId "CUFF.7.1"; tss_id "TSS2"; +chr1 Cufflinks transcript 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; oId "CUFF.7.1"; tss_id "TSS2"; num_samples "1"; chr1 Cufflinks exon 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; exon_number "1"; -chr1 Cufflinks transcript 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000003"; oId "CUFF.7.1"; contained_in "TCONS_00000002"; tss_id "TSS3"; +chr1 Cufflinks transcript 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000003"; oId "CUFF.7.1"; contained_in "TCONS_00000002"; tss_id "TSS3"; num_samples "1"; chr1 Cufflinks exon 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000003"; exon_number "1"; -chr1 Cufflinks transcript 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000003"; oId "CUFF.9.1"; tss_id "TSS3"; +chr1 Cufflinks transcript 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000003"; oId "CUFF.9.1"; tss_id "TSS3"; num_samples "1"; chr1 Cufflinks exon 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000003"; exon_number "1"; -chr1 Cufflinks transcript 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000004"; oId "CUFF.10.1"; tss_id "TSS4"; +chr1 Cufflinks transcript 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000004"; oId "CUFF.10.1"; tss_id "TSS4"; num_samples "1"; chr1 Cufflinks exon 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000004"; exon_number "1"; -chr1 Cufflinks transcript 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000005"; oId "CUFF.1.1"; tss_id "TSS5"; +chr1 Cufflinks transcript 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000005"; oId "CUFF.1.1"; tss_id "TSS5"; num_samples "2"; chr1 Cufflinks exon 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000005"; exon_number "1"; -chr1 Cufflinks transcript 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000006"; oId "CUFF.3.1"; tss_id "TSS6"; +chr1 Cufflinks transcript 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000006"; oId "CUFF.3.1"; tss_id "TSS6"; num_samples "1"; chr1 Cufflinks exon 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000006"; exon_number "1"; -chr1 Cufflinks transcript 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000007"; oId "CUFF.5.1"; tss_id "TSS7"; +chr1 Cufflinks transcript 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000007"; oId "CUFF.5.1"; tss_id "TSS7"; num_samples "1"; chr1 Cufflinks exon 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000007"; exon_number "1"; |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out1.stats --- a/test-data/gffcompare_out1.stats Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out1.stats Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,5 +1,5 @@ -# gffcompare v0.11.2 | Command line was: -#gffcompare -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf +# gffcompare v0.12.6 | Command line was: +#gffcompare -V -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf # #= Summary for dataset: gffcompare_in1_gtf |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2-1.refmap --- a/test-data/gffcompare_out2-1.refmap Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2-1.refmap Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,2 +1,2 @@ -ref_gene_id ref_id class_code qry_id_list -Lypla1 Lypla1 c CUFF.7|CUFF.7.1 +ref_gene ref_id class_code qry_id_list +CUFF.1 CUFF.1.1 = CUFF.1|CUFF.1.1 |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2-1.tmap --- a/test-data/gffcompare_out2-1.tmap Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2-1.tmap Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,6 +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 +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +CUFF.1 CUFF.1.1 = CUFF.1 CUFF.1.1 1 20.607936 0.000000 1.317073 9 CUFF.1.1 9 +CUFF.3 CUFF.3.1 x CUFF.3 CUFF.3.1 1 27.255658 0.000000 1.741935 6 CUFF.3.1 9 +CUFF.3 CUFF.3.1 p CUFF.7 CUFF.7.1 1 9.999117 0.000000 0.639053 9 CUFF.7.1 9 +CUFF.7 CUFF.7.1 k CUFF.9 CUFF.9.1 1 17.776896 0.000000 1.136139 9 CUFF.9.1 6 +CUFF.7 CUFF.7.1 p CUFF.10 CUFF.10.1 1 17.776896 0.000000 1.136139 9 CUFF.10.1 6 |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2-2.refmap --- a/test-data/gffcompare_out2-2.refmap Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2-2.refmap Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,2 +1,4 @@ -ref_gene_id ref_id class_code qry_id_list -Lypla1 Lypla1 c CUFF.7|CUFF.7.1 +ref_gene ref_id class_code qry_id_list +CUFF.3 CUFF.3.1 = CUFF.3|CUFF.3.1 +CUFF.7 CUFF.7.1 = CUFF.7|CUFF.7.1 +CUFF.5 CUFF.5.1 = CUFF.5|CUFF.5.1 |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2-2.tmap --- a/test-data/gffcompare_out2-2.tmap Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2-2.tmap Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,5 +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 +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +CUFF.1 CUFF.1.1 = CUFF.1 CUFF.1.1 1 35.211287 0.000000 2.000000 9 CUFF.1.1 9 +CUFF.3 CUFF.3.1 = CUFF.3 CUFF.3.1 1 35.211287 0.000000 2.000000 9 CUFF.3.1 9 +CUFF.5 CUFF.5.1 = CUFF.5 CUFF.5.1 1 21.226627 0.000000 1.205672 9 CUFF.5.1 9 +CUFF.7 CUFF.7.1 = CUFF.7 CUFF.7.1 1 29.709524 0.000000 1.687500 6 CUFF.7.1 6 |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2.gtf --- a/test-data/gffcompare_out2.gtf Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2.gtf Fri Feb 03 10:57:30 2023 +0000 |
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| @@ -1,16 +1,16 @@ -chr1 Cufflinks transcript 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS1"; +chr1 Cufflinks transcript 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; gene_name "CUFF.3"; oId "CUFF.3.1"; cmp_ref "CUFF.3.1"; class_code "="; tss_id "TSS1"; num_samples "1"; chr1 Cufflinks exon 12 20 . + . transcript_id "TCONS_00000006"; gene_id "XLOC_000001"; exon_number "1"; -chr1 Cufflinks transcript 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; gene_name "Lypla1"; oId "CUFF.7.1"; cmp_ref "Lypla1"; class_code "c"; tss_id "TSS2"; +chr1 Cufflinks transcript 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; oId "CUFF.7.1"; cmp_ref "CUFF.3.1"; class_code "p"; cmp_ref_gene "CUFF.3"; tss_id "TSS2"; num_samples "1"; chr1 Cufflinks exon 32 40 . + . transcript_id "TCONS_00000001"; gene_id "XLOC_000002"; exon_number "1"; -chr1 