ลอง biopython

สีดำ = คำสั่ง  สีน้ำเงิน = ผล

Python 2.5.2 (r252:60911, Jul 31 2008, 17:28:52)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.Seq import Seq
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq('AGTACACTGGT', Alphabet())
>>> my_seq.complement()
Seq('TCATGTGACCA', Alphabet())

เข้าไปในไดเรกตอรี่ที่มีไฟล์ ls_orchid.fasta (หรือไฟล์ fasta อะไรที่มีลำดับเบส/โปรตีน จาก GenBank)


>>> from Bio import SeqIO
>>> handle = open("ls_orchid.fasta")
>>> for seq_record in SeqIO.parse(handle, "fasta") :print seq_record.id
... (กด enter)
gi|2765658|emb|Z78533.1|CIZ78533
gi|2765657|emb|Z78532.1|CCZ78532
gi|2765656|emb|Z78531.1|CFZ78531
gi|2765655|emb|Z78530.1|CMZ78530
gi|2765654|emb|Z78529.1|CLZ78529
gi|2765652|emb|Z78527.1|CYZ78527
gi|2765651|emb|Z78526.1|CGZ78526
gi|2765650|emb|Z78525.1|CAZ78525
gi|2765649|emb|Z78524.1|CFZ78524
gi|2765648|emb|Z78523.1|CHZ78523
gi|2765647|emb|Z78522.1|CMZ78522
gi|2765646|emb|Z78521.1|CCZ78521
gi|2765645|emb|Z78520.1|CSZ78520
gi|2765644|emb|Z78519.1|CPZ78519
gi|2765643|emb|Z78518.1|CRZ78518
gi|2765642|emb|Z78517.1|CFZ78517
gi|2765641|emb|Z78516.1|CPZ78516
gi|2765640|emb|Z78515.1|MXZ78515
gi|2765639|emb|Z78514.1|PSZ78514
gi|2765638|emb|Z78513.1|PBZ78513
gi|2765637|emb|Z78512.1|PWZ78512
gi|2765636|emb|Z78511.1|PEZ78511
gi|2765635|emb|Z78510.1|PCZ78510
gi|2765634|emb|Z78509.1|PPZ78509
gi|2765633|emb|Z78508.1|PLZ78508
gi|2765632|emb|Z78507.1|PLZ78507
gi|2765631|emb|Z78506.1|PLZ78506
gi|2765630|emb|Z78505.1|PSZ78505
gi|2765629|emb|Z78504.1|PKZ78504
gi|2765628|emb|Z78503.1|PCZ78503
gi|2765627|emb|Z78502.1|PBZ78502
gi|2765626|emb|Z78501.1|PCZ78501
gi|2765625|emb|Z78500.1|PWZ78500
gi|2765624|emb|Z78499.1|PMZ78499
gi|2765623|emb|Z78498.1|PMZ78498
gi|2765622|emb|Z78497.1|PDZ78497
gi|2765621|emb|Z78496.1|PAZ78496
gi|2765620|emb|Z78495.1|PEZ78495
gi|2765619|emb|Z78494.1|PNZ78494
gi|2765618|emb|Z78493.1|PGZ78493
gi|2765617|emb|Z78492.1|PBZ78492
gi|2765616|emb|Z78491.1|PCZ78491
gi|2765615|emb|Z78490.1|PFZ78490
gi|2765614|emb|Z78489.1|PDZ78489
gi|2765613|emb|Z78488.1|PTZ78488
gi|2765612|emb|Z78487.1|PHZ78487
gi|2765611|emb|Z78486.1|PBZ78486
gi|2765610|emb|Z78485.1|PHZ78485
gi|2765609|emb|Z78484.1|PCZ78484
gi|2765608|emb|Z78483.1|PVZ78483
gi|2765607|emb|Z78482.1|PEZ78482
gi|2765606|emb|Z78481.1|PIZ78481
gi|2765605|emb|Z78480.1|PGZ78480
gi|2765604|emb|Z78479.1|PPZ78479
gi|2765603|emb|Z78478.1|PVZ78478
gi|2765602|emb|Z78477.1|PVZ78477
gi|2765601|emb|Z78476.1|PGZ78476
gi|2765600|emb|Z78475.1|PSZ78475
gi|2765599|emb|Z78474.1|PKZ78474
gi|2765598|emb|Z78473.1|PSZ78473
gi|2765597|emb|Z78472.1|PLZ78472
gi|2765596|emb|Z78471.1|PDZ78471
gi|2765595|emb|Z78470.1|PPZ78470
gi|2765594|emb|Z78469.1|PHZ78469
gi|2765593|emb|Z78468.1|PAZ78468
gi|2765592|emb|Z78467.1|PSZ78467
gi|2765591|emb|Z78466.1|PPZ78466
gi|2765590|emb|Z78465.1|PRZ78465
gi|2765589|emb|Z78464.1|PGZ78464
gi|2765588|emb|Z78463.1|PGZ78463
gi|2765587|emb|Z78462.1|PSZ78462
gi|2765586|emb|Z78461.1|PWZ78461
gi|2765585|emb|Z78460.1|PCZ78460
gi|2765584|emb|Z78459.1|PDZ78459
gi|2765583|emb|Z78458.1|PHZ78458
gi|2765582|emb|Z78457.1|PCZ78457
gi|2765581|emb|Z78456.1|PTZ78456
gi|2765580|emb|Z78455.1|PJZ78455
gi|2765579|emb|Z78454.1|PFZ78454
gi|2765578|emb|Z78453.1|PSZ78453
gi|2765577|emb|Z78452.1|PBZ78452
gi|2765576|emb|Z78451.1|PHZ78451
gi|2765575|emb|Z78450.1|PPZ78450
gi|2765574|emb|Z78449.1|PMZ78449
gi|2765573|emb|Z78448.1|PAZ78448
gi|2765572|emb|Z78447.1|PVZ78447
gi|2765571|emb|Z78446.1|PAZ78446
gi|2765570|emb|Z78445.1|PUZ78445
gi|2765569|emb|Z78444.1|PAZ78444
gi|2765568|emb|Z78443.1|PLZ78443
gi|2765567|emb|Z78442.1|PBZ78442
gi|2765566|emb|Z78441.1|PSZ78441
gi|2765565|emb|Z78440.1|PPZ78440
gi|2765564|emb|Z78439.1|PBZ78439

