KosinskiLab / AlphaPulldownSnakemake

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download_uniprot fails for uniprot codes with '.' #21

Closed DimaMolod closed 2 months ago

DimaMolod commented 2 months ago

When providing uniprot codes with dotes: JG004_prot_IDs.csv I got a list of broken fasta files: 004327151..fasta 007002401..fasta 007002425..fasta 007002447..fasta 007002470..fasta 007002493..fasta 007002516..fasta 007002543..fasta 004327179..fasta 007002402..fasta 007002426..fasta 007002448..fasta 007002471..fasta 007002495..fasta 007002518..fasta 007002545..fasta 004327181..fasta 007002403..fasta 007002427..fasta 007002449..fasta 007002472..fasta 007002497..fasta 007002520..fasta 007002546..fasta 004327183..fasta 007002404..fasta 007002428..fasta 007002450..fasta 007002473..fasta 007002498..fasta 007002521..fasta 007003112..fasta 004327199..fasta 007002405..fasta 007002429..fasta 007002451..fasta 007002474..fasta 007002499..fasta 007002522..fasta 007003113..fasta 004327205..fasta 007002406..fasta 007002431..fasta 007002452..fasta 007002475..fasta 007002500..fasta 007002523..fasta 007003114..fasta 004327259..fasta 007002407..fasta 007002432..fasta 007002453..fasta 007002477..fasta 007002501..fasta 007002524..fasta 007003116..fasta 004327262..fasta 007002408..fasta 007002433..fasta 007002455..fasta 007002478..fasta 007002502..fasta 007002525..fasta 007003117..fasta 004327263..fasta 007002411..fasta 007002434..fasta 007002456..fasta 007002479..fasta 007002503..fasta 007002526..fasta 007003118..fasta 004327273..fasta 007002412..fasta 007002435..fasta 007002457..fasta 007002480..fasta 007002504..fasta 007002527..fasta 007003119..fasta 004327282..fasta 007002414..fasta 007002436..fasta 007002458..fasta 007002481..fasta 007002505..fasta 007002528..fasta 007003120..fasta 004327283..fasta 007002415..fasta 007002437..fasta 007002459..fasta 007002482..fasta 007002506..fasta 007002529..fasta 007003121..fasta 007002391..fasta 007002416..fasta 007002438..fasta 007002460..fasta 007002483..fasta 007002507..fasta 007002531..fasta 007003122..fasta 007002392..fasta 007002417..fasta 007002439..fasta 007002461..fasta 007002484..fasta 007002508..fasta 007002533..fasta 007003123..fasta 007002393..fasta 007002418..fasta 007002440..fasta 007002462..fasta 007002485..fasta 007002509..fasta 007002535..fasta YP..fasta 007002394..fasta 007002419..fasta 007002441..fasta 007002463..fasta 007002486..fasta 007002510..fasta 007002536..fasta 007002395..fasta 007002420..fasta 007002442..fasta 007002464..fasta 007002487..fasta 007002511..fasta 007002537..fasta 007002396..fasta 007002421..fasta 007002443..fasta 007002465..fasta 007002488..fasta 007002512..fasta 007002538..fasta 007002397..fasta 007002422..fasta 007002444..fasta 007002466..fasta 007002489..fasta 007002513..fasta 007002539..fasta 007002398..fasta 007002423..fasta 007002445..fasta 007002467..fasta 007002491..fasta 007002514..fasta 007002540..fasta 007002399..fasta 007002424..fasta 007002446..fasta 007002468..fasta 007002492..fasta 007002515..fasta 007002541..fasta

they are empty inside:

cat 007002458..fasta
>007002458.
The 'accession' value has invalid format. It should be a valid UniProtKB accession