Shell Programming and Scripting

Group   Centre      Branches       Id_of_Branches
 3       006          6         009,004,008,007,005,006
 5       012          2         012,013

Group: 0 Number of Branches: 1
0    001
Centre: 001 Branches: 1
Group: 1 Number of Branches: 1
0    002
Centre: 002 Branches: 1
Group: 2 Number of Branches: 1
0    003
Centre: 003 Branches: 1
Group: 3 Number of Branches: 6
0    009
1    004
2    008
3    007
4    005
5    006
Centre: 006 Branches: 6
Group: 4 Number of Branches: 2
0    010
1    011
Centre: 010 Branches: 2
Group: 5 Number of Branches: 2
0    012
1    013
Centre: 012 Branches: 2
Upto more than 600 groups

Group No:
 3        Centre: 006 Branches: 6                   
 5        Centre: 012 Branches: 2

(1) g3.txt
#009
ATOM 1 N SER A 1 35.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#004
ATOM 1 N SER A 1 34.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#008
ATOM 1 N SER A 1 45.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 35.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#007
ATOM 1 N SER A 1 50.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 65.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#005
ATOM 1 N SER A 1 90.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 89.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#006
ATOM 1 N SER A 1 67.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 23.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

(2)g5.txt
#012
ATOM 1 N SER A 1 37.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 37.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#13
ATOM 1 N SER A 1 40.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 31.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

(3) Centre.txt (For Id from centre of all groