Intro
abed
is annotation tool for bed files.
It annotates bed files with gene names, gene ids, and feature information from a provided annotations file (GTF).
Examples
$ abed -b K27AC_chip1_peaks.bed -g hg38.83.gtf -s hg38.83.genome \
-c "chr,start,end,name,signal_value,strand,fold_change,p_value,Benjamini_Hochberg_FDR" \
-p 1000,200 -o annotated.bed.tsv
Output files
annotated.bed.tsv
chr start end name signal_value strand fold_change p_value Benjamini_Hochberg_FDR annotated_gene_features
1 1205710 1205930 chip1_peak_2799 241.68113891 . 12.1486518993 1.18025200195e-06 0.00504618822857 TNFRSF18/ENSG00000186891: promoter
1 1616560 1616780 chip1_peak_5889 71.050614487 . 3.57152066778 5.81256160902e-06 0.0113928182561 RP11-345P4.9/ENSG00000272106: promoter; MIB2/ENSG00000197530: five_prime_utr, exon, promoter, CDS
1 1892440 1892660 chip1_peak_3527 243.582136289 . 12.2442098543 1.93910073064e-06 0.00651852531479 RP1-140A9.1/ENSG00000231050: exon
1 2212540 2212870 chip1_peak_25 81.3040545107 . 4.08693314134 9.22431065693e-12 4.99354651514e-06 FAAP20/ENSG00000162585: exon, promoter; RP11-181G12.4/ENSG00000234396: exon, promoter
1 3712500 3712720 chip1_peak_6234 38.8954679096 . 1.95516912169 6.52541908518e-06 0.0120595193967 TP73/ENSG00000078900; RP5-1092A11.2/ENSG00000235131
1 3772780 3773000 chip1_peak_4768 120.93909338 . 6.0792784787 3.69904369916e-06 0.00905667169324 SMIM1/ENSG00000235169: five_prime_utr, exon, promoter
1 4680280 4680500 chip1_peak_7707 110.246753848 . 5.54180372353 9.96101899764e-06 0.014735318932 AJAP1/ENSG00000196581
1 5652020 5652240 chip1_peak_526 145.04841094 . 7.29118813738 2.00633103721e-08 0.000477258277665 RP11-154H17.1/ENSG00000236948
1 6330720 6330940 chip1_peak_7213 153.651918104 . 7.72366298467 8.71110008982e-06 0.0138290963917 ACOT7/ENSG00000097021
1 6362730 6362950 chip1_peak_7153 87.6949697748 . 4.40818702657 8.54621275409e-06 0.0136908694171 ACOT7/ENSG00000097021
1 6421360 6421580 chip1_peak_5440 279.339262378 . 14.0416230896 4.90344812744e-06 0.0104638228061 HES2/ENSG00000069812
1 6423890 6424220 chip1_peak_3597 398.194019503 . 20.0161276677 2.01692509039e-06 0.00664985446589 ESPN/ENSG00000187017: promoter; HES2/ENSG00000069812
1 6859710 6860040 chip1_peak_53 79.510332304 . 3.99676761667 4.53361213715e-11 1.10018291319e-05 CAMTA1/ENSG00000171735
1 7400250 7400470 chip1_peak_5957 122.230907584 . 6.14421445654 5.936688264e-06 0.011503154056 CAMTA1/ENSG00000171735
1 7705060 7705390 chip1_peak_1184 96.6376920702 . 4.85771329365 1.53921999586e-07 0.001601221552 CAMTA1/ENSG00000171735
1 7745650 7745870 chip1_peak_746 105.6964562 . 5.31307266734 4.97095836632e-08 0.000833924420617 CAMTA1/ENSG00000171735: exon, CDS
Help
$ abed --help
usage: abed [-h] [-b BED] [-g GTF] [-s SIZES] [-c COLUMNS] [-p PROMOTER]
[-o OUTPUT]
abed is an annotation tool for bed files.
optional arguments:
-h, --help show this help message and exit
-b BED, --bed BED /path/to/file.bed (default: None)
-g GTF, --gtf GTF /path/to/file.gtf (default: None)
-s SIZES, --sizes SIZES
/path/to/file.genome. Tab separated values of
'chromosome name' and 'size' information. (default:
None)
-c COLUMNS, --columns COLUMNS
A comma separated string of column headers to use when
reading in the bed file. eg.: 'chr,start,end,name'.
(default: None)
-p PROMOTER, --promoter PROMOTER
A comma separated list containing the upstream start
of the promoter region from the TSS and the downstream
end of the promoter region from the TSS. eg.:
'1000,200'. (default: None)
-o OUTPUT, --output OUTPUT
/path/to/output.tsv. (default: None)