update May 28, 2011
NAME
phylcnv.py - Convert Phylip files into other formats
SYNOPSIS
phylcnv.py [-ini|-ins] [-ocsv|-otsv] [-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
-ini - input is interleaved (default)
-ins - input is sequential
-ocsv - output is csv format ie. field separator is a comma
-otsv - output is tsv format ie. field separator is a TAB character (default)
-inv - invert characters so that 0 -> 1 and 1 - > 0


INPUT
The input is a Phylip data file. There are two Phylip formats, interleaved and sequential.

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 teh 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