StephenBaca
commented
1 year ago Hi, I am also looking for some of this information, specifically the format of the config file. Closed threads have pointed to the phyluce documentation but I've searched high and low and can only find these barcode extracting programs listed in the "List of Phyluce programs" with brief description but no usage details. I've tried to reconstruct it from the phyluce_assembly_extract_contigs_to_barcodes python script, but I'm failing. Does anyone have any insight on this? Thanks!
Hello, I used phyluce_assembly_match_contigs_to_barcodes for extracting barcodes from my assemblies. It worked well. Then I found out that by using phyluce_assembly_extract_contigs_to_barcodes it is possible to create a table format file which as far as I understand is basically the information contained I the log file but in a table. However there is no argument provided to identify a path to the LOG file as input. The only required arguments are --contigs, --config and --output. But it is asking for the assembled contigs as input instead of the log file, and it says you will get a fasta file as output, but in the description of the program it says the output should be a table. Of course a fasta file containing all sequences found previously using phyluce_assembly_match_contigs_to_barcodes should be good so I would think that there is a different command for it but it is not. Also, for the phyluce_assembly_extract_contigs_to_barcodes it s necessary a config file so if someone could provide an example of it I would really appreciate it. Thanks a lot!