# HG changeset patch # User fubar # Date 1718347640 0 # Node ID 49c6f715bc82bc52331409a62286206130560177 # Parent 4eadb56fa31479df85bd0681e5934e33f2da81e8 planemo upload for repository https://www.encodeproject.org/software/bedgraphtobigwig/ diff -r 4eadb56fa314 -r 49c6f715bc82 bam_bed_gff_to_bigwig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_bed_gff_to_bigwig.xml Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,104 @@ + + + ucsc-bedgraphtobigwig + bedtools + coreutils + python + + + + + input2 && +#else: + ln -s '$input1' input2 && +#end if +#if $input1.ext == "bam": + bedtools genomecov -bg -split -ibam input2 | +#else + bedtools genomecov -bg -i input2 -g ./CHROMFILE | +#end if +LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg && +bedGraphToBigWig temp.bg ./CHROMFILE '$output' + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Estimates coverage of a reference genome for bam, bed or gff as a bigwig, suitable for viewing in JBrowse2 or other browser. + + If the input does not have a dbkey, a chromosome lengths file must be provided. The actual reference is not needed. + + This can be useful in workflows with assemblies in progress before a stable reference is available for a custom or built in reference dbkey. + + + + 10.1093/bioinformatics/btq351 + + diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/.shed.yml --- a/bbgbigwig/.shed.yml Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -name: bbgbigwig -owner: iuc -categories: -- Convert Formats -description: Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. -long_description: | - Designed for assembly visualisation JBrowse2 workflows where dbkey is not ready to be assigned even with a custom - genome. A bigwig track is very useful when there are too many features to display -type: unrestricted -remote_repository_url: https://www.encodeproject.org/software/bedgraphtobigwig/ -homepage_url: https://www.encodeproject.org/software/bedgraphtobigwig/ diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/bam_bed_gff_to_bigwig.xml --- a/bbgbigwig/bam_bed_gff_to_bigwig.xml Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,103 +0,0 @@ - - - ucsc-bedgraphtobigwig - bedtools - coreutils - python - - - - - input2 && -#else: - ln -s '$input1' input2 && -#end if -#if $input1.ext == "bam": - bedtools genomecov -bg -split -ibam input2 | -#else - bedtools genomecov -bg -i input2 -g ./CHROMFILE | -#end if -LC_COLLATE=C sort -k1,1 -k2,2n > temp.bg && -bedGraphToBigWig temp.bg ./CHROMFILE '$output' - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Converter for bam, bed or gff to bigwig - If the input does not have a dbkey, a chromosome lengths file is needed. - This can be useful in workflows with assemblies in progress before a stable reference is available for - a custom or built in reference dbkey. - - - - 10.1093/bioinformatics/btq351 - - diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/gff_to_bed_converter.py --- a/bbgbigwig/gff_to_bed_converter.py Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ -#!/usr/bin/env python - -import sys - -assert sys.version_info[:2] >= (2, 6) - - -def __main__(): - skipped_lines = 0 - first_skipped_line = None - # was sys.argv[2] but we need stdout for a pipe in bam_bed_gff_to_bigwig.xml - for i, line in enumerate(sys.stdin): - line = line.rstrip("\r\n") - if line and not line.startswith("#"): - try: - elems = line.split("\t") - start = str(int(elems[3]) - 1) - endoff = str(int(elems[4]) - 1) - # GFF format: chrom, source, name, chromStart, chromEnd, score, strand - # bedtools puts out only 4 fields: chrom, chromStart, chromEnd, score - sys.stdout.write(f"{elems[0]}\t{start}\t{endoff}\t0\n") - except Exception: - skipped_lines += 1 - if not first_skipped_line: - first_skipped_line = i + 1 - else: - skipped_lines += 1 - if not first_skipped_line: - first_skipped_line = i + 1 - - -if __name__ == "__main__": - __main__() diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/dbkeys.loc.test --- a/bbgbigwig/test-data/dbkeys.loc.test Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -# -hg38 hg38 ${__HERE__}/testing.len diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/featureCounts_input1.bam Binary file bbgbigwig/test-data/featureCounts_input1.bam has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/featureCounts_input1.bigwig Binary file bbgbigwig/test-data/featureCounts_input1.