python - BioPython AlignIO ValueError 表示字符串的长度必须相同？

Question

输入fasta格式的文本文件:

http://www.jcvi.org/cgi-bin/tigrfams/DownloadFile.cgi?file=/opt/www/www_tmp/tigrfams/fa_alignment_PF00205.txt

#!/usr/bin/python

from Bio import AlignIO

seq_file = open('/path/to/fa_alignment_PF00205.txt')
alignment = AlignIO.read(seq_file, "fasta")

错误:

ValueError: Sequences must all be the same length

输入序列的长度不必相同，因为在 ClustalOmega 上您可以对齐不同长度的序列。

这也不起作用...得到同样的错误:

alignment = AlignIO.parse(seq_file,"fasta")

for record in alignment:
    print(record.id)

有没有熟悉 BioPython 的人知道如何绕过这个问题来比对来自 fasta 文件的序列？

Answer 1

填充太短的序列并将记录写入临时 FASTA 文件。比你的对齐方式按预期工作:

from Bio import AlignIO
from Bio import SeqIO
from Bio import Seq
import os

input_file = '/path/to/fa_alignment_PF00205.txt'
records = SeqIO.parse(input_file, 'fasta')
records = list(records) # make a copy, otherwise our generator
                        # is exhausted after calculating maxlen
maxlen = max(len(record.seq) for record in records)

# pad sequences so that they all have the same length
for record in records:
    if len(record.seq) != maxlen:
        sequence = str(record.seq).ljust(maxlen, '.')
        record.seq = Seq.Seq(sequence)
assert all(len(record.seq) == maxlen for record in records)

# write to temporary file and do alignment
output_file = '{}_padded.fasta'.format(os.path.splitext(input_file)[0])
with open(output_file, 'w') as f:
    SeqIO.write(records, f, 'fasta')
alignment = AlignIO.read(output_file, "fasta")
print alignment

这个输出:

SingleLetterAlphabet() alignment with 104 rows and 275 columns
TKAAIELIADHQ.......LTVLADLLVHRLQ..AVKELEALLA...QAL SP|A2VGF0.1/208-339
LQELASVINQHE...KV..MLFCGHGCR...Y..AVEEVMALAK...EDL SP|A3D4X6.1/190-319
IKKIAQAIEKAK...KP..VICAGGGVINS.N..ASEELLTLSR...KEL SP|A3DID9.1/192-327
IDEAAEAINKAE...RP..VILAGGGVSIA.G..ANKELFEFAT...QLL SP|A3DIY4.1/192-327
IEKAIELINSSQ...RP..FICSGGGVISS.E..ASEELIQFAE...KIL SP|A4XHS0.1/191-326
IKRAVEAIENSQ...RP..VICSGGGVIAS.R..ASDELKILVE...SEI SP|A4XIL5.1/194-328
VRQAARIIMESE...RP..VIYAGGGVRIS.G..AAPELLELSE...RAL SP|A5D4V9.1/192-327
LQALAQRILRAQ...RP..VIITGDEIVKS.D..ALQAAADFAS...LQL SP|A5ECG1.1/192-328
VEKAVELLWSAR...RV..LVISGRGAR...G..AGPELIGLLD...RAM SP|A5EDH4.1/198-324
IQKAARLIETAE...KP..VIIAGHGVNIS.G..ANEELKTLAE...KSL SP|A5FR34.1/193-328
LDALARDLDSAA...RV..TIYAGIGAR...G..AAARVVQLAG...EAL SP|A5FTR0.1/189-317
VADVAALLRAAR...RP..VIVAGGGVIHSG...AEERLATFAA...DAL SP|A5G0X6.1/217-351
IAEAVSALKGAK...RP..IIYTGGGLINS.GPESAELIVQLAK...RAL SP|A5G2E1.1/199-336
LKKAAEIINRAK...RP..LIYAGGGITLA.G..ASAELRALAA...ALL SP|A5GC69.1/192-327
CRDIVGKLLQSH...RP..VVLGGTGVRLS.R..TEQRLLALVE...DVF SP|A5W0I1.1/200-336
LDQAALKLAAAE...RP..MIIAGGGA..L.H..AAEQLAQLSA...AGL SP|A5W220.1/196-326
LQRAADILNTGH...KV..AILVGAGAL...Q..ATEQVIAIAE...RAL SP|A5W364.1/198-328
IRKAAEMLLAAK...RP..VVYSGGGVILG.G..GSEALTEIAK...SEM SP|A5W954.1/196-331
...
LTELQERLANAQ...RP..VVILGGSRWSD.A..AVQQFTRFAE...... SP|Q220C3.1/190-328