GTHBSSMTRAIN(1)

💖 GTHBSSMTRAIN 💖

okay bestie, welcome to the manual page for gthbssmtrain — that's the gthbssmtrain(1) page, section 1, for when you need to train a splice site model 🧬✨

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✨ NAME ✨

gthbssmtrain — train splice site model 🎀

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🌸 SYNOPSIS 🌸

gthbssmtrain [option ...] GFF3_file

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🦋 DESCRIPTION 🦋

Create BSSM training data from annotation given in GFF3_file. that's literally it, that's the whole vibe 💅

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👑 OPTIONS 👑

• -outdir — set name of output directory to which the training files are written. default: training_data
• -gcdonor — extract training data for GC donor sites. default: yes
• -filtertype — set type of features to used for filtering (usually 'exon' or 'CDS'). default: exon
• -goodexoncount — set the minimum number of good exons a feature must have to be included into the training data. default: 1
• -cutoff — set the minimum score an exon must have to count towards the "good exon count" (exons without a score count as good). default: 1.00
• -extracttype — set type of features to be extracted as exons (usually 'exon' or 'CDS'). default: CDS
• -seqfile — set the sequence file from which to take the sequences. default: undefined
• -encseq — set the encoded sequence indexname from which to take the sequences. default: undefined
• -seqfiles — set the sequence files from which to extract the features. use -- to terminate the list of sequence files
• -matchdesc — search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match. default: no
• -matchdescstart — exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace. default: no
• -usedesc — use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID ('III') and the first range position as offset ('1000001'). default: no
• -regionmapping — set file containing sequence-region to sequence file mapping. default: undefined
• -seed — set seed for random number generator manually. 0 generates a seed from the current time and the process id. default: 0
• -v — be verbose. default: no
• -gzip — write gzip compressed output files. default: no
• -bzip2 — write bzip2 compressed output files. default: no
• -force — force writing to output files. default: no
• -help — display help and exit 🙈
• -version — display version information and exit 🌈

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and that's the whole page, bestie 🫶 mwah, no notes, go train those splice site models 💜

signing off from the GTHBSSMTRAIN(1) corner of the manual — same title top and bottom, that's just how this page rolls ✨💅