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/merlin.bed.bigwig Binary file bbgbigwig/test-data/merlin.bed.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/merlin.gff.bigwig Binary file bbgbigwig/test-data/merlin.gff.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/srma_out2.bam Binary file bbgbigwig/test-data/srma_out2.bam has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/srma_out2.bigwig Binary file bbgbigwig/test-data/srma_out2.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/test-6.bed --- a/bbgbigwig/test-data/test-6.bed Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Merlin 49 1452 chromosomal_replication_initiator_protein_DnaA 0 + -Merlin 1457 2557 DNA_polymerase_III_subunit_beta 0 + -Merlin 2557 3630 DNA_replication_and_repair_protein_RecF 0 + diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/test5.bed --- a/bbgbigwig/test-data/test5.bed Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + -chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + -chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + -chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + -chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + -chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + -chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + -chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + -chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + -chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + -chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + -chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + -chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 + -chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 + -chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 + -chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 + -chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 + diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/test5.bed.bigwig Binary file bbgbigwig/test-data/test5.bed.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/test5.gff.bigwig Binary file bbgbigwig/test-data/test5.gff.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/test5.gff3 --- a/bbgbigwig/test-data/test5.gff3 Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -##gff-version 3 -##date Tue Jun 26 10:48:17 2007 -##sequence-region ctgA 1 50000 -##source gbrowse GFFToGalaxyDumper plugin -##NOTE: All features dumped. -ctgA example my_feature 22132 24633 . + . ID=My_feature:f15 -ctgA example my_feature 46990 48410 . - . ID=My_feature:f11 -ctgA example my_feature 44705 47713 . - . ID=My_feature:f01 -ctgA example my_feature 36649 40440 . - . ID=My_feature:f03 -ctgA example my_feature 23072 23185 . + . ID=My_feature:f14 -ctgA example my_feature 37242 38653 . + . ID=My_feature:f04 -ctgA example motif 37497 40559 . - . ID=Motif:m15;Note=7-transmembrane -ctgA example my_feature 36034 38167 . + . ID=My_feature:f09 -ctgA example motif 28332 30033 . - . ID=Motif:m02;Note=HOX -ctgA example my_feature 4715 5968 . - . ID=My_feature:f05 -ctgA example motif 48253 48366 . + . ID=Motif:m01;Note=WD40 -ctgA example BAC 1000 20000 . . . ID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads -ctgA example right_end_read 19500 20000 . - . Parent=BAC:b101.2 -ctgA example left_end_read 1000 1500 . + . Parent=BAC:b101.2 -ctgA example motif 13801 14007 . - . ID=Motif:m05;Note=helix+loop+helix -ctgA example coding 1050 9000 . + . ID=mRNA:EDEN.1;Gene=EDEN -ctgA example CDS 1201 1500 . + 0 Parent=mRNA:EDEN.1 -ctgA example CDS 3000 3902 . + 0 Parent=mRNA:EDEN.1 -ctgA example CDS 5000 5500 . + 0 Parent=mRNA:EDEN.1 -ctgA example CDS 7000 7608 . + 0 Parent=mRNA:EDEN.1 -ctgA example