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analyze_bed
Martin Asser Hansen edited this page Oct 2, 2015
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analyze_bed analyzes all BED entries in the stream and add the follow keys to each record which is practical for filtering BED records using grab.
- EXONS - The number of exons in the current record.
- EXON_LEN_0 - The length of the first exon in the current record.
- EXON_LEN_1 - The lenght of the second exon (_2,_3, _4 for subsequent exons) in the current record.
- EXON_LEN_-1 - The length of the last exon in the current record.
- EXON_MAX_LEN - The maximum exon length in the stream.
- EXON_MIN_LEN - The minimum exon length in the stream.
- EXON_MEAN_LEN - The mean exon length in the stream.
- INTRONS - The number of introns in the current record.
- INTRON_LEN_0 - The length of the first intron in the current record.
- INTRON_LEN_-1 - The length of the last intron in the current record.
- INTRON_MAX_LEN - The maximum intron length in the stream.
- INTRON_MIN_LEN - The minimum intron length in the stream.
- INTRON_MEAN_LEN - The mean intron length in the stream._
See read_bed for more information about BED records.
... | analyze_bed [options]
[-? | --help] # Print full usage description.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following 5 BED entries in the file `test.bed':
chr4 31176 31602 AA695812 0 - 31176 31602 0 1 426, 0,
chr4 44448 44874 AA695812 0 - 44448 44874 0 1 426, 0,
chr4 50522 50841 AA142091 0 - 50522 50841 0 2 81,237, 0,82,
chr4 57489 57808 AA142091 0 - 57489 57808 0 2 81,237, 0,82,
chr4 59352 59778 AA695812 0 - 59352 59778 0 1 426, 0,
To analyze these entries read the BED file with read_bed:
read_bed -i test.bed | analyze_bed
EXON_MAX_LEN: 426
INTRONS: 0
Q_ID: AA695812
EXON_LEN_-1: 426
BED_LEN: 426
BLOCKCOUNT: 1
CHR: chr4
EXON_MEAN_LEN: 426
THICK_BEG: 31176
BLOCKSIZES: 426,
STRAND: -
CHR_END: 31601
THICK_END: 31601
SCORE: 0
CHR_BEG: 31176
REC_TYPE: BED
EXONS: 1
Q_BEGS: 0,
ITEMRGB: 0
EXON_MIN_LEN: 426
BED_COLS: 12
EXON_LEN_0: 426
---
EXON_MAX_LEN: 426
INTRONS: 0
Q_ID: AA695812
EXON_LEN_-1: 426
BED_LEN: 426
BLOCKCOUNT: 1
CHR: chr4
EXON_MEAN_LEN: 426
THICK_BEG: 44448
BLOCKSIZES: 426,
STRAND: -
CHR_END: 44873
THICK_END: 44873
SCORE: 0
CHR_BEG: 44448
REC_TYPE: BED
EXONS: 1
Q_BEGS: 0,
ITEMRGB: 0
EXON_MIN_LEN: 426
BED_COLS: 12
EXON_LEN_0: 426
---
INTRON_LEN_-1: 1
EXON_MAX_LEN: 237
INTRON_MEAN_LEN: 1
INTRON_MAX_LEN: 1
INTRONS: 1
Q_ID: AA142091
EXON_LEN_1: 237
EXON_LEN_-1: 237
BED_LEN: 319
BLOCKCOUNT: 2
CHR: chr4
EXON_MEAN_LEN: 159
THICK_BEG: 50522
BLOCKSIZES: 81,237,
STRAND: -
CHR_END: 50840
THICK_END: 50840
SCORE: 0
CHR_BEG: 50522
REC_TYPE: BED
INTRON_LEN_0: 1
EXONS: 2
INTRON_MIN_LEN: 1
Q_BEGS: 0,82,
ITEMRGB: 0
EXON_MIN_LEN: 81
BED_COLS: 12
EXON_LEN_0: 81
---
INTRON_LEN_-1: 1
EXON_MAX_LEN: 237
INTRON_MEAN_LEN: 1
INTRON_MAX_LEN: 1
INTRONS: 1
Q_ID: AA142091
EXON_LEN_1: 237
EXON_LEN_-1: 237
BED_LEN: 319
BLOCKCOUNT: 2
CHR: chr4
EXON_MEAN_LEN: 159
THICK_BEG: 57489
BLOCKSIZES: 81,237,
STRAND: -
CHR_END: 57807
THICK_END: 57807
SCORE: 0
CHR_BEG: 57489
REC_TYPE: BED
INTRON_LEN_0: 1
EXONS: 2
INTRON_MIN_LEN: 1
Q_BEGS: 0,82,
ITEMRGB: 0
EXON_MIN_LEN: 81
BED_COLS: 12
EXON_LEN_0: 81
---
EXON_MAX_LEN: 426
INTRONS: 0
Q_ID: AA695812
EXON_LEN_-1: 426
BED_LEN: 426
BLOCKCOUNT: 1
CHR: chr4
EXON_MEAN_LEN: 426
THICK_BEG: 59352
BLOCKSIZES: 426,
STRAND: -
CHR_END: 59777
THICK_END: 59777
SCORE: 0
CHR_BEG: 59352
REC_TYPE: BED
EXONS: 1
Q_BEGS: 0,
ITEMRGB: 0
EXON_MIN_LEN: 426
BED_COLS: 12
EXON_LEN_0: 426
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
analyze_bed is part of the Biopieces framework.