>>> print repr(seq_record.seq)
Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC', SingleLetterAlphabet())
>>> print len(seq_record)
592
>>> handle.close()
>>>
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("AGTACACTGGT", IUPAC.unambiguous_dna)
>>> my_seq
Seq('AGTACACTGGT', IUPACUnambiguousDNA())
>>> my_seq.alphabet
IUPACUnambiguousDNA()

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("GATCGATGGGCCTATATAGGATCGAAAATCGC", IUPAC.unambiguous_dna)
>>> for index, letter in enumerate(my_seq) :print index, letter
... (กด enter)
0 G
1 A
2 T
3 C
4 G
5 A
6 T
7 G
8 G
9 G
10 C
11 C
12 T
13 A
14 T
15 A
16 T
17 A
18 G
19 G
20 A
21 T
22 C
23 G
24 A
25 A
26 A
27 A
28 T
29 C
30 G
31 C
>>>
>>> print my_seq[0] #first element
G
>>> print my_seq[2] #third element
T
>>> print my_seq[-1] #last element
C
>>> len(my_seq)
32
>>> my_seq.count("G")
9
>>> 100*float(my_seq.count("G") + my_seq.count("C"))/len(my_seq)
46.875
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> from Bio.SeqUtils import GC
>>> my_seq = Seq('GATCGATGGGCCTATATAGGATCGAAAATCGC', IUPAC.unambiguous_dna)
>>> GC(my_seq)
46.875

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