crops-cropseq options

Cropping and Renumbering Operations for PDB structure and Sequence files (CROPS) v.1.0.2 This script will remove a number of residues from a sequence file in agreement to the intervals and other details supplied.

usage: crops-cropseq [-h] [-o Output_Directory]
                     [-p Oligoseq_ids [Oligoseq_ids ...]] [-s Sort_type | -i]
                     [-t | -u Uniprot_ratio_threshold Sequence_database]
                     [--version]
                     Sequence_filepath Intervals_database

Positional Arguments

Sequence_filepath
	Input sequence filepath.
Intervals_database
	Input intervals database filepath.

Named Arguments

-o, --outdir	Set output directory path. If not supplied, default is the one containing the input sequence.
-p, --preselect
	From all the sequences in the input sequence file, just print out this preselected subset.
-s, --sort	Sort output sequences in descending order by criteria provided - ‘ncrops’ or ‘percent’. Add ‘IN’ (‘ncropsIN’, ‘percentIN’) to ignore numbers from terminals. Only for multiple ID fasta inputs.
-i, --individual
	One separated fasta file per each sequence. Default: False
-t, --terminals
	Ignore interval discontinuities and only crop the ends off. Default: False
-u, --uniprot_threshold
	Act if SIFTS database is used as intervals source AND % residues from single Uniprot sequence is above threshold. Threshold: [MIN,MAX)=[0,100). Database path: uniclust##_yyyy_mm_consensus.fasta-path or server-only. The latter requires internet connexion.
--version	show program’s version number and exit