Cufflinks transcript 42 47 . + . transcript_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"; -chr1 Cufflinks exon 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000002"; exon_number "1"; -chr1 Cufflinks transcript 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000002"; gene_name "Lypla1"; oId "CUFF.9.1"; cmp_ref "Lypla1"; class_code "c"; tss_id "TSS3"; -chr1 Cufflinks exon 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000002"; exon_number "1"; -chr1 Cufflinks transcript 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000003"; gene_name "Lypla1"; oId "CUFF.10.1"; cmp_ref "Lypla1"; class_code "p"; tss_id "TSS4"; -chr1 Cufflinks exon 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000003"; exon_number "1"; -chr1 Cufflinks transcript 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000004"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS5"; -chr1 Cufflinks exon 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000004"; exon_number "1"; -chr1 Cufflinks transcript 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000005"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS6"; -chr1 Cufflinks exon 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000005"; exon_number "1"; -chr1 Cufflinks transcript 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000006"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS7"; -chr1 Cufflinks exon 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000006"; exon_number "1"; +chr1 Cufflinks transcript 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000003"; gene_name "CUFF.7"; oId "CUFF.7.1"; contained_in "TCONS_00000002"; cmp_ref "CUFF.7.1"; class_code "="; tss_id "TSS3"; num_samples "1"; +chr1 Cufflinks exon 42 47 . + . transcript_id "TCONS_00000007"; gene_id "XLOC_000003"; exon_number "1"; +chr1 Cufflinks transcript 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000003"; gene_name "CUFF.7"; oId "CUFF.9.1"; cmp_ref "CUFF.7.1"; class_code "k"; tss_id "TSS3"; num_samples "1"; +chr1 Cufflinks exon 42 50 . + . transcript_id "TCONS_00000002"; gene_id "XLOC_000003"; exon_number "1"; +chr1 Cufflinks transcript 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000004"; oId "CUFF.10.1"; cmp_ref "CUFF.7.1"; class_code "p"; cmp_ref_gene "CUFF.7"; tss_id "TSS4"; num_samples "1"; +chr1 Cufflinks exon 52 60 . + . transcript_id "TCONS_00000003"; gene_id "XLOC_000004"; exon_number "1"; +chr1 Cufflinks transcript 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000005"; gene_name "CUFF.1"; oId "CUFF.1.1"; cmp_ref "CUFF.1.1"; class_code "="; tss_id "TSS5"; num_samples "2"; +chr1 Cufflinks exon 2 10 . - . transcript_id "TCONS_00000004"; gene_id "XLOC_000005"; exon_number "1"; +chr1 Cufflinks transcript 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000006"; oId "CUFF.3.1"; cmp_ref "CUFF.3.1"; class_code "x"; cmp_ref_gene "CUFF.3"; tss_id "TSS6"; num_samples "1"; +chr1 Cufflinks exon 15 20 . - . transcript_id "TCONS_00000005"; gene_id "XLOC_000006"; exon_number "1"; +chr1 Cufflinks transcript 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000007"; gene_name "CUFF.5"; oId "CUFF.5.1"; cmp_ref "CUFF.5.1"; class_code "="; tss_id "TSS7"; num_samples "1"; +chr1 Cufflinks exon 22 30 . - . transcript_id "TCONS_00000008"; gene_id "XLOC_000007"; exon_number "1"; |
