fnafile

3.4

The fnafile command provides similar functionality for FASTA files as the sfffile command provides for SFF files, and in addition provides a mechanism to easily generate and add annotation strings to the description lines of reads in the file. The command constructs a single FASTA file containing the reads from a list of FASTA, PHD or SCF files, or directories containing FASTA, PHD or SCF files. The reads written to the new FASTA file can be filtered using inclusion and exclusion lists of accession numbers, and their sequence trimming points or annotation strings can be adjusted. This command is used to pool the results of many Sanger reads into a single FASTA file, to simplify further handling of the combined data.

The fnafile command uses the following syntax:

fnafile [options] (fastafile or PHDfile or SCFfile or directory)...

Command	Description
fnafile	Constructs a single FASTA file (plus associated quality score file) containing the reads from a list of FASTA files (possibly with associated quality score files), PHD files, SCF files or directories containing FASTA, PHD or SCF files.

Option / Argument	Description
-o output	The “‑o” option allows the user to specify a different filename for the output fna and qual files.
-i accnofile	By default, all reads in the inputs are written to the output file. If the “-i” (Include only these reads in output) or “-e” (Exclude these reads from output) options are used, the accession numbers given in the files specified will change the reads that are output. The associated accnofile files should list the accession numbers one per line. These options are cumulative, i.e. if multiple -i options are given, the reads included will be the union of the -i accession lists.
-e accnofile
-t trimfile or -tr trimfile	These two options adjust the trim points for some or all reads in the output file. The specified “trimfile” should contain one or more lines consisting of (1) a read accession number, (2) a starting trimpoint and (3) an ending trimpoint, separated by whitespace characters or where the trimpoints are separated by a dash (e.g., “accno 12 543” or “accno 12-543”). The trimpoint values are 1-based position values that denote the first and last base of the trimmed region (e.g. for a read 800 bases in length, the example above specify that bases 1-11 and 544-800 should be ignored, and bases 12-543 form the trimmed region of the read). A value of 0 specifies that the beginning or end of the read should be used (e.g. for a read 800 bases in length, the line “accno 12 0” sets the trimmed region to 12-800). The –t option will merge the given trimpoints with any existing trim points for the input read, writing the largest starting trimpoint and smallest ending trimpoint into the output. The –tr option will “reset” the trimpoints, using only the trimpoint information occurring in this file. Note: The use of this option does not limit the reads that will be written into the output file. To only output the reads whose accessions appear in the trim file, the –i option must also be used, with the same file as its argument.
-af filename	This option specifies a file that contains adjustments to the description line for some or all reads. Each line should contain the adjustments for a single read, and the line must begin with the accession number of the read. The text that follows the accession number (and subsequent whitespace characters) can take one of two forms. (1) If the text to the right of the accession number does not begin with a ‘>’, it is appended to the description line for the read. For example, the line DJS045A03F template=DJS045A03 dir=F library=DJS045 will append the text “template=DJS045A03 dir=F library=DJS045” to the end of the current description line for read “DJS045A03F”. (2) If the text to the right of the accession number does begins with a ‘>’, it will completely replace the description line for the input read, including changing the accession number for the read. For example, the line gi\|tl\|00103402131 >DJS045A03F template=DJS045A03... will change the description line for input read “gi\|tl\|00103402131” to be “>DJS045A03F template=DJS045A03…” in the output FASTA file that is written (and effectively change the accession number of the read for any program which uses the output FASTA file). This feature is useful for translating less descriptive read accession numbers (such as the NCBI Trace Archive accessions) into more descriptive read accession numbers (such as the genome project accession numbers, which encode library, plate-well and direction in the accession numbers).
-ac command	This option specifies a command to be executed for each input read, to determine adjustments to make to the read’s description line in the output FASTA file. The fnafile command will execute the command string “command accno ‘description’” for each read, where “command” is the value of the –ac option, “accno” is the first non-whitespace string on the input read’s description line, and “description” is the input read’s full description line (including the accno). The command processes each line of the file individually and writes the result to standard output. The output should be formatted as described above for the “text after the accession” for the –af option and will be processed by the fnafile command the same way. If no line of output is written, the input read’s description line will remain unchanged.
[--help]	Displays a usage line and short description of the command.
[--version]	Displays the current software version of the command.
fastafile or PHD file or SCF file or directory	Path to a FASTA file, PHD file, SCF file or a directory containing FASTA, PHD or SCF files. The reads in any input files are merged directly into the single output FASTA file generated by this command. If a directory is given, all the files it contains are read, and any files in the directory that are FASTA, PHD or SCF are processed and their reads are included in the output. Note: This command is not aware of consed’s phd_dir versioning of reads. If a phd_dir directory is given that contains multiple versions of the PHD file for a single read, all versions will be read and used by the command, and multiple versions of those reads will appear in the output FASTA file. The same holds true if a phd.ball file and individual PHD files are given on the command line.