processed_transcript 1050 9000 . + . ID=mRNA:EDEN.1 -ctgA example 5'-UTR 1050 1200 . + . Parent=mRNA:EDEN.1 -ctgA example 3'-UTR 7609 9000 . + . Parent=mRNA:EDEN.1 -ctgA est match 5410 7503 . - . ID=EST:agt830.3;Target=agt830.3+1+595 -ctgA est HSP 7000 7503 . - . Parent=EST:agt830.3;Target=agt830.3+1+504 -ctgA est HSP 5410 5500 . - . Parent=EST:agt830.3;Target=agt830.3+505+595 -ctgA example motif 46012 48851 . + . ID=Motif:m09;Note=kinase -ctgA example match 6885 8999 . - . ID=Match:seg03 -ctgA example HSP 8306 8999 . - . Parent=Match:seg03 -ctgA example HSP 8055 8080 . - . Parent=Match:seg03 -ctgA example HSP 7410 7737 . - . Parent=Match:seg03 -ctgA example HSP 6885 7241 . - . Parent=Match:seg03 -ctgA example my_feature 13280 16394 . + . ID=My_feature:f08 diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/test-data/testing.len --- a/bbgbigwig/test-data/testing.len Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -dummy_chr 100000000 -chr1 1000000000 -X 1000000000 -16 1000000000 -ctgA 1000000000 -Merlin 10000000 -super_1 1000000000 -chr1 1000000000 -chr7 2000000000 -chrX 2000000000 -phiX174 100000000 -random_phiX_region_1 100000000 -random_phiX_region_2 100000000 -random_phiX_region_3 100000000 -random_phiX_region_4 100000000 -random_phiX_region_5 100000000 -random_phiX_region_6 100000000 -random_phiX_region_7 100000000 -random_phiX_region_8 100000000 -random_phiX_region_9 100000000 -random_phiX_region_10 100000000 -random_phiX_region_11 100000000 -random_phiX_region_12 100000000 -random_phiX_region_13 100000000 -random_phiX_region_14 100000000 -random_phiX_region_15 100000000 -random_phiX_region_16 100000000 -random_phiX_region_17 100000000 -random_phiX_region_18 100000000 -random_phiX_region_19 100000000 diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/tool-data/dbkeys.loc.sample --- a/bbgbigwig/tool-data/dbkeys.loc.sample Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -# diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/tool-data/testing.len --- a/bbgbigwig/tool-data/testing.len Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -dummy_chr 100000000 -chr1 1000000000 -X 1000000000 -16 1000000000 -ctgA 1000000000 -Merlin 10000000 -super_1 1000000000 -chr1 1000000000 -chr7 2000000000 -chrX 20000000000 -phiX174 100000000 -random_phiX_region_1 100000000 -random_phiX_region_2 100000000 -random_phiX_region_3 100000000 -random_phiX_region_4 100000000 -random_phiX_region_5 100000000 -random_phiX_region_6 100000000 -random_phiX_region_7 100000000 -random_phiX_region_8 100000000 -random_phiX_region_9 100000000 -random_phiX_region_10 100000000 -random_phiX_region_11 100000000 -random_phiX_region_12 100000000 -random_phiX_region_13 100000000 -random_phiX_region_14 100000000 -random_phiX_region_15 100000000 -random_phiX_region_16 100000000 -random_phiX_region_17 100000000 -random_phiX_region_18 100000000 -random_phiX_region_19 100000000 diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/tool_data_table_conf.xml.sample --- a/bbgbigwig/tool_data_table_conf.xml.sample Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ - - - - value, name, len_path - -

- \ No newline at end of file diff -r 4eadb56fa314 -r 49c6f715bc82 bbgbigwig/tool_data_table_conf.xml.test --- a/bbgbigwig/tool_data_table_conf.xml.test Fri Jun 14 06:06:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ - - - - value, name, len_path - -

- diff -r 4eadb56fa314 -r 49c6f715bc82 gff_to_bed_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff_to_bed_converter.py Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,33 @@ +#!