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| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2.loci --- a/test-data/gffcompare_out2.loci Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2.loci Fri Feb 03 10:57:30 2023 +0000 |
| [ |
| @@ -1,6 +1,7 @@ -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 +XLOC_000001 chr1[+]12-20 CUFF.3|CUFF.3.1 - CUFF.3.1 +XLOC_000002 chr1[+]32-40 - CUFF.7.1 - +XLOC_000003 chr1[+]42-50 CUFF.7|CUFF.7.1 CUFF.9.1 CUFF.7.1 +XLOC_000004 chr1[+]52-60 - CUFF.10.1 - +XLOC_000005 chr1[-]2-10 CUFF.1|CUFF.1.1 CUFF.1.1 CUFF.1.1 +XLOC_000006 chr1[-]15-20 - CUFF.3.1 - +XLOC_000007 chr1[-]22-30 CUFF.5|CUFF.5.1 - CUFF.5.1 |
| b |
| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2.stats --- a/test-data/gffcompare_out2.stats Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2.stats Fri Feb 03 10:57:30 2023 +0000 |
| b |
| @@ -1,47 +1,47 @@ -# gffcompare v0.11.2 | Command line was: -#gffcompare -r ref_annotation -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf +# gffcompare v0.12.6 | Command line was: +#gffcompare -V -r reference_annotation -T -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf # #= 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 +# Reference mRNAs : 4 in 4 loci (0 multi-exon) +# Super-loci w/ reference transcripts: 2 #-----------------| Sensitivity | Precision | - Base level: 94.7 | 42.9 | - Exon level: 100.0 | 40.0 | - Transcript level: 0.0 | 0.0 | - Locus level: 0.0 | 0.0 | + Base level: 45.5 | 35.7 | + Exon level: 50.0 | 40.0 | + Transcript level: 25.0 | 20.0 | + Locus level: 25.0 | 20.0 | Matching intron chains: 0 - Matching transcripts: 0 - Matching loci: 0 + Matching transcripts: 1 + Matching loci: 1 - Missed exons: 0/1 ( 0.0%) + Missed exons: 2/4 ( 50.0%) Novel exons: 3/5 ( 60.0%) - Missed loci: 0/1 ( 0.0%) + Missed loci: 2/4 ( 50.0%) Novel loci: 3/5 ( 60.0%) #= 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 +# Reference mRNAs : 4 in 4 loci (0 multi-exon) +# Super-loci w/ reference transcripts: 4 #-----------------| 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 | + Base level: 100.0 | 100.0 | + Exon level: 100.0 | 100.0 | + Transcript level: 100.0 | 100.0 | + Locus level: 100.0 | 100.0 | Matching intron chains: 0 - Matching transcripts: 0 - Matching loci: 0 + Matching transcripts: 4 + Matching loci: 4 - Missed exons: 0/1 ( 0.0%) - Novel exons: 3/4 ( 75.0%) - Missed loci: 0/1 ( 0.0%) - Novel loci: 3/4 ( 75.0%) + Missed exons: 0/4 ( 0.0%) + Novel exons: 0/4 ( 0.0%) + Missed loci: 0/4 ( 0.0%) + Novel loci: 0/4 ( 0.0%) - Total union super-loci across all input datasets: 6 - (0 multi-transcript, ~1.3 transcripts per locus) + Total union super-loci across all input datasets: 7 + (0 multi-transcript, ~1.1 transcripts per locus) 8 out of 8 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant) |
| b |
| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out2.tracking --- a/test-data/gffcompare_out2.tracking Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out2.tracking Fri Feb 03 10:57:30 2023 +0000 |
| b |
| @@ -1,8 +1,8 @@ -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 +TCONS_00000001 XLOC_000002 CUFF.3|CUFF.3.1 p q1:CUFF.7|CUFF.7.1|1|9.999117|0.000000|0.639053|9 - +TCONS_00000002 XLOC_000003 CUFF.7|CUFF.7.1 k q1:CUFF.9|CUFF.9.1|1|17.776896|0.000000|1.136139|9 - +TCONS_00000003 XLOC_000004 CUFF.7|CUFF.7.1 p q1:CUFF.10|CUFF.10.1|1|17.776896|0.000000|1.136139|9 - +TCONS_00000004 XLOC_000005 CUFF.1|CUFF.1.1 = 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_000006 CUFF.3|CUFF.3.1 x q1:CUFF.3|CUFF.3.1|1|27.255658|0.000000|1.741935|6 - +TCONS_00000006 XLOC_000001 CUFF.3|CUFF.3.1 = - q2:CUFF.3|CUFF.3.1|1|35.211287|0.000000|2.000000|9 +TCONS_00000007 XLOC_000003 CUFF.7|CUFF.7.1 = - q2:CUFF.7|CUFF.7.1|1|29.709524|0.000000|1.687500|6 +TCONS_00000008 XLOC_000007 CUFF.5|CUFF.5.1 = - q2:CUFF.5|CUFF.5.1|1|21.226627|0.000000|1.205672|9 |
| b |
| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out3.gtf --- a/test-data/gffcompare_out3.gtf Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out3.gtf Fri Feb 03 10:57:30 2023 +0000 |
| b |
| b'@@ -1,8 +1,8 @@\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\ttranscript\t160930303\t160940234\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; gene_name "MSTRG.3"; xloc "XLOC_000001"; cmp_ref "MSTRG.3.1"; class_code "="; 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\ttranscript\t160940817\t160967997\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; gene_name "MSTRG.4"; xloc "XLOC_000002"; cmp_ref "MSTRG.4.1"; class_code "="; 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@@ -19,21 +19,21 @@\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\ttranscript\t160968644\t160972020\t.\t+\t.\ttranscript_id "MSTRG.5.1"; gene_id "MSTRG.5"; gene_name "MSTRG.5"; xloc "XLOC_000003"; cmp_ref "MSTRG.5.1"; class_code "="; 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\ttranscript\t160972938\t160974977\t.\t+\t.\ttranscript_id "MSTRG.6.1"; gene_id "MSTRG.6"; gene_name "MSTRG.6"; xloc "XLOC_000004"; cmp_ref "MSTRG.6.1"; class_code "="; 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\ttranscript\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; gene_name "MSTRG.7"; xloc "XLOC_000005"; cmp_ref "MSTRG.7.1"; class_code "="; 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\ttranscript\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; gene_name "MSTRG.10"; xloc "XLOC_000006"; cmp_ref "MSTRG.10.1"; class_code "="; 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\ttranscript\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; gene_name "MSTRG.12"; xloc "XLOC_'..b'0504\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; gene_name "MSTRG.19"; xloc "XLOC_000026"; cmp_ref "MSTRG.19.1"; class_code "="; tss_id "TSS29";\n chr1\tStringTie\texon\t161051330\t161051438\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "1";\n chr1\tStringTie\texon\t161053941\t161054120\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "2";\n chr1\tStringTie\texon\t161056461\t161056530\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "3";\n@@ -176,7 +176,7 @@\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\ttranscript\t161051331\t161070649\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; gene_name "MSTRG.19"; xloc "XLOC_000026"; cmp_ref "MSTRG.19.2"; class_code "="; 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@@ -187,9 +187,9 @@\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\ttranscript\t161088915\t161090275\t.\t-\t.\ttranscript_id "MSTRG.25.1"; gene_id "MSTRG.25"; gene_name "MSTRG.25"; xloc "XLOC_000027"; cmp_ref "MSTRG.25.1"; class_code "="; 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\ttranscript\t161090412\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "MSTRG.27"; xloc "XLOC_000028"; cmp_ref "MSTRG.27.1"; 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@@ -202,5 +202,5 @@\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\ttranscript\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; gene_name "MSTRG.29"; xloc "XLOC_000029"; cmp_ref "MSTRG.29.1"; class_code "="; 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 0f710191a66d -r f99dd58de04f test-data/gffcompare_out3.loci --- a/test-data/gffcompare_out3.loci Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out3.loci Fri Feb 03 10:57:30 2023 +0000 |
| [ |
| @@ -1,21 +1,29 @@ -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[+]160930303-160940234 MSTRG.3|MSTRG.3.1 MSTRG.3.1 +XLOC_000002 chr1[+]160940817-160967997 MSTRG.4|MSTRG.4.1 MSTRG.4.1 +XLOC_000003 chr1[+]160968644-160972020 MSTRG.5|MSTRG.5.1 MSTRG.5.1 +XLOC_000004 chr1[+]160972938-160974977 MSTRG.6|MSTRG.6.1 MSTRG.6.1 +XLOC_000005 chr1[+]161003085-161003516 MSTRG.7|MSTRG.7.1 MSTRG.7.1 +XLOC_000006 chr1[+]161006151-161006466 MSTRG.10|MSTRG.10.1 MSTRG.10.1 +XLOC_000007 chr1[+]161008375-161008625 MSTRG.12|MSTRG.12.1 MSTRG.12.1 +XLOC_000008 chr1[+]161009768-161010195 MSTRG.13|MSTRG.13.1 MSTRG.13.1 +XLOC_000009 chr1[+]161019713-161019962 MSTRG.14|MSTRG.14.1 MSTRG.14.1 +XLOC_000010 chr1[+]161034351-161038539 MSTRG.16|MSTRG.16.1,MSTRG.16|MSTRG.16.2,MSTRG.16|MSTRG.16.3,MSTRG.16|MSTRG.16.4,MSTRG.16|MSTRG.16.5 MSTRG.16.1,MSTRG.16.2,MSTRG.16.3,MSTRG.16.4,MSTRG.16.5 +XLOC_000011 chr1[+]161041562-161070639 MSTRG.18|MSTRG.18.1,MSTRG.18|MSTRG.18.2 MSTRG.18.1,MSTRG.18.2 +XLOC_000012 chr1[+]161070945-161078458 MSTRG.20|MSTRG.20.1 MSTRG.20.1 +XLOC_000013 chr1[+]161082956-161083421 MSTRG.21|MSTRG.21.1 MSTRG.21.1 +XLOC_000014 chr1[+]161084121-161084344 MSTRG.22|MSTRG.22.1 MSTRG.22.1 +XLOC_000015 chr1[+]161085014-161086329 MSTRG.23|MSTRG.23.1 MSTRG.23.1 +XLOC_000016 chr1[+]161088497-161088913 MSTRG.24|MSTRG.24.1 MSTRG.24.1 +XLOC_000017 chr1[+]161089415-161131512 MSTRG.26|MSTRG.26.1 MSTRG.26.1 +XLOC_000018 chr1[+]161123665-161123877 MSTRG.28|MSTRG.28.1 MSTRG.28.1 +XLOC_000019 chr1[-]29485012-29485458 MSTRG.1|MSTRG.1.1 MSTRG.1.1 +XLOC_000020 chr1[-]86909344-86909692 MSTRG.2|MSTRG.2.1 MSTRG.2.1 +XLOC_000021 chr1[-]161003658-161004769 MSTRG.8|MSTRG.8.1 MSTRG.8.1 +XLOC_000022 chr1[-]161005030-161005802 MSTRG.9|MSTRG.9.1 MSTRG.9.1 +XLOC_000023 chr1[-]161007444-161007700 MSTRG.11|MSTRG.11.1 MSTRG.11.1 +XLOC_000024 chr1[-]161032044-161032396 MSTRG.15|MSTRG.15.1 MSTRG.15.1 +XLOC_000025 chr1[-]161041525-161050001 MSTRG.17|MSTRG.17.1 MSTRG.17.1 +XLOC_000026 chr1[-]161051330-161070649 MSTRG.19|MSTRG.19.1,MSTRG.19|MSTRG.19.2 MSTRG.19.1,MSTRG.19.2 +XLOC_000027 chr1[-]161088915-161090275 MSTRG.25|MSTRG.25.1 MSTRG.25.1 +XLOC_000028 chr1[-]161090412-161131492 MSTRG.27|MSTRG.27.1 MSTRG.27.1 +XLOC_000029 chr1[-]192074156-192074378 MSTRG.29|MSTRG.29.1 MSTRG.29.1 |
