AttributeError: module 'array' has no attribute 'typecode'

[weishwu]

I got an error that seems to be related to pysam (version 0.20.0 with python 3.10.9):

Traceback (most recent call last):
  File "/usr/share/NanoMethPhase/nanomethphase.py", line 2242, in <module>
    main()
  File "/usr/share/NanoMethPhase/nanomethphase.py", line 2236, in main
    args.func(args)
  File "/usr/share/NanoMethPhase/nanomethphase.py", line 1194, in main_phase
    alignmentwriter(result, outHP22BisSam)
  File "/usr/share/NanoMethPhase/nanomethphase.py", line 411, in alignmentwriter
    out_samRead.set_tags(all_tags)
  File "pysam/libcalignedsegment.pyx", line 2656, in pysam.libcalignedsegment.AlignedSegment.set_tags
  File "pysam/libcalignedsegment.pyx", line 385, in pysam.libcalignedsegment.pack_tags
AttributeError: module 'array' has no attribute 'typecode'

One line in my BAM:

0a8e9d66-3338-4578-a7ff-fbe08d4e2434	2048	chr1	10001	23	169S15M1D32M1D20M1D11M1D34M1D29M1D30M7I57M1D18M2D5M1D63M12D3M1D13M4D32M1D13M1I18M1I6M1I15M3602S	*	0	0	CCCTAACCCTAACCCTCACCCCTAACCCCTAACCCTAACCCTAACCCTGACCCCTAACCCTAACCCTGACCCTAACCCTAACCCTAACCCTAACCCTCACCCTGACCCTCACCCTGACCCTGACCCTGACCCATAACCCATAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCTAACCCTAACCTAACCCTAACCCTAACCCTAACCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCGACCCTGACCCTAACCCTAACCCTAACCCTAACCCTGACCCTGACCCTAACCCTAACCCCAACCCCAACCCCAACCCCGGCCCAACCCCAACCCTAACCCTAACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCTAAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCAAATAATCACTCAAAATCATCCTTACACTAAAAATGCTAAACTATACAATTTCTAGAAGAAACAATAGAAGAAAAGCTATGTGCCTTTGGGTTTGGTAATGAATTTTAACAAATGATACAAAAGGTTGACATACACAAAAGAAATGACATTGTGGATTTCTTAATATTTAAAGTTTATACTCTGGAAGACACCTTGTTAAGAGAACAAAAAGACAAGCCACATATTGAAGAAAATATTTGCAAAATACACATCTGAGAAAGAATTTGTCTTCAAAATATATAAAAAAGTATTAAAACTAAACAATAAGTTAAACAGCCCAACTAAAAATGCACACATCTGAACAGACACCTCACCAAAGAAGATCTACAGATGGCAAGTAAAGAAACATCAAAAAGATGCTCAACATACTAGAAAACTGAAAACCACAATGAGATAGCACAGCTGGTCTATATCTCTTAGAACTGCTAAACTCCCTAAAAAATGACAAATTGCTGGAGGAAAAACAAGAACTCTTTTCATTGCCGGTGGAACACAATGTACAAGACCAAAACATGCCACCCCAAAATATAATGGTAGGAAACCAGAATATGCCACCCCAAAATATGTCCCTTTGGCTTAAGAATTATTCCAAGCTGATTATTTTGAAAAAATAAATGCTAACAAAGGAAGTTCTGAAAACAGAGTAGAAGTTACCCTTGTGTAAGGAAAATTTACATCTATAAAGGAAATCCCCATTTAAAAGCTACCTCTCTCTACACCAAGAAGAGAAGGATAACTAAATCACTAAAGAGTCTTTAATAGTGGGATATCTGCCACAACACATTTATACAGATACACAGAATTTTATGGCCAAATGGGTAAATCAAATTCTATTCAAATTAAACAAAATTACTCAGGATGTGGCGTATCCCAGGACAGAATGCATCATGTTGAAAAAGAATTTATGCTACAAATTACTATGGTTTGGATGTGGTTTGTCCCCAAGCCATGTTGAAATTTGACCCCCAATGTGGCAGTGTGGGGCGGTGGGGCCTAGTGGATGGTGTTTGGGTCATGGGGATGGATCCCTCATGAATAGATTAATGTCCTCCATGGGGGTCAGTGGGTACTGCTTCTCATAGGAATGGATTAATTCCTGCAGGAGTAGGTAATTAAAAGAGTCTGGCTTCCTTGGCTTCCCTTTTGCTTTCACTTCTGCTATGTGATCTCTGGTGCACCCCTTGCTCCCCTTCCGCTTTCCACCATGAGGTGAAAAAGACTGAAGCCCCACCAGATGCAACTGCCCAATCTCGGACATTCCAGCTACCAGTATTGTGAGCCAAATGAATCTTTTTCACTTATAAATTACCCAGCCTCAGGTATTCTGTTACAGGAAGCACAAGATGGACTAAGACACAAATGTAGGTAAAAACTCACTGAAGGTGGAGGGAAAATGGTGTTGACCTAAGTCACTTTGAAAATCAATAGAATCTGGAGGCTGAAGGCACATGAACTATACTTCATAATTGGATTACATTTTATAAAGTTATTTCCAACAGAAGCAATTGTGAACAATTGTAAAACCACAGTGTCTGTATCTGGAGTAAAACAATGACTTACATAAGTCGCAGATGGTGGGAACCAGCTTTCTCACTGTTGAAGTGGGAGGTTACAAATTAGCAAGACGAGAAGGCTAGAATGATTCCTGTGATAATAGAGATTGGGAGGATGAAGTCAACGTAAACTTATGCTTAGTTTAATATAGATACACACAGTTCTACATAGAAAACTTTATAATTAGGTGTGTGTAGGTAGGTTAGACACACACATATACTTCCTAGCATTGCTAATGAGGGACAAGATACAATGTGCATTCAGCAGCCAGATGTAAGTTTTCCCACCATTCTGAAAGGAATCAGGCTCTTTGAAGAAATGTCTGATACTAGAACTGGGACAGTATAAATATAGGAGCCAGGATAATCTGGAAGTATCAGAAAGTAAGTACTAAAAAAATTAAAATATATCAAACAAAAATAAAAGCCAATAAAAACAGCTACCGATGGCCAACACAGGAAGGAATTGTGCAACATAATGCTATAGTGTTGAATAATAACTAAAGCTTAAAGTAATTATCTAGGTGTCTGTATTTGTATACCTAGGTGAATAAGCAAATGGAGTTGCATAGAAATCTCCTTTGCAAAAGAATTCCAATAACTGATGTAGACACTCAGGCCATCAAGAAGGTGGAGCCAACTCCTCACTCCGTAAGTGTGGGCTCTGCATAGTGACTTGCTCCAAAAGAACACATGCAGTACGGACAAGGAGGAAAAATAACTTCACAGTGGAGAAATCTGACAAACAGTAGCTCTGCCAAATGATCCAAGTGAACATCAAAGCTGACAGTTCACCTTAGAACATGAAGTGACAATGGGGGACATTCTTTAAAATGCCTGACCAATCCTCCTCAGTGCTATGAAGGTCATCATGAGGTGGAAAGCCTGACACACTGTCACTGCCAGGAAGAGCCTACGTGATGACTACATGTCATGCGGGATCCTGGATGGGATCCTGGGTCAGAGTAAGATAGAACTAAGGGAATCCAAATGAAATATGAACTTTAGTTAATAACAGTCTATCAGTATTGGTTCATTAAGTGTGACAAATTCTGTAAGATAATAATAAGCCATGTGAGACACACTGATTGATAGGAGATGTTAATAACAGAGGAAACTAGGTTGCGGCTACATGGGAAATCTCTGCTTTTTTTTTTTTTTTTTCTGACGATTTCTGTGTAAGTAAAAAGCAGATGTAAAATAAAACTTTATTTAAAACACTTTTTAACACTTCCTTGTTTAATTATTTATACCATGAATTACTAGTAATTGACACTGTTAACTAGTCCTGTTTTTAAAAATAAGAGCATTTATGACACAAAAAATTAAACAGTGCAGACTGATATATAAATCAAAACAAATATTCTTTACACGTTTTCTGTTACAGTAGTAACACATATGTGTAAATTTAAGTATCATATTTTTTTCTTGTGCTATGGTTGTGTCCTAGGTTCATTCTCTAAAATGCTGTTCACCTTAGACCAGGAAAAATATTAACCATACAGACTCTGTTTCCAGTCATAGCTAAATATTTTCAAAAGAGTGACTTTGTAAAAACATGTTCCAATGGCAAATTGATTCATTATGATGGGATCAATTGTACGAGTTCCTGTCTTATTATTTCTTTGCCATGCCTACCTTTTAGCCATAATACAACAGAATCAAATCTGGCCACTGGGAAAAAAAGAAAAAAAAAAGAAAAAAGAAAGGTAGGGTCAGGGAAAAAAAAAGAAAGAATGTGAACAGAACTTATGACCATGATGATTAAATATTTTACCACAATGCTTTCTAAAACAGAAGAGTGTAAAAGGATATTCAAAGTCAATTTCCTCAGCGAGGCTTTGCAGAAAATGAGGAAACTAGAAAAACAAAAATGGCAGGACATTCTATGGGTGATTTTAAATGTTGCTATGTTTTATGGGAAAAAAATACTTTACCTTTTAAAGAATCACAAAGAATTATTGGAAACCCAAACTCTGGAATGTTTCAAATTTAGTTCAGCTTCTATG	''((+8653-8<;?A;5332488<=<=>/-=9:;<:=?A@@<<<<;<<,++++1+;;<=?AD>BAB@11111>@DB?DDEDACECC>AACBD@@??=65555976678;86666778777:98889;/....,***,8;20001;=AF@C@CFA=@ACCD<CDEED:7745;<=B?:;;<@A@;;;78BCEHEICCBFDEBCFSCKA@?A=AAAA>6666<A?8>ACEFHECGEHDDFABD@BEA<===99:?@@ACIBCDCBHDCEA>8:844<>?@BC>>><;@@BCDICB@EEF@BDEEGBDBFGJECFGCSEF@IJECEEE@JIFHJDFA<AD@F@??@=::;;<>10001<>?@BDDLGFFIED@DDCBSICBD=33333455556?ABADFHIA@@A66655;88877;233113-*)()('',.367878?BOSGEGHO8>BDHK@@?A99888?87777=:::99@99888>55545=::999>33323?DDFCEFCDD<9;BEEFEEFEBBACFDEGIGFFB@A@@11111=>B@>>@88555>A:9@@=C<<=:<EEAG@?@>,*6611864=9<>@>B???@;>?>>>?@>>??ACCCBDCB:8778:CDCA@@@AA>>>>>??@?????@??88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My guess is that some tags in my BAM are not compatible with pysam. Any help? Thanks.

[jmarshall]

The AttributeError was a pysam bug. Some of the tagged fields being added in out_samRead.set_tags(all_tags) must have had invalid value types, and future pysam will report this via a more useful message.