How to ignore errors when working with multiple variants?

[Tarun karthik kumar Mamidi]

Hello all,

I have a column of variants and want to convert them all to genomic co-ordinates. I'm using the following code 

def c2g(hgvs_c):

    var_c = hp.parse_hgvs_variant(hgvs_c)

    g = am.c_to_g(var_c)

    

    return g.posedit.pos.end.base

known['Variant1_pos']  = known.apply(lambda  row: c2g(row.Variant1) if 'NM' in row.Variant1 else '', axis=1)


Error:

HGVSInvalidIntervalError: ('The given coordinate is outside the bounds of the reference sequence.', 'occurred at index 6')

As expected, some of the variants are not formatted well, maybe cause of human error or something. I want to ignore those and print all others in the column. Is there a way to do that? I really hate using loops. Please help!

Thank you,

[Reece Hart]

You need to catch exceptions. Something like:

import logging

_logger = logging.getLogger(__name__)

def c2g(hgvs_c):

    try:

        var_c = hp.parse_hgvs_variant(hgvs_c)

        g = am.c_to_g(var_c)

    except HGVSError as e:

        _logger.exception(e)

        return None

    return g.posedit.pos.end.base

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[Tarun karthik kumar Mamidi]

Thanks for the help. I still get an error. Please see below.

NameError: ("name 'HGVSError' is not defined", 'occurred at index 6')

So, there was an unrecognized variant in the column at that position. I would like to ignore and convert all others.

Thanks for the help!

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