/usr/bin/env python + +import sys + +assert sys.version_info[:2] >= (2, 6) + + +def __main__(): + skipped_lines = 0 + first_skipped_line = None + # was sys.argv[2] but we need stdout for a pipe in bam_bed_gff_to_bigwig.xml + for i, line in enumerate(sys.stdin): + line = line.rstrip("\r\n") + if line and not line.startswith("#"): + try: + elems = line.split("\t") + start = str(int(elems[3]) - 1) + endoff = str(int(elems[4]) - 1) + # GFF format: chrom, source, name, chromStart, chromEnd, score, strand + # bedtools puts out only 4 fields: chrom, chromStart, chromEnd, score + sys.stdout.write(f"{elems[0]}\t{start}\t{endoff}\t0\n") + except Exception: + skipped_lines += 1 + if not first_skipped_line: + first_skipped_line = i + 1 + else: + skipped_lines += 1 + if not first_skipped_line: + first_skipped_line = i + 1 + + +if __name__ == "__main__": + __main__() diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/dbkeys.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbkeys.loc.test Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,2 @@ +# +hg38 hg38 ${__HERE__}/testing.len diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/featureCounts_input1.bam Binary file test-data/featureCounts_input1.bam has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/featureCounts_input1.bigwig Binary file test-data/featureCounts_input1.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/merlin.bed.bigwig Binary file test-data/merlin.bed.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/merlin.gff.bigwig Binary file test-data/merlin.gff.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/srma_out2.bam Binary file test-data/srma_out2.bam has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/srma_out2.bigwig Binary file test-data/srma_out2.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/test-6.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-6.bed Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,3 @@ +Merlin 49 1452 chromosomal_replication_initiator_protein_DnaA 0 + +Merlin 1457 2557 DNA_polymerase_III_subunit_beta 0 + +Merlin 2557 3630 DNA_replication_and_repair_protein_RecF 0 + diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/test5.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5.bed Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,17 @@ +chr7 115444712 115444739 CCDS5763.1_cds_0_0_chr7_115444713_f 0 + +chr7 115468538 115468624 CCDS5763.1_cds_1_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5763.1_cds_2_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5763.1_cds_3_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5763.1_cds_4_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5763.1_cds_5_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5763.1_cds_6_0_chr7_115491299_f 0 + +chr7 115468538 115468624 CCDS5764.1_cds_0_0_chr7_115468539_f 0 + +chr7 115483024 115483277 CCDS5764.1_cds_1_0_chr7_115483025_f 0 + +chr7 115484165 115484501 CCDS5764.1_cds_2_0_chr7_115484166_f 0 + +chr7 115485764 115485980 CCDS5764.1_cds_3_0_chr7_115485765_f 0 + +chr7 115486322 115486481 CCDS5764.1_cds_4_0_chr7_115486323_f 0 + +chr7 115491298 115491487 CCDS5764.1_cds_5_0_chr7_115491299_f 0 + +chr7 115733786 115733936 CCDS5766.1_cds_0_0_chr7_115733787_f 0 + +chr7 115734264 115734452 CCDS5766.1_cds_1_0_chr7_115734265_f 0 + +chr7 115739975 115740126 CCDS5766.1_cds_2_0_chr7_115739976_f 0 + +chr7 115733786 115733936 CCDS5765.1_cds_0_0_chr7_115733787_f 0 + diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/test5.bed.bigwig Binary file test-data/test5.bed.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/test5.gff.bigwig Binary file test-data/test5.gff.bigwig has changed diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/test5.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test5.gff3 Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,38 @@ +##gff-version 3 +##date Tue Jun 26 10:48:17 2007 +##sequence-region ctgA 1 50000 +##source gbrowse GFFToGalaxyDumper plugin +##NOTE: All features dumped. +ctgA example my_feature 22132 24633 . + . ID=My_feature:f15 +ctgA example my_feature 46990 48410 . - . ID=My_feature:f11 +ctgA example my_feature 44705 47713 . - . ID=My_feature:f01 +ctgA example my_feature 36649 40440 . - . ID=My_feature:f03 +ctgA example my_feature 23072 23185 . + . ID=My_feature:f14 +ctgA example my_feature 37242 38653 . + . ID=My_feature:f04 +ctgA example motif 37497 40559 . - . ID=Motif:m15;Note=7-transmembrane +ctgA example my_feature 36034 38167 . + . ID=My_feature:f09 +ctgA example motif 28332 30033 . - . ID=Motif:m02;Note=HOX +ctgA example my_feature 4715 5968 . - . ID=My_feature:f05 +ctgA example motif 48253 48366 . + . ID=Motif:m01;Note=WD40 +ctgA example BAC 1000 20000 . . . ID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads +ctgA example right_end_read 19500 20000 . - . Parent=BAC:b101.2 +ctgA example left_end_read 1000 1500 . + . Parent=BAC:b101.2 +ctgA example motif 13801 14007 . - . ID=Motif:m05;Note=helix+loop+helix +ctgA example coding 1050 9000 . + . ID=mRNA:EDEN.1;Gene=EDEN +ctgA example CDS 1201 1500 . + 0 Parent=mRNA:EDEN.1 +ctgA example CDS 3000 3902 . + 0 Parent=mRNA:EDEN.1 +ctgA example CDS 5000 5500 . + 0 Parent=mRNA:EDEN.1 +ctgA example CDS 7000 7608 . + 0 Parent=mRNA:EDEN.1 +ctgA example processed_transcript 1050 9000 . + . ID=mRNA:EDEN.1 +ctgA example 5'-UTR 1050 1200 . + . Parent=mRNA:EDEN.1 +ctgA example 3'-UTR 7609 9000 . + . Parent=mRNA:EDEN.1 +ctgA est match 5410 7503 . - . ID=EST:agt830.3;Target=agt830.3+1+595 +ctgA est HSP 7000 7503 . - . Parent=EST:agt830.3;Target=agt830.3+1+504 +ctgA est HSP 5410 5500 . - . Parent=EST:agt830.3;Target=agt830.3+505+595 +ctgA example motif 46012 48851 . + . ID=Motif:m09;Note=kinase +ctgA example match 6885 8999 . - . ID=Match:seg03 +ctgA example HSP 8306 8999 . - . Parent=Match:seg03 +ctgA example HSP 8055 8080 . - . Parent=Match:seg03 +ctgA example HSP 7410 7737 . - . Parent=Match:seg03 +ctgA example HSP 6885 7241 . - . Parent=Match:seg03 +ctgA example my_feature 13280 16394 . + . ID=My_feature:f08 diff -r 4eadb56fa314 -r 49c6f715bc82 test-data/testing.len --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testing.len Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,30 @@ +dummy_chr 100000000 +chr1 1000000000 +X 1000000000 +16 1000000000 +ctgA 1000000000 +Merlin 10000000 +super_1 1000000000 +chr1 1000000000 +chr7 2000000000 +chrX 2000000000 +phiX174 100000000 +random_phiX_region_1 100000000 +random_phiX_region_2 100000000 +random_phiX_region_3 100000000 +random_phiX_region_4 100000000 +random_phiX_region_5 100000000 +random_phiX_region_6 100000000 +random_phiX_region_7 100000000 +random_phiX_region_8 100000000 +random_phiX_region_9 100000000 +random_phiX_region_10 100000000 +random_phiX_region_11 100000000 +random_phiX_region_12 100000000 +random_phiX_region_13 100000000 +random_phiX_region_14 100000000 +random_phiX_region_15 100000000 +random_phiX_region_16 100000000 +random_phiX_region_17 100000000 +random_phiX_region_18 100000000 +random_phiX_region_19 100000000 diff -r 4eadb56fa314 -r 49c6f715bc82 tool-data/dbkeys.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/dbkeys.loc.sample Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,1 @@ +# diff -r 4eadb56fa314 -r 49c6f715bc82 tool-data/testing.len --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/testing.len Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,30 @@ +dummy_chr 100000000 +chr1 1000000000 +X 1000000000 +16 1000000000 +ctgA 1000000000 +Merlin 10000000 +super_1 1000000000 +chr1 1000000000 +chr7 2000000000 +chrX 20000000000 +phiX174 100000000 +random_phiX_region_1 100000000 +random_phiX_region_2 100000000 +random_phiX_region_3 100000000 +random_phiX_region_4 100000000 +random_phiX_region_5 100000000 +random_phiX_region_6 100000000 +random_phiX_region_7 100000000 +random_phiX_region_8 100000000 +random_phiX_region_9 100000000 +random_phiX_region_10 100000000 +random_phiX_region_11 100000000 +random_phiX_region_12 100000000 +random_phiX_region_13 100000000 +random_phiX_region_14 100000000 +random_phiX_region_15 100000000 +random_phiX_region_16 100000000 +random_phiX_region_17 100000000 +random_phiX_region_18 100000000 +random_phiX_region_19 100000000 diff -r 4eadb56fa314 -r 49c6f715bc82 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,7 @@ + + + + value, name, len_path + +

+ \ No newline at end of file diff -r 4eadb56fa314 -r 49c6f715bc82 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Jun 14 06:47:20 2024 +0000 @@ -0,0 +1,7 @@ + + + + value, name, len_path + +