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BioPython AlignIO ValueError says strings must be same length?

Input fasta-format text file:

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")

Error:

ValueError: Sequences must all be the same length

The input sequences shouldn't have to be the same length since on ClustalOmega you can align sequences of differing lengths.

This also doesn't work...gets the same error:

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

for record in alignment:
    print(record.id)

Does anybody who is familiar with BioPython know how to get around this to align sequences from fasta files?

2个回答

    最佳答案
  1. Pad the sequence that is too short and write the records to to a temporary FASTA file. Than your alignments works as expected:

    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
    

    This outputs:

    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
    
  2. 参考答案2
  3. your problem is last record of fasta ... tail -9 fa_alignment_PF00205.txt

    >SP|Q21VK8.1/229-357
    LQAALAALAKAE...RP..LLVIGSQALVLSK..QAEHLAEAVARL.GIPV.YLSGMA..RGLLG.R..........DH.
    ...............PLQ..................MRHQRRQALRE..ADCVLLAG.VP...CDFRLD......YGKHV
    RR..............S.AT.........L..IAA.N......................RSA.........KDARLNR..
    .......K...PD.IAAIGDAG.......LFLQAL
    >SP|Q220C3.1/190-328
    LTELQERLANAQ...RP..VVILGGSRWSD.A..AVQQFTRFAEAF.SLPV.FCSFRR..QMLFS.A..........NH.
    ...............ACY...AG.DLGLG.A.....NQRLLARI.RQ..SDLILLLG.GR...MSEVPS......QGYEL
    LGIPAPQQ...........D
    

    Sequence with id SP|Q220C3.1/190-328 has different length than other sequences