Command Line Interface

tcdo_pg_tools

tcdo_pg_tools [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

coverage-calculator

calculate wt mean AA coverage for multi-enzyme digests

tcdo_pg_tools coverage-calculator [OPTIONS]

Options

--fragpipe_dir <fragpipe_dir>

Required fragpipe out dir; MUST have subdirs starting with enzyme (e.g., “trypsin_diaPASEF”)

--enzymes <enzymes>

Required enzyme names, comma separated (e.g., “trypsin,chymotrypsin”)

--output_tsv <output_tsv>

output tsv filename

--unique_proteins

just calculate coverage for proteins with unique peptides

--unique_peptides

just calculate coverage using unique peptides

fusion-merge

Merge fusion calls across multiple samples based on gene symbols and breakpoints.

tcdo_pg_tools fusion-merge [OPTIONS]

Options

-i, --input_metadata <input_metadata>

Required Metadata sheet from isabl_utils with paths to FusionInspector results

-v, --app_version <app_version>

Required Filter for results from a specific Isabl app version

-r, --result_type <result_type>

Required Filter on result type in metadata sheet

-t, --fusion_table <fusion_table>

Required Path to output fusion info table

-fa, --output_fasta <output_fasta>

Required Path to output FASTA file

--ill

specify if Illumina (default assumes ONT)

merge-fasta

merge multiple fasta on sequence identity

tcdo_pg_tools merge-fasta [OPTIONS]

Options

-i, --input_csv <input_csv>

Required three column csv (fasta: fasta path, name: sample name, condition: condition)

-t, --info_table <info_table>

Path to index tsv for merged protein IDs

Default:

'info_table.tsv'

-fa, --merged_fasta <merged_fasta>

Path to merged fasta file

Default:

'merged.fasta'

--upset

plot upset

--upset_path <upset_path>

Path to upset plot

Default:

'upset_plot.svg'

--filter_by_header <filter_by_header>

filter out proteins by header prefix (provide comma separated list)

Default:

'contam_,rev_,tr|GF'

--filter_crap <filter_crap>

filter out contaminants

Default:

PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/tcdo-pg-tools/checkouts/latest/src/tcdo_pg_tools/philosopher.crap-gpmdb.fas')

--no_uniprot_headers

if fasta headers are not uniprot header-style

merge-pg-results

merge proteomegenerator results across multiple samples on AA seq identity

tcdo_pg_tools merge-pg-results [OPTIONS]

Options

-i, --input_csv <input_csv>

Required four column csv (fasta: fasta path, protein_table: protein.tsv path, name: sample name, condition: condition)

-t, --info_table <info_table>

Path to index tsv for merged protein IDs

Default:

'info_table.tsv'

-fa, --merged_fasta <merged_fasta>

Path to merged fasta file

Default:

'merged.fasta'

--upset

plot upset

--upset_path <upset_path>

Path to upset plot

Default:

'upset_plot.svg'

--filter_by_header <filter_by_header>

filter out proteins by header prefix (provide comma separated list)

Default:

'contam_,rev_,tr|GF'

--filter_crap <filter_crap>

filter out contaminants

Default:

PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/tcdo-pg-tools/checkouts/latest/src/tcdo_pg_tools/philosopher.crap-gpmdb.fas')

--no_uniprot_headers

if fasta headers are not uniprot header-style