update September 24, 2011

NAME

phylcnv.py - Convert Phylip files into other formats

SYNOPSIS

phylcnv.py [-inf format] [-outf format] [-inv] infile outfile

DESCRIPTION


This script reads a file containing sequence data or discrete data (eg. molecular markers) in Phylip format and writes it in  the indicated format. The output formats supported currently are comma-seperated value (.csv) or tab-seperated value (.tsv).  The csvfile is a comma-separated value file of the type produced by exporting a spreadsheet (eg. OpenOffice Calc or MS-Excell) to a .csv file.  If  csv file is specified, the script will read the csv file and write a Phylip file removing the .csv or .CSV extension (if any) and replacing it with .phyl. Otherwise, phylcnv.py will take input from the standard input and write to the standard output.

If no input or output file names are specified, input is from the standard input and output is the standard output.


OPTIONS

-inf - input file format. pint (default): Phylip interleaved format; pseq: Phylip sequential format; csv: comma-separated value; tsv: tab-separated value

-outf – output file format. csv (default): comma-separated value; tsv: tab-separated value; pint: Phylip interleaved; pseq: Phylip sequential; fasta – Fasta; flatdna, flatpro, flattext: BioLegato flat file formats.
-inv - invert marker characters so that 0 -> 1 and 1 - > 0; + -> - and - -> +



INPUT

CSV,TSV
comma-separated value and tab-separated value, as generated by most spreadsheets. When exporting to these formats, many spreadsheets will enclose each item in double quotes. phylcnv.py strips out double quotes during input, and does not write them during output.


Phylip

The input is a Phylip data file. There are two Phylip formats, interleaved and sequential. Examples are shown for molecular marker data, but DNA or protein sequence files would be handled exactly the same way.

Interleaved - The first line has integers telling the number of isolates/species/strains, and the number of markers. Each subsequent line has an isolate/species/strain name of exactly 10 characters, followed by marker data. If the name is greater than 10 characters, it is truncated. If it is less than 10 characters, it is padded with blanks to 10 characters.


          3   319
G-A1 01001100110011000011100101011001001001011010000011
G-A2 01001000110111010011101101010000000001111001001011
G-A3 01000100110011000011100000011010101001011100111011
11010000010111011011101001110101110001001100010011
00010000000100111011101001100011110011011110011010
00110000010100111011100011100011100011011101010010
01000111111111011010101011100111111111000101100011
00000110010111110100000010110101001100000000010111
010001100101110000000010101001111111000???????????
01101011000101110011110100110101111101000001010111
01111011000100010101110000111101011100000001010011
??????????????????????????111101111000000001010011
11010110001110011110000000001001101100001000000000
11110111001111010110001010000001100010100000000111
10010110001110010110001010001000101111011001101111
00000000000000101011000101000101100100011000100001
11111001011000000000000101000101100000011100011101
01111000010000000010000101000001100100111000001101
0000100000000010100
0000101100001110100
0000101100100010100


Sequential- The first line has integers telling the number of isolates/species/strains, and the number of markers. Each sequence is represented by a sequence name, on one line, followed by one or more lines of sequence. Unlike fasta format, which uses a '>' character to indicate a new sequence name, Phylip sequential format detects the end of the sequence by reading the number of non-blank characters represented by the second number on the first line. This is an inherently dangerous file format for that reason.



                   3       319
G-A1
01001100110011000011100101011001001001011010000011
11010000010111011011101001110101110001001100010011
01000111111111011010101011100111111111000101100011
01101011000101110011110100110101111101000001010111
11010110001110011110000000001001101100001000000000
00000000000000101011000101000101100100011000100001
0000100000000010100
G-A2
01001000110111010011101101010000000001111001001011
00010000000100111011101001100011110011011110011010
00000110010111110100000010110101001100000000010111
01111011000100010101110000111101011100000001010011
11110111001111010110001010000001100010100000000111
11111001011000000000000101000101100000011100011101
0000101100001110100
G-A3
01000100110011000011100000011010101001011100111011
00110000010100111011100011100011100011011101010010
010001100101110000000010101001111111000???????????
??????????????????????????111101111000000001010011
10010110001110010110001010001000101111011001101111
01111000010000000010000101000001100100111000001101
0000101100100010100



OUTPUT

The output file consists of one or more lines lines of comma-separated marker data, in which the first field is the name of the marker, and all other fields are single characters.

Example:
LR210,1,0,1,1,0,1,0,0,0,1,0,0,1,0,0,0,1,0,0,1,0,1,1,0,1,0,1
LR211,0,1,1,1,0,1,1,0,1,1,0,0,1,0,0,0,1,0,0,1,0,1,1,1,1,0,1
LR212,0,0,1,1,0,1,0,0,1,1,0,0,1,0,0,1,1,0,0,1,0,1,1,1,1,0,1
LR213,1,0,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,0,0,0,0,1,0,1,1,0,1
LR214,0,0,1,1,1,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0
LR215,1,0,1,1,1,1,0,1,1,1,0,1,1,0,1,1,1,0,0,0,0,1,0,1,1,0,1
LR216,1,1,1,1,0,1,1,0,1,1,1,0,0,0,0,1,1,0,0,1,1,1,1,1,0,0,1
LR217,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,0,0,0,1,0,1,1,0,1



NOTES

1. This script is used by blmarker for File --> Import Discrete Data from CSV file.

 
AUTHOR

Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB  Canada R3T 2N2
frist@cc.umanitoba.ca
http://home.cc.umanitoba.ca/~frist