sortgrcd(1)

💖 sortgrcd — the group chat version 💖

okay bestie, so this is sortgrcd, a General Commands Manual page, and honestly? she's the post-processing queen. Full name: Postprocess of the output of spaln with -O12 option, Version 2. iykyk. 💅

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✨ SYNOPSIS ✨

sortgrcd [options] xxx1.grd(.gz) [xxx2.grd(.gz) ...]

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🌸 DESCRIPTION 🌸

so sortgrcd is literally here to recover the output of spaln with -O12 option, apply some filtering, and also rearrange the outputs of multiple Spaln runs. she's giving cleanup crew, main character energy. 🧹✨

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🎀 OPTIONS 🎀

• -C# — Minimum cover rate = % nucleotides in predicted exons / length of query (x 3 if query is protein) (0-100). math but make it fashion.
• -F# — Filter level. #=0: no; #=1: mild; #=2: medium; #=3: stringent (0). pick ur vibe of picky. 🍓
• -H# — Minimum alignment score.
• -M# — Maximum total number of mismatches near boundaries.
• -N# — Maximum number of non-canonical boundaries.
• -O# — Output format. 0:Gff3, 4:Native, 5:Intron, 15: unique intron.
• -P# — Minimum overall % sequence identity (0-100).
• -S[a|b|c|r] — sort order of chromosomes/contigs: a:alphabetical, b:abundance, c:input order, r:reverse for minus strand. so many ways to be organized, we love a flexible icon.
• -U# — Maximum total number of unpaired bases in gaps.
• -V# — Maximum internal memory size used for core sort. Suffix k (or K) or m (or M) may be attached to specify kilo or mega bytes. memory limits, but make it cute.
• -m# — Maximum number of mismatches within 10bp from the nearest exon-intron boundary.
• -n# — Allow non-canonical (other than GT..AG, GC..AG, AT..AC) intron ends (0: no).
• -u# — Maximum number of unpaired (gap) sites within 10bp from the nearest exon-intron boundary.

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💜 COMMENTS 💜

okay so this part is the lore, listen up. 📢

The output format of spaln -O12 has been changed since version 2; in addition to *.grd and *.erd files, *.qrd file will be generated. This change has removed the limitations on the lengths of the identifiers of both target (genomic) and query sequences. The database files that was specified by -d option of spaln must not be changed before running sortgrcd.

not me warning u: do NOT touch those -d database files before running sortgrcd, fr fr. that's a whole situation we are not doing. 💀

By default, no filter listed above is applied. (so she's chill by default, no gatekeeping)

When the output of Spaln is separated in several files, the combined results are subjected to the sorting. Although *.grd(.gz) files are assigned as the argument, there must be corresponding *.erd(.gz) and *.qrd(.gz) files in the same directory. like, bring ur whole friend group or don't come at all. 🫶

In the default output format, the gene structure corresponding to each transcript is delimited by a line starting with @, whereas each gene locus is delimited by a line starting with !. Two transcripts belong to the same locus if their corresponding genomic regions overlap by at least one nucleotide on the same strand. the way that @ and ! are carrying this whole structure... iconic.

The -O0, -O3, -O4, -O5, -O6, and -O7 options work in the same manner as those of spaln.

In particular, with -O0 option, the outputs follow the Gff3 gene format (http://www.sequenceontology.org/gff3.shtml) where a gene locus is defined as described above.

With -O4 (default) and -O5 options, the outputs follow the exon-oriented and intron-oriented spaln formats, respectively.

With -O15 option, introns are uniqued, i.e., introns inferred from different transcripts with the same 5' and 3' boundaries are output only once. dedupe slay ✨

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📚 REFERENCES 📚

1. "A Space-Efficient and Accurate Method for Mapping and Aligning cDNA Sequences onto Genomic Sequence", O. Gotoh, Nucleic Acid Res., 36 (8), 2630-2638 (2008).
2. "Direct Mapping and Alignment of Protein Sequences onto Genomic Sequence", O. Gotoh, Bioinformatics, 24 (21) 2438-2444 (2008).

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👑 AUTHOR 👑

Osamu Gotoh <o.gotoh@aist.go.jp>

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and that's the whole page bestie, go forth and sort ur grd files 💖✨

this was sortgrcd(1) from the General Commands Manual, dated 2018-09-06, and yes she ate. periodt. 💅🦋