BP_FAS...O_TABLE(1p)

🌸 NAME 🌸

fastm9_to_table — the lil glow-up that turns your FASTA -m 9 output into NCBI -m 9 tabular output 💅✨

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✨ SYNOPSIS ✨

fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...

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💖 DESCRIPTION 💖

Okay bestie, here's the whole command line situation, laid out all pretty:

• -e, --evalue evalue — filter by evalue 🔍
• -b, --bitscore bitscore — filter by bitscore 🔍
• --header — boolean flag to print the column header 🏷️
• -o, --out — optional outputfile to write data to; otherwise it will write to STDOUT 📝
• -h, --help — show this documentation 🫶

Not technically a SearchIO script, since this doesn't use any Bioperl components — but it's a useful and fast one, no cap. The output is tabular output with the standard NCBI -m9 columns 👑

• queryname
• hit name
• percent identity
• alignment length
• number mismatches
• number gaps
• query start (if on rev-strand start > end)
• query end
• hit start (if on rev-strand start > end)
• hit end
• evalue
• bit score

Additionally 3 more columns are provided 🌈

• fasta score
• sw-score
• percent similar
• query length
• hit length
• query gaps
• hit gaps

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👑 AUTHOR - Jason Stajich 👑

Jason Stajich jason_at_bioperl-dot-org

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That's the whole vibe, bestie — sending you off with the receipts: this page is from perl v5.32.1, dated 2021-08-15, under BP_FAS...O_TABLE(1p) in the User Contributed Perl Documentation. Go turn those FASTA hits into a table, you're gonna eat 💅🦋💖