usr$ python vespa.py translate –input=USR_INPUT Command-specific options: The function incorporates a single unique option ‘translate’ and the previously described options of the clean functions (Section 1.6.1). ‘cleave_terminal’ The option is enabled by default and is designed to cleave the terminal stop ‘cleave_terminal’ codon of each sequence (Figure 3d). The function and default status of the remaining options are detailed in Section 1.6.1. usr$ python vespa.py translate –input=USR_INPUT -cleave_terminal=False Supported file format(s): formatted files ‘input’: fasta Figure 3: Overview of function. ‘translate’ Figure 3 Legend FastA formatted files are shown as grey boxes and their filenames are given in white boxes. (a) Translating an input file using initiates the translation procedure by separating ‘translate’ the sequence (as in (b)) into each codon to determine the respective amino acid, (c) translated sequences are saved in the output file. (d) If the option is ‘Translated’ ‘cleave_terminal’ invoked, terminal stop codons will be removed from each applicable sequence. 1.6.3: Create Database Function The function was designed for users to concatenate multiple genomes into ‘create_database’ the single database required for homology searching. The function operates by building the database a single sequence at a time (Figure 4a and b). The command-line version of BLAST requires additional commands to create a BLAST-formatted database. If the user enables the option and BLAST is installed on the system the function will attempt to ‘format_blast’ automate the additional steps required for producing a BLAST-ready database (Figure 4c). If is unable to create the BLAST-formatted database, a warning message will ‘create_database’ be produced (see Section 1.12 BLAST version requirements). usr$ python vespa.py create_database –input=USR_INPUT Supported file format(s): formatted files ‘input’: fasta
usr$ python vespa.py translate –input=USR_INPUT Command-specific options: The ‘translate’ function incorporates a single unique option ‘cleave_terminal’ and the previously described options of the clean functions (Section 1.6.1). The ‘cleave_terminal’ option is enabled by default and is designed to cleave the terminal stop codon of each sequence (Figure 3d). The function and default status of the remaining options are detailed in Section 1.6.1. usr$ python vespa.py translate –input=USR_INPUT -cleave_terminal=False Supported file format(s): ‘input’: fasta formatted files Figure 3: Overview of ‘translate’ function. Figure 3 Legend FastA formatted files are shown as grey boxes and their filenames are given in white boxes. (a) Translating an input file using ‘translate’ initiates the translation procedure by separating the sequence (as in (b)) into each codon to determine the respective amino acid, (c) translated sequences are saved in the ‘Translated’ output file. (d) If the ‘cleave_terminal’ option is invoked, terminal stop codons will be removed from each applicable sequence. 1.6.3: Create Database Function The ‘create_database’ function was designed for users to concatenate multiple genomes into the single database required for homology searching. The function operates by building the database a single sequence at a time (Figure 4a and b). The command-line version of BLAST requires additional commands to create a BLAST-formatted database. If the user enables the option ‘format_blast’ and BLAST is installed on the system the function will attempt to automate the additional steps required for producing a BLAST-ready database (Figure 4c). If ‘create_database’ is unable to create the BLAST-formatted database, a warning message will be produced (see Section 1.12 BLAST version requirements). usr$ python vespa.py create_database –input=USR_INPUT Supported file format(s): ‘input’: fasta formatted files