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Fix invalid-type message for creating header from dictionary #1334

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gtamazian
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The message for the type error when creating a SAM header from a dictionary misses type names. The following MWE causes the error by passing a dictionary instead of a list of dictionaries under the PG tag in the SAM header:

import pysam

header = {"PG": {"ID": "my-tool"}}
output = pysam.AlignmentFile("test.sam", "w", header=header)

The current invalid-type error message:

ValueError: invalid type for record %s: %s, expected %s

The fixed error message:

ValueError: invalid type for record PG: <class 'dict'>, expected <class 'collections.abc.Sequence'>

@jmarshall jmarshall force-pushed the fix-invalid-type-message branch from 5b3a528 to cbd830b Compare March 25, 2025 09:36
@jmarshall jmarshall merged commit cbd830b into pysam-developers:master Mar 25, 2025
@jmarshall
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Thanks. For new code we're mostly switching to f-strings for formatting, but this is the easiest fix for this thinko.

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2 participants