This repository has been discontinued in favor of the TriFusion software.
TriFusion github: https://github.com/ODiogoSilva/TriFusion
TriFusion webpage: http://odiogosilva.github.io/TriFusion/
Note: Name under consideration
PhD_Easy is a python program developed for the UNIX OS (but should work in any operating system with python 3.x) that converts, concatenates and manipulates common population genetics and phylogenetics data file types (such as Fasta, Phylip and Nexus). For the moment, the program works through command line exclusively, which makes it fast and scriptable, but a GUI version is being worked on. It requires the wingman library.
It currently supports as input file formats:
- Fasta
- Phylip
- Nexus (Alignment files and partition files)
- RAxML partition files
And its able to convert/concatenate any of these file formats into:
- Fasta
- Phylip (Including the *.parts file required for multilocus datasets in RAxML)
- Nexus
- ZORRO weigths files (these weigths files that are associated with their respective alignment files can be jointly concatenated)
Recently, PhD_Easy has received several new features:
- Collapse alignments into unique haplotypes. Taxa in the output alignment will be Haplotypes and their correspondance to the original taxa will be provided in a secondary file with the '.haplotypes' extension
- Code gaps into a binary state matrix that is appended at the end of the alignment, following the method of Simmons and Ochoterena (2000). This will only work when the output format is Nexus, and it can be red by MrBayes
- Columns of the alignment with excessive missing data can be filtered according to two user-specified thresholds (a threshold for the maximum proportion of gap and missing data, and another for missing data only).
Other minor improvements include:
- Specific taxa can be removed from the output alignments when converting/concatenating files
- In the Nexus output format, the outgroup may be set when converting/cocatenating
There is no need for instalation. The only requirement is that the wingman library must be on the same directory as PhD_Easy.py (or you can use any other way to let the main script know where the module is). I do recommend, to make it easier to call the program, that you add it to your $PATH variable. This can be done by declaring "export $PATH=$PATH:/path/to/PhD_Easy" on your .bashrc, or your shell specific rc file.
Finally, please note that PhD_Easy.py is not immune to bugs, and I'll be happy to know about them through my e-mail (o.diogosilva@gmail.com) so that I can fix them. Any suggestions or comments are also welcome.
PhD_Easy.py has the following options (which can also be consulted by typing "PhD_Easy.py -h" or "PhD_Easy.py --help" in the command line):
####optional arguments:
-h, --help show this help message and exit
####Main execution:
-in INFILE [INFILE ...] Provide the input file name. If multiple files are provided, plase separated the names with spaces
-if {fasta,nexus,phylip,guess} Format of the input file(s). The default is 'guess' in which the program tries to guess the input format and genetic code automatically
-of {nexus,phylip,fasta} [{nexus,phylip,fasta} ...] Format of the ouput file(s). You may select multiple output formats simultaneously (default is 'nexus')
-o OUTFILE Name of the output file
####Alternative execution modes:
-c Used for convertion of the input files passed as arguments with the -in option. This flag precludes the usage of the -o option, as the output file name is automatically generated based on the input file name
-r REVERSE Reverse a concatenated file into its original single locus alignments. A partition file similar to the one read by RAxML or a file containing a NEXUS charset block must be provided
-z ZORRO, --zorro-suffix ZORRO Use this option if you wish to concatenate auxiliary Zorro files associated with each alignment. Provide the sufix for the concatenated zorro file
-p PARTITION_FILE, --partition-file PARTITION_FILE Using this option and providing the partition file will convert it between a RAxML or Nexus format
-collapse Use this flag if you would like to collapse the input alignment(s) into unique haplotypes
-gcoder Use this flag to code the gaps of the alignment into a binary state matrix that is appended to the end of the alignment
-filter FILTER FILTER Use this option if you wish to filter the alignment's missing data. Along with this option provide the threshold percentages for gap and missing data, respectively (e.g. -filter 50 75 - filters alignments columns with more than 50% of gap+missing data and columns with more than 75% of true missing data)
####Formatting options:
-model {DAYHOFF,DCMUT,JTT,MTREV,WAG,RTREV,CPREV,VT,BLOSUM62,MTMAM,LG} This option only applies for the concatenation of protein data into phylip format. Specify the model for all partitions defined in the partition file (default is 'LG')
-interleave Specificy this option to write output files in interleave format (currently only supported for nexus files
-g GAP Symbol for gap (default is '-')
-m MISSING Symbol for missing data (default is 'n')
####Data manipultation:
-rm [REMOVE [REMOVE ...]] Removes the specified taxa from the final alignment. Unwanted taxa my be provided in a csv file containing 1 column with a species name in each line or they may be specified in the command line and separated by whitespace
-outgroup [OUTGROUP_TAXA [OUTGROUP_TAXA ...]] **Provide taxon names/number for the outgroup (This option is only supported for NEXUS output format files)**xxxxxxxx
####Miscellaneous:
-quiet Removes all terminal output
#####Note: The order of the options does not matter.
PhD_Easy.py -c -of nexus -in input_file.fas
PhD_Easy.py -c -of nexus -in input_file.phy
PhD_Easy.py -c -of phylip fasta -in input_file.nex
PhD_Easy.py -c -of nexus -in input_file1.fas input_file2.fas input_file3.fas input_file4.fas [...] input_fileN.fas
or
PhD_Easy.py -c -of nexus -in *.fas
ElConcetenero.py -of nexus -in input_file1.nex input_file2.nex input_file3.nex (...) input_fileN.nex -o concatenated_file
or
ElConcetenero.py -of nexus -in *.nex -o concatenated_file
PhD_Easy.py -of phylip -in input_file1.fas input_file2.fas (...) input_fileN.fas -o concatenated_file
or
PhD_Easy.py -of phylip -in *.fas -o concatenated_file
#####Collapse alignment
PhD_Easy.py -in *.fas -of fasta -collapse -o Collapsed_alignment
PhD_Easy.py -in *.fas -of nexus -gcoder -c
PhD_Easy.py -in *.fas -of fasta nexus phylip -filter 50 75
PhD_Easy.py -in *.fas -of fasta -rm taxon1 taxon2 taxon3 (...) taxonN