Removal of primers from matched sequences

I have a list of two matched sequences:

[[('---------------C----C---GT----GTR-GGK---AC-TGM-GGA-GGW--CATTGTCGAA-CATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAARAACGTAGCGAAATGCGATACTTGGTGTGAATTGCARAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGTCGG--GAACACC-CGCTGAATTTAAGCATATCAATAAGCGGAGG', 'GGKAARKWAAAAAGTCGTAACAAGGTTTCCGT-AGG-TGAACCTG-CGGAAGG-ATCATTGTCGAAACATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGT---YAGAAC-CCACG-----TT----------------------', 1312.2000000000025, 0, 743)], [('------------C------------CC-TGWAGGK---AC-TGCGGA-GGW--CATTGTCGAA-CATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGAC-TGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAR-AACGTAGCGAAATGCGATACTTGGTGTGAATTGCAR-AATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGR-ATGGCCTAAW-TTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAG-TCGG--GAA-CACCCGCTGA-ATTTAAGCATATCAATAAGCGGARGAA', 'KAAGTATAAAGTCGTAACAAGGTTTCCGT--AGG-TGAACCTGCGGAAGG-ATCATTGTCGAAACATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGA-YTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAA-GAACGTAGCGAAATGCGATACTTGGTGTGAATTGCA-GAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCG-GATGGCCTAA-ATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCA-GTCA-KT---YAGAAMC-CCC----AMAT-----C----C--T-----------', 1304.0000000000023, 0, 747)]]

I would like to remove primers in these sequences. Going from the middle right and left to find the first character "-". And then delete everything that is in front of this sign. For example, for the first match I would like to receive:

[('CATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAARAACGTAGCGAAATGCGATACTTGGTGTGAATTGCARAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGTCGG', 'ATCATTGTCGAAACATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGT', 1312.2000000000025, 0, 743)]

And the same for the others.

Thanks for any answer.

biopython

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updated 6.1 years ago by Joe

• written 6.1 years ago by adrian18_07 •

I am reasonably certain bbduk.sh from BBMap suite can do this. A guide is available here.

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written 6.1 years ago by GenoMax

1 answer

The data structure you have is pretty confusing and heavily nested, but I think this is correct. I get the right result for your first example at least, but the second seems very short as there are "-" characters quite near the centre of the string (you may need to rethink your strategy?).

data = #...
for entry in data:
    new_strings = []
    for string in (entry[0][0], entry[0][1]):
        first_half = string[0:round(len(string)/2)]
        second_half = string.replace(first_half, "") # Using this replace method rather than string slicing again, as the mid point for an odd versus even string will differ and might cause chars to be missed.
        new_strings.append(first_half[first_half.rfind("-")+1:] + second_half[:second_half.find("-")])
    print([(new_strings[0], new_strings[1]) +  entry[0][2:]])

Gives me:

[('CATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAARAACGTAGCGAAATGCGATACTTGGTGTGAATTGCARAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGTCGG', 'ATCATTGTCGAAACATGCCCGACAGAGCGACCCGCGAACACGTTACAAACACTACGCGGGGTGGCCCCGGCTGCCTCGCGCGGAGGTGCTGCGGCTGAGTGCGCAAACTAGCTGCGCGCACGCTGTCCGTGCCACCTCCACTAACAGAACCCCGGCGCGGACTGCGCCAAGGAATAAAAAACGAATGAGAGCGAGCGCGCCCCCCTCGCCCCGGAGACGGTGCGCGATGGTGTGTGCCTCGCTGTCCATTGATAAACTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACGCAACGTCGCCGCCAACCCCACCCCTAGGGGCGGGAAGTTGGGGGCGGACTCTGGCCTCCCGTGCGCCTCGGCGCGCGGATGGCCTAAATTTCAGCTCCTGGCGAGGATCGCCACGACAAGCGGTGGTTTTTTGAACTAAGGACCTCGGGTGTTGTCGTGCGGCCTCCCGGAGGGAACGGACCCTGTGCGCTCGCGCACCATCCTATCGAGACCCCAGGTCAGT', 1312.2000000000025, 0, 743)]
[('AACGTAGCGAAATGCGATACTTGGTGTGAATTGCAR', 'GAACGTAGCGAAATGCGATACTTGGTGTGAATTGCA', 1304.0000000000023, 0, 747)]

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written 6.1 years ago by Joe