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feat(IPVC-2195): add script to generate alignment metrics #30

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merged 2 commits into from
May 3, 2024

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bsgiles73
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This pull request adds a script to the repo that can be used to generate alignment metrics for build 37 alignments.

Usage:

python generate_alignment_metrics.py <output_file> --db-url <db_url> --schema-name <schema_name>

Output:

hgnc	tx_ac	seq_length	exon_count	alt_ac	alt_aln_method	alt_strand	aligned_exon_count	exon_structure_mismatch	matches	mismatches	gap_count	aln_length	identity_gap	identity_ungap	coverage
AADACL3	NM_001103169.1	3832	3	NC_000001.10	splign	1	3	False	3832	0	0	3832	1.000000	1.000000	1.000000
AAK1	NM_014911.3	21265	22	NC_000002.11	splign	-1	22	False	21264	1	0	21265	0.999953	0.999953	1.000000
ABCF1	NM_001090.2	3350	24	NC_000006.11	splign	1	24	False	3350	0	0	3350	1.000000	1.000000	1.000000
ACTL8	NM_030812.2	1861	3	NC_000001.10	splign	1	3	False	1861	0	0	1861	1.000000	1.000000	1.000000

@bsgiles73 bsgiles73 requested review from sptaylor and nvta1209 May 2, 2024 03:33
@bsgiles73 bsgiles73 merged commit 875e428 into main May 3, 2024
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@bsgiles73 bsgiles73 deleted the IPVC-2195-add-metrics-script branch May 3, 2024 14:05
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3 participants