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https://github.com/pwwang/wigtools
A set of tools for wiggle file
https://github.com/pwwang/wigtools
bigwig wiggle-files
Last synced: 14 days ago
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A set of tools for wiggle file
- Host: GitHub
- URL: https://github.com/pwwang/wigtools
- Owner: pwwang
- License: mit
- Created: 2020-05-03T21:56:01.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-05-05T15:27:59.000Z (over 4 years ago)
- Last Synced: 2024-12-10T04:27:01.752Z (24 days ago)
- Topics: bigwig, wiggle-files
- Language: Python
- Size: 23.4 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# wigtools
A set of tools for wiggle file
## Installation
```
pip install wigtools
```
## Usage
```bash console
> wigtools
Description:
A set of tools for wiggle file
Usage:
wigtools [OPTIONS]
Global optional options:
-h, -H, --help - Show help message and exit.
Available commands:
switch-base - Switch the coordinate base of a wiggle file.
sort - Sort the blocks in a wiggle file by chrom and start. Chromosomes will be \
sorted the way sort -V does.
stats - Statistics for data in a wiggle file for each block
reshape - Generate a new wiggle file and reshape the blocks to the query regions
query - Find the blocks that intersect with the query regions
help [COMMAND] - Print help message for the command and exit.
```
### Switch coordinate base for a wiggle file
```bash console
> cat test.wig
variableStep chrom=chr
1 1.0
2 2.0
> cat test.wig | wigtools switch-base --to 0
variableStep chrom=chr span=1
0 1.0
1 2.0
```
### Sort a wiggle file
```bash console
> cat test-unsorted.wig
variableStep chrom=chr
5 1.0
6 2.0
variableStep chrom=chr
1 1.0
2 2.0
> cat test.wig-unsorted.wig | wigtools sort
variableStep chrom=chr span=1
1 1.0
2 2.0
variableStep chrom=chr span=1
5 1.0
6 2.0
```
### Calculate the statistics of each block
```bash console
> cat test-unsorted.wig | wigtools sort | wigtools stats
Chrom Start End min max mean median sum count bp
chr 1 2 1.0 2.0 1.5 1.5 3.0 2 2
chr 5 6 1.0 2.0 1.5 1.5 3.0 2 2
> cat test-unsorted.wig | wigtools sort | wigtools stats --stats mean count --nohead
chr 1 2 1.5 2
chr 5 6 1.5 2
```
### Query a wiggle file to find blocks
```bash console
> cat query.bed
chr 2 3
> wigtools query -i test-unsorted.wig --qfile query.bed
variableStep chrom=chr span=1
1 1.0
2 2.0
> wigtools query -i test-unsorted.wig --qfile query.bed --qbase 0
# No overlapping blocks
```
### Reshape the blocks in query regions
```bash console
> cat reshape.bed
chr 1 8
> cat test-unsorted.wig | wigtools sort | wigtools reshape --qfile reshape.bed
variableStep chrom=chr span=1
1 1.0
2 2.0
5 1.0
6 2.0
```
### Split blocks into different files
```bash console
> wigtools split -i test-unsorted.wig --outprefix outdir/split
> ls outdir/
split_chr_1_2.wig split_chr_5_6.wig
> cat split_chr_1_2.wig
variableStep chrom=chr span=1
1 1.0
2 2.0
```