Recreate vcf from variants in scout #6
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mutacc_auto/parse/parse_scout.py
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| @@ -2,6 +2,7 @@ | |||
| from datetime import datetime, timedelta | |||
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| from mutacc_auto.commands.scout_command import ScoutExportCases | |||
| from mutacc_auto.parse.vcf_constants import * | |||
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Does this mean import all? If so, it is usually better to be explicit. Otherwise your namespace might be polluted without you knowing it.
mutacc_auto/parse/parse_scout.py
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| #Write header of vcf | ||
| for header_line in HEADER: | ||
| vcf_string += header_line + '\n' |
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Looks like a named constant + NEWLINE
mutacc_auto/parse/parse_scout.py
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| #Get samples | ||
| samples = [sample['sample_id'] for sample in scout_vcf_output[0]['samples']] | ||
| samples = '\t'.join(samples) |
mutacc_auto/parse/parse_scout.py
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| samples = [sample['sample_id'] for sample in scout_vcf_output[0]['samples']] | ||
| samples = '\t'.join(samples) | ||
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| vcf_string += f"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t{samples}\n" |
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I would like a simple "TAB.join(#CHROM, POS, ...etc)" if possible or even better
header_column_names = ["#CHROM", "POS", ..etc]
TAB.join(header_column_names, samples) + NEWLINE
That is a better description of what the parts are and more readable. You will have to excuse my python, but I think you get the idea
mutacc_auto/parse/parse_scout.py
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| #Write variants | ||
| for variant in scout_vcf_output: | ||
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| entry= [] |
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And a line is vcf is usually called a "record" I think...
mutacc_auto/parse/parse_scout.py
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| for variant in scout_vcf_output: | ||
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| entry= [] | ||
| entry.append(str(variant['chromosome'])) #CHROM |
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Why do you not make this into a for loop and append each iteration using the key as iterator.
something like:
entry = []
for column in scout_header_column_names:
if column in variant:
entry.append(str(variant[column] or '.')) # Since it was only uninitilized place
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Handle the PASS outside loop if it is not part of variant
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Make this into a def
mutacc_auto/parse/parse_scout.py
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| entry.append('PASS') #FILTER | ||
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| #write INFO | ||
| info = [] |
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make this into a def
mutacc_auto/parse/parse_scout.py
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| entry.append(format) | ||
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| samples = [] |
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make this into a def
Now recreates vcf files from the 'scout export variants --json --case-id ...' output