4.6.4 Gene density retrieval¶

Function¶

rpf_Retrieve extracts selected gene or transcript density records from a merged density table. It can optionally normalize density values to RPM, reshape three-frame sample columns into a more plotting-friendly format, and split the result into one file per gene.

Input files¶

Input	Required	Description
Merged density table	Yes	RPF or RNA density table generated by `rpf_Merge`, usually `RIBO_merged.txt` or `RNA_merged.txt`.
Gene list	No	One-column gene or transcript list used to retrieve selected entries. If omitted, all genes passing the minimum-count filter are retained.

Parameters¶

Parameter	Required	Description
`-r`	Yes	Input RPF or RNA density table in TXT format.
`-o`	Yes	Output prefix. Although the parser does not enforce this option, the current implementation uses it directly when writing `<prefix>_retrieve.txt`.
`-l`	No	Gene or transcript list in TXT format. The current implementation passes this value to the density parser as the target gene list.
`-m`	No	Retain transcripts with more than this minimum number of RPFs. Default: `0`.
`-n`	No	Normalize read counts to RPM before output. Disabled by default.
`-f`	No	Reformat three frame-specific columns for each sample into a long, plotting-friendly table. Disabled by default.
`-s`	No	Split retrieved density into individual per-gene TXT files. Disabled by default.

Output files¶

Assuming -o RIBO, the command writes:

Output	Description
`RIBO_retrieve.txt`	Retrieved density table. Generated when `-s` is not used.
`<gene_id>_retrieve.txt`	Per-gene retrieved density file. Generated for each gene when `-s` is used.

Example¶

rpf_Retrieve \
    -l gene.list.txt \
    -r ../05.merge/RIBO_merged.txt \
    -m 50 \
    -f \
    -n \
    -o RIBO \
    &> RIBO.retrieve.log

Notes¶

-f is useful when preparing data for custom line plots or gene-level visualization because it expands frame-specific density columns into a tidy table.
-n converts raw RPF counts into RPM using total RPF counts from the merged density parser.
Use -s only when individual gene files are needed. It can generate many files for large gene lists.
Provide -o explicitly in normal use, because current output writing depends on this prefix.