Repository revision
0:9cff9a1176ea

Repository 'get_orfs_or_cdss'

Get open reading frames (ORFs) or coding sequences (CDSs) tool metadata
Miscellaneous
e.g. to get peptides from ESTs
get_orfs_or_cdss
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.1
0.0.1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.2
toolshed.g2.bx.psu.edu/repos/peterjc/get_orfs_or_cdss/get_orfs_or_cdss/0.0.1 (this tool)
get_orfs_or_cdss
Requirements (dependencies defined in the <requirements> tag set)
name version type
Bio not provided python-module
Additional information about this tool
get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file
	
python
False
False
Functional tests
name inputs outputs required files
Test-1 input_file: get_orf_input.fasta
table: 1
ftype: CDS
ends: open
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t1_nuc_out.fasta
out_prot_file: get_orf_input.t1_prot_out.fasta
get_orf_input.fasta
get_orf_input.t1_nuc_out.fasta
get_orf_input.t1_prot_out.fasta
Test-2 input_file: get_orf_input.fasta
table: 11
ftype: CDS
ends: closed
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t11_nuc_out.fasta
out_prot_file: get_orf_input.t11_prot_out.fasta
get_orf_input.fasta
get_orf_input.t11_nuc_out.fasta
get_orf_input.t11_prot_out.fasta
Test-3 input_file: get_orf_input.fasta
table: 11
ftype: CDS
ends: open
mode: all
min_len: 10
strand: forward
out_nuc_file: get_orf_input.t11_open_nuc_out.fasta
out_prot_file: get_orf_input.t11_open_prot_out.fasta
get_orf_input.fasta
get_orf_input.t11_open_nuc_out.fasta
get_orf_input.t11_open_prot_out.fasta