| b |
| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out3.stats --- a/test-data/gffcompare_out3.stats Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out3.stats Fri Feb 03 10:57:30 2023 +0000 |
| b |
| @@ -1,30 +1,30 @@ -# gffcompare v0.11.2 | Command line was: -#gffcompare -r ref_annotation -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf +# gffcompare v0.12.6 | Command line was: +#gffcompare -V -r reference_annotation -R --strict-match -e 100 -T -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 : 19 in 6 loci (19 multi-exon) -# Super-loci w/ reference transcripts: 6 +# Reference mRNAs : 35 in 29 loci (15 multi-exon) +# Super-loci w/ reference transcripts: 29 #-----------------| Sensitivity | Precision | - Base level: 72.7 | 60.7 | - Exon level: 81.0 | 55.7 | - Intron level: 81.2 | 64.4 | -Intron chain level: 10.5 | 13.3 | - Transcript level: 10.5 | 5.7 | - Locus level: 33.3 | 6.9 | + Base level: 100.0 | 100.0 | + Exon level: 100.0 | 100.0 | + Intron level: 100.0 | 100.0 | +Intron chain level: 100.0 | 100.0 | + Transcript level: 100.0 | 100.0 | + Locus level: 100.0 | 100.0 | - Matching intron chains: 2 - Matching transcripts: 2 - Matching loci: 2 + Matching intron chains: 15 + Matching transcripts: 35 + Matching loci: 29 - Missed exons: 2/84 ( 2.4%) - Novel exons: 46/122 ( 37.7%) - Missed introns: 11/69 ( 15.9%) - Novel introns: 28/87 ( 32.2%) - Missed loci: 0/6 ( 0.0%) - Novel loci: 15/29 ( 51.7%) + Missed exons: 0/122 ( 0.0%) + Novel exons: 0/122 ( 0.0%) + Missed introns: 0/87 ( 0.0%) + Novel introns: 0/87 ( 0.0%) + Missed loci: 0/29 ( 0.0%) + Novel loci: 0/29 ( 0.0%) - Total union super-loci across all input datasets: 21 + Total union super-loci across all input datasets: 29 35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) |
| b |
| diff -r 0f710191a66d -r f99dd58de04f test-data/gffcompare_out3.tracking --- a/test-data/gffcompare_out3.tracking Thu Oct 17 03:01:26 2019 -0400 +++ b/test-data/gffcompare_out3.tracking Fri Feb 03 10:57:30 2023 +0000 |
| b |
| @@ -1,35 +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 +TCONS_00000001 XLOC_000001 MSTRG.3|MSTRG.3.1 = q1:MSTRG.3|MSTRG.3.1|3|0.000000|0.000000|0.000000|403 +TCONS_00000002 XLOC_000002 MSTRG.4|MSTRG.4.1 = q1:MSTRG.4|MSTRG.4.1|16|0.000000|0.000000|0.000000|3003 +TCONS_00000003 XLOC_000003 MSTRG.5|MSTRG.5.1 = q1:MSTRG.5|MSTRG.5.1|1|0.000000|0.000000|0.000000|3377 +TCONS_00000004 XLOC_000004 MSTRG.6|MSTRG.6.1 = q1:MSTRG.6|MSTRG.6.1|1|0.000000|0.000000|0.000000|2040 +TCONS_00000005 XLOC_000005 MSTRG.7|MSTRG.7.1 = q1:MSTRG.7|MSTRG.7.1|1|0.000000|0.000000|0.000000|432 +TCONS_00000006 XLOC_000006 MSTRG.10|MSTRG.10.1 = q1:MSTRG.10|MSTRG.10.1|1|0.000000|0.000000|0.000000|316 +TCONS_00000007 XLOC_000007 MSTRG.12|MSTRG.12.1 = q1:MSTRG.12|MSTRG.12.1|1|0.000000|0.000000|0.000000|251 +TCONS_00000008 XLOC_000008 MSTRG.13|MSTRG.13.1 = q1:MSTRG.13|MSTRG.13.1|1|0.000000|0.000000|0.000000|428 +TCONS_00000009 XLOC_000009 MSTRG.14|MSTRG.14.1 = q1:MSTRG.14|MSTRG.14.1|1|0.000000|0.000000|0.000000|250 +TCONS_00000010 XLOC_000010 MSTRG.16|MSTRG.16.1 = q1:MSTRG.16|MSTRG.16.1|11|0.000000|0.000000|0.000000|800 +TCONS_00000011 XLOC_000010 MSTRG.16|MSTRG.16.2 = q1:MSTRG.16|MSTRG.16.2|12|0.000000|0.000000|0.000000|608 +TCONS_00000012 XLOC_000010 MSTRG.16|MSTRG.16.3 = q1:MSTRG.16|MSTRG.16.3|11|0.000000|0.000000|0.000000|1008 +TCONS_00000013 XLOC_000010 MSTRG.16|MSTRG.16.4 = q1:MSTRG.16|MSTRG.16.4|11|0.000000|0.000000|0.000000|531 +TCONS_00000014 XLOC_000010 MSTRG.16|MSTRG.16.5 = q1:MSTRG.16|MSTRG.16.5|11|0.000000|0.000000|0.000000|807 +TCONS_00000015 XLOC_000011 MSTRG.18|MSTRG.18.1 = q1:MSTRG.18|MSTRG.18.1|16|0.000000|0.000000|0.000000|2459 +TCONS_00000016 XLOC_000011 MSTRG.18|MSTRG.18.2 = q1:MSTRG.18|MSTRG.18.2|6|0.000000|0.000000|0.000000|903 +TCONS_00000017 XLOC_000012 MSTRG.20|MSTRG.20.1 = q1:MSTRG.20|MSTRG.20.1|3|0.000000|0.000000|0.000000|716 +TCONS_00000018 XLOC_000013 MSTRG.21|MSTRG.21.1 = q1:MSTRG.21|MSTRG.21.1|1|0.000000|0.000000|0.000000|466 +TCONS_00000019 XLOC_000014 MSTRG.22|MSTRG.22.1 = q1:MSTRG.22|MSTRG.22.1|1|0.000000|0.000000|0.000000|224 +TCONS_00000020 XLOC_000015 MSTRG.23|MSTRG.23.1 = q1:MSTRG.23|MSTRG.23.1|1|0.000000|0.000000|0.000000|1316 +TCONS_00000021 XLOC_000016 MSTRG.24|MSTRG.24.1 = q1:MSTRG.24|MSTRG.24.1|1|0.000000|0.000000|0.000000|417 +TCONS_00000022 XLOC_000017 MSTRG.26|MSTRG.26.1 = q1:MSTRG.26|MSTRG.26.1|12|0.000000|0.000000|0.000000|3033 +TCONS_00000023 XLOC_000018 MSTRG.28|MSTRG.28.1 = q1:MSTRG.28|MSTRG.28.1|1|0.000000|0.000000|0.000000|213 +TCONS_00000024 XLOC_000019 MSTRG.1|MSTRG.1.1 = q1:MSTRG.1|MSTRG.1.1|1|0.000000|0.000000|0.000000|447 +TCONS_00000025 XLOC_000020 MSTRG.2|MSTRG.2.1 = q1:MSTRG.2|MSTRG.2.1|1|0.000000|0.000000|0.000000|349 +TCONS_00000026 XLOC_000021 MSTRG.8|MSTRG.8.1 = q1:MSTRG.8|MSTRG.8.1|1|0.000000|0.000000|0.000000|1112 +TCONS_00000027 XLOC_000022 MSTRG.9|MSTRG.9.1 = q1:MSTRG.9|MSTRG.9.1|1|0.000000|0.000000|0.000000|773 +TCONS_00000028 XLOC_000023 MSTRG.11|MSTRG.11.1 = q1:MSTRG.11|MSTRG.11.1|1|0.000000|0.000000|0.000000|257 +TCONS_00000029 XLOC_000024 MSTRG.15|MSTRG.15.1 = q1:MSTRG.15|MSTRG.15.1|1|0.000000|0.000000|0.000000|353 +TCONS_00000030 XLOC_000025 MSTRG.17|MSTRG.17.1 = q1:MSTRG.17|MSTRG.17.1|6|0.000000|0.000000|0.000000|1029 +TCONS_00000031 XLOC_000026 MSTRG.19|MSTRG.19.1 = q1:MSTRG.19|MSTRG.19.1|11|0.000000|0.000000|0.000000|1514 +TCONS_00000032 XLOC_000026 MSTRG.19|MSTRG.19.2 = q1:MSTRG.19|MSTRG.19.2|10|0.000000|0.000000|0.000000|1478 +TCONS_00000033 XLOC_000027 MSTRG.25|MSTRG.25.1 = q1:MSTRG.25|MSTRG.25.1|1|0.000000|0.000000|0.000000|1361 +TCONS_00000034 XLOC_000028 MSTRG.27|MSTRG.27.1 = q1:MSTRG.27|MSTRG.27.1|12|0.000000|0.000000|0.000000|2016 +TCONS_00000035 XLOC_000029 MSTRG.29|MSTRG.29.1 = q1:MSTRG.29|MSTRG.29.1|1|0.000000|0.000000|0.000000|223 |