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biodata-0.0.6
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مشاهده بیشترتوضیحات
A python package for common biological data I/O
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biodata-0.0.6 |
| نام | biodata |
| نسخه کتابخانه | 0.0.6 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Alden Leung |
| ایمیل نویسنده | alden.leung@gmail.com |
| آدرس صفحه اصلی | https://github.com/aldenleung/biodata/ |
| آدرس اینترنتی | https://pypi.org/project/biodata/ |
| مجوز | - |
# biodata - A standard biological data processing package
The biodata package provides a standard API to access all different kinds of biological data using similar syntax. For each data type, data is processed by the corresponding reader (XX-Reader) and writer (XX-Writer) as a stream of entries. For example, `FASTAReader` is used to process FASTA file. A call to the method `read()` from `FASTAReader` yields a `FASTA` object. For indexed file, random access is supported through the XX-IReader. For example, an indexed FASTA file can be access by `FASTAIReader`.
## Installation
```
pip install biodata
```
## Quick Start
For more advanced use, please see the Basic Usage section.
```python
# Reading file contents
from biodata.fasta import FASTAReader
seq_dict = FASTAReader.read_all(lambda fr: {f.name:f.seq for f in fr}, "input.fa")
from biodata.bed import BEDReader
from genomictools import GenomicCollection
beds = BEDReader.read_all(GenomicCollection, "input.bed")
from biodata.gff import GFF3Reader
from genomictools import GenomicCollection
gff3s = GFF3Reader.read_all(GenomicCollection, "input.gff3")
from biodata.gff import GTFReader
from genomictools import GenomicCollection
gtfs = GTFReader.read_all(GenomicCollection, "input.gtf")
```
## Basic usage
We will demonstrate the use of biodata package using FASTA file.
```
>seq1
ACGT
>seq2
CCCGGGAAA
```
### Read the first entry
```python
from biodata.fasta import FASTAReader
with FASTAReader(filename) as fr:
f = fr.read()
print(f.name, f.seq) # seq1 ACGT
```
### Read entry by entry
```python
from biodata.fasta import FASTAReader
with FASTAReader(filename) as fr:
for f in fr:
print(f.name, f.seq)
# seq1 ACGT
# seq2 CCCGGGAAA
with BEDReader(bedfile) as br:
for b in br:
print(b.name, str(b.genomic_pos))
```
### Read all entries at once
```python
from biodata.fasta import FASTAReader
fasta_entries = FASTAReader.read_all(list, filename) # list of FASTA
seq_dict = FASTAReader.read_all(lambda fr: {f.name:f.seq for f in fr}, filename)
# A dictionary with fasta name as key and fasta sequence as value
# {"seq1": "ACGT", "seq2": "CCCGGGAAA"}
# For genomic range data, one could also use GenomicCollection to store them:
from biodata.bed import BEDReader
from genomictools import GenomicCollection
beds = BEDReader.read_all(GenomicCollection, filename)
```
### Peek an entry
```python
from biodata.fasta import FASTAReader
with FASTAReader(filename) as fr:
f = fr.peek() # Only peek the entry without proceeding to the next entry
print(f.name, f.seq) # seq1 ACGT
f = fr.read() # Read the entry and proceed to the next entry
print(f.name, f.seq) # seq1 ACGT
f = fr.read()
print(f.name, f.seq) # seq2 CCCGGGAAA
```
### Read an entry from StringIO
```python
# TextIOBase can be used as input
import io
from biodata.fasta import FASTAReader
FASTAReader.read_all(list, io.StringIO(">seq1\nACGT\n>seq2\nCCCGGGAAA\n"))
```
### Read an indexed file
```python
from biodata.fasta import FASTAIReader
from genomictools import GenomicPos, StrandedGenomicPos
from biodata.bed import BED
fir = FASTAIReader(filename, faifilename) # fai file can be created using 'samtools faidx filename'
f = fir[GenomicPos("seq2:1-4")] # Read from a region without strand
print(f.name, f.seq) # seq2:1-4 CCCG
f = fir[StrandedGenomicPos("seq2:1-4:-")] # Read from a region with strand
print(f.name, f.seq) # seq2:1-4:- CGGG
f = fir[BED("seq2", 0, 4, strand="-")] # Equivalent to StrandedGenomicPos but a BED entry is used
print(f.name, f.seq) # seq2:1-4:- CGGG
fir.close()
```
### Write entry by entry
```python
from biodata.fasta import FASTA, FASTAWriter
with FASTAWriter(output_file) as fw:
fw.write(FASTA("seq1", "ACGT"))
fw.write(FASTA("seq2", "CCCGGGAAA"))
```
### Write all entries at once
```python
from biodata.fasta import FASTA, FASTAWriter
fasta_entries = [FASTA("seq1", "ACGT"), fw.write(FASTA("seq2", "CCCGGGAAA"))]
FASTAWriter.write_all(fasta_entries, output_file)
```
## List of supported format
1. Delimited - tsv, csv (`biodata.delimited`)
2. FASTA, FASTQ (`biodata.fasta`)
3. BED3, BED, BEDX, BEDGraph, BEDPE (`biodata.bed`)
4. GFF3, GTF (GFF2) (`biodata.gff`)
5. bwa FastMap (`biodata.bwa.fastmap`)
6. MEME Motif Format (`biodata.meme`)
Future supported formats.
1. VCF (`biodata.vcf`)
3. BigBed (`biodata.bed`)
4. BigWig (`biodata.bigwig`)
## Extension of BaseReader
Users can extend the `BaseReader` and `BaseWriter` class easily.
```python
class ExampleNode(object):
def __init__(self, value1, value2):
self.value1 = value1
self.value2 = value2
class ExampleNodeReader(BaseReader):
def __init__(self, filename):
super(ExampleNodeReader, self).__init__(filename)
def _read(self):
if self.line is None:
return None
words_array = self.line.split('\t')
value1 = words_array[0]
value2 = words_array[1]
self.proceed_next_line()
return ExampleNode(value1, value2)
filename = "SomeDocument.txt"
with ExampleNodeReader(filename) as er:
for node in er:
print(node.value1, node.value2)
```
نیازمندی
| مقدار | نام |
|---|---|
| >=0.0.5 | genomictools |
نحوه نصب
نصب پکیج whl biodata-0.0.6:
pip install biodata-0.0.6.whl
نصب پکیج tar.gz biodata-0.0.6:
pip install biodata-0.0.6.tar.gz