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Minor description edits
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smlmbrt committed Aug 23, 2022
1 parent c8ef7c9 commit 50999ac
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4 changes: 4 additions & 0 deletions pgscatalog_utils/download/download_scorefile.py
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Expand Up @@ -88,6 +88,10 @@ def _description_text() -> str:
The PGS Catalog API is queried to get a list of scoring file
URLs. Scoring files are downloaded via FTP to a specified
directory. PGS Catalog scoring files are staged with the name:
{PGS_ID}.txt.gz
If a valid build is specified harmonized files are downloaded as:
{PGS_ID}_hmPOS_{genome_build}.txt.gz
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8 changes: 4 additions & 4 deletions pgscatalog_utils/match/match_variants.py
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Expand Up @@ -123,12 +123,12 @@ def _description_text() -> str:
makes matching faster and simpler.
Target genomes can be in plink1 bim format or plink2 pvar
format. Variant IDs should be unique.
format. Variant IDs should be unique so that they can be specified
in the scoring file as: variant_id|effect_allele|[effect_weight column(s)...]
Only one set of target genomes should be matched at a time. Don't
try to match target genomes from different plink
filesets. Matching against a set of chromosomes from the same
fileset is OK (see --split).
try to match target genomes from different plink filesets. Matching
against a set of chromosomes from the same fileset is OK (see --split).
''')


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3 changes: 2 additions & 1 deletion pgscatalog_utils/scorefile/combine_scorefiles.py
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Expand Up @@ -43,7 +43,8 @@ def _read_and_melt(path, drop_missing: bool = False):

def _description_text() -> str:
return textwrap.dedent('''\
Combine multiple scoring files in PGS Catalog format to a 'long'
Combine multiple scoring files in PGS Catalog format (see
https://www.pgscatalog.org/downloads/ for details) to a 'long'
table, and optionally liftover genomic coordinates to GRCh37 or
GRCh38. Custom scorefiles in PGS Catalog format can be combined
with PGS Catalog scoring files. The program can accept a mix of
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