SPACER_DATA_CONVERT
Write a data file for SPACER

SPACER_DATA_CONVERT is a FORTRAN77 program which takes a simple file of object names and distances, and writes out a data file suitable for input with SPACER.

The input file is very simple. The first line lists N, the number of objects. The next line lists the name of object #1, and the N "distances" to the other objects (including itself). Similar lines follow for objects 2 through N. Spaces are used to separate the data.

Example of a legal input file to SPACER_DATA_CONVERT:

       5
       London            0.0  125.0  250.0   75.0  450.0
       Manchester      125.0    0.0   83.0  327.0  154.0
       Dunwich         250.0   83.0    0.0  223.0  243.0
       East-Grinstead   75.0  327.0  223.0    0.0   93.0
       Burnt-Norton    450.0  154.0  243.0   93.0    0.0
      

Usage:

spacer_data_convert input output

input

the input file to be processed;

output

the output file, suitable for use with SPACER;

Languages:

SPACER_DATA_CONVERT is available in a FORTRAN77 version and a FORTRAN90 version.

Related Data and Programs:

DISTANCES is a FORTRAN77 program which can read a file in PIR format and create a distance matrix.

READ_ALIGN is a FORTRAN77 program which can read a multiple sequence alignment file and write out the relevant information into a file in PIR format.

SPACER is a FORTRAN77 program which reads a distance matrix and computes a principal coordinate analysis.

Author:

Des Higgins,
EMBL Data Library,
April 1992

Source Code:

• spacer_data_convert.f, the source code;
• spacer_data_convert.csh, commands to compile and load the source code;

Examples and Tests:

CITIES is the simple data example discussed above, with distances between 5 cities.

• cities_convert.txt, output printed by SPACER_DATA_CONVERT during the process of conversion.
• cities_input.txt, the input data file;
• cities_output.txt, the converted data file;

PROTEIN is a data file involving "distances" between 66 proteins.

• protein_convert.txt, output printed by SPACER_DATA_CONVERT during the process of conversion.
• protein_input.txt, the input data file;
• protein_output.txt, the converted data file;

List of Routines:

• SPACER_DATA_CONVERT converts a data file to SPACER format.
• CH_CAP capitalizes a single character.
• CH_EQI is a case insensitive comparison of two characters for equality.
• CH_TO_DIGIT returns the integer value of a base 10 digit.
• GET_UNIT returns a free FORTRAN unit number.
• I4_EXTRACT "extracts" an integer from the beginning of a string.
• INPUT_PRINT prints the input data.
• INPUT_READ reads the distance data from a file.
• OUTPUT_WRITE writes the distance data to a file in SPACER format.
• R4_EXTRACT "extracts" a real from the beginning of a string.
• S_SHIFT_LEFT shifts the characters in a string to the left and blank pads.
• S_TO_I4 reads an integer value from a string.
• S_TO_R4 reads a real number from a string.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• WORD_EXTRACT extracts the next word from a string.

You can go up one level to the FORTRAN77 source codes.