BP_DOW...GENBANK(1p)

🌸 NAME 🌸

bp_download_query_genbank — it's a script that queries Genbank and pulls records for you, bestie 💖

Okay so this is a Perl script (from the User Contributed Perl Documentation collection, manual page BP_DOW...GENBANK(1p), iykyk) and it does exactly what it says on the tin: you give it a query, it goes and asks Genbank for the records, and it hands them back. Literally that simple. Slay. ✨

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🎀 USAGE 🎀

Two ways to run it, both iconic:

bp_download_query_genbank --query "Neurospora[ORGN]" --db nucest -o Ncrassa_ESTs.fa --format fasta

bp_download_query_genbank --queryfile 'filewithquery' --db nucest -o Ncrassa_ESTs.fa --format fasta

💅 Other options

Provide ONE of these — like, pick one, not all three, okay? 🫶

• -q, --query query string — OR
• --queryfile profile file with query — OR
• --gi, --gis, --gifile file with list of GIs to download

Database type:

• -d, --db database — the choices are nucleotide [this is the default], nucest, protein, )

Then the output-y ones:

• -o, --out, --outfile output file — and if you don't give one? Results just get displayed on screen instead 🙈
• -f, --format sequence file output format — fasta by default, no cap
• -v, --verbose — debugging output, for when you need to see everything 👑

🦋 Query options

• --maxids — maximum number of IDs to retrieve in a set (it's 100 at a time by default)
• --reldate
• --maxdate — maxdate for a record
• --mindate — minimum date for record
• --datetype — edat or mdat (entered or modified)

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👑 AUTHOR 👑

Jason Stajich — Jason Stajich, jason-AT-bioperl.org 💜

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That's the whole vibe, bestie. Go download some sequences. Periodt. 💅✨

This page is perl v5.36.0, dated 2023-12-17 — so yeah, she's got a lil vintage energy but she's still serving 🎀🦋