This program will find and stitch together exons from targeted assemblies using amino acid targets and DNA assemblies.
-h, --help
Show this help message and exit.
--version
Show program's version number and exit.
-T TAXA, --taxa TAXA
A text file of all of your taxon names.
-r FASTA, --reference-genes FASTA, --refs FASTA
Reference amino acid sequences in a FASTA file.
-a PATH, --assemblies-dir PATH
The path to the DNA contigs.
-O OVERLAP, --overlap OVERLAP
Contigs must overlap by this many codons before it is considered a real overlap.
-t DIR, --temp-dir DIR
Place temporary files in this directory. All files will be deleted after aTRAM completes. The directory must exist.
--keep-temp-dir
This flag will keep the temporary files in the --temp- dir around for debugging.
-l LOG_FILE, --log-file LOG_FILE
Log file (full path). The default is "atram_stitcher_.log".
-i N, --iterations N
The number of times to run the main stitcher loop. This must be either 1 or 2, the default is 2.
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
This is the prefix of all of the output files. So you can identify different stitcher output file sets. You may include a directory as part of the prefix. The stitcher will add suffixes to differentiate output files.
-f FILE_FILTER, --file-filter FILE_FILTER
Use this to filter files in the assemblies directory. For example 'filtered.fasta' will select all fasta files in the assemblies directory with the word filtered in them. The default is to select all fasta files in the assemblies directory '*.fasta'.
--reference-name
Prepend the reference name to the final assembled gene name? if false the gene name in the reference file with just be the if you select this then the assembled gene name will be ..