b2ct

name	b2ct
description	Use when converting ViennaRNA-style sequence-plus-dot-bracket records on stdin into RNA connectivity-table output.
disable-model-invocation	true
user-invocable	true

b2ct

b2ct is a small legacy ViennaRNA converter that turns a sequence plus structure record into CT-format rows. The only confirmed healthy path in this environment is stdin-driven conversion to stdout.

Quick Start

• Command: b2ct
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/b2ct
• Confirmed positive path: printf '>test\nAAAA\n.... (0.00)\n' | b2ct

When To Use This Tool

• Convert a ViennaRNA / RNAfold-like record into CT rows for downstream structure tooling.
• Inspect a single dot-bracket structure in a tabular partner-index layout.
• Turn ephemeral stdin structure output into a file you can archive or pass downstream.

Common Patterns

# 1) Convert a simple structure record from stdin
printf '>test\nAAAA\n.... (0.00)\n' | b2ct

# 2) Save CT output to a file
printf '>test\nAAAA\n.... (0.00)\n' | b2ct > test.ct

# 3) Reuse an existing RNAfold-style output file through stdin redirection
b2ct < fold.out > fold.ct

Recommended Workflow

1. Normalize the input to the ViennaRNA-style three-line form: record name, sequence, and dot-bracket structure with optional energy in parentheses.
2. Feed the record through stdin or shell redirection rather than relying on a positional filename.
3. Capture stdout into a .ct file if you need to reuse the result.
4. Verify sequence length and bracket balance before trusting the CT table downstream.

Guardrails

• No real help or version interface was observed: bare b2ct and b2ct -h were both silent in local testing.
• The confirmed positive path is stdin to stdout. In contrast, b2ct fold.out exited 0 but produced no stdout and no sidecar file in repeated smoke tests.
• Live good input printf '>test\nAAAA\n.... (0.00)\n' | b2ct emitted CT rows beginning with 4 ENERGY = 0.0 test.
• An invalid sample with mismatched sequence and structure lengths emitted sequence and structure have unequal length.
• Binary strings also expose an unbalanced brackets error path, so bracket balance matters even if you do not hit it in the happy path.
• The converter writes CT text to stdout on the confirmed path; it does not automatically create a .ct file for you.