fastaconvtr_help.txt

#fastaconvtr v.1.0.0 (20250107034050) Sebastian E. Ramos-Onsins.

Flags:
      -F [input format file: f (fasta), t (tfasta)]
      -i [path and name of the input file (text or gz indexed)]
      -f [output format file: t (tfasta), f (fasta), m (ms), 0(nothing)]
      -o [path and name of the output file (include extension .gz except ms files)]
      -n [name of the file containing the name(s) of scaffold(s) and their length (separated by a tab), one per line (ex. fai file)]
   OPTIONAL PARAMETERS:
      -h [help and exit]
      -P [define window lengths in 'physical' positions (1) or in 'effective' positions (0)]. DEFAULT: 1
      -O [#_nsam] [Reorder samples: number order of first sample, number 0 is the first sample] [second sample] ...etc.
      -W [for ms and fasta outputs, file with the coordinates of each window: (one header plus nlines with init end]
      -N [#_pops] [#samples_pop1] ... [#samples_popN] (necessary in case to indicate the outgroup population)
      -G [outgroup included (1) or not (0), last population (1/0)]. DEFAULT: 0
      -u [Missing counted (1) or not (0) in weights given GFF annotation]. DEFAULT: 0
      -m [masking regions: file indicating the start and the end of regions to be masked by Ns]
     Outputing ms format:
      -w [window size]. DEFAULT: Total_length
      -s [slide size]. DEFAULT: Total_length
     Inputing fasta format:
      -p [if fasta input,
             haplotype: 1 (single sequence)
             genotype:  2 or 4 (two diploid mixed sequences in IUPAC format. If p=4 lowercase will be considered as one haplotype missing!). DEFAULT: 1
     Annotation file and weight options:
      -g [GFF_file]
         [add also: coding,noncoding,synonymous,nonsynonymous,silent, others (whatever annotated)]
         [if 'synonymous', 'nonsynonymous', 'silent' add: Genetic_Code: Nuclear_Universal,mtDNA_Drosophila,mtDNA_Mammals,Other]
         [if 'Other', introduce the single letter code for the 64 triplets in the order UUU UUC UUA UUG ... etc.]
      -c [in case use coding regions, criteria to consider transcripts (max/min/first/long)]. DEFAULT: long
      -E [instead -g & -c, input file with weights for positions: include three columns with a header, first the physical positions (1...end), second the weight for positions and third a boolean weight for the variant (eg. syn variant but nsyn position)]
      -T [in case define -g and -c and output is TFasta, option to print (1) or not (0) the DNA sequence]. DEFAULT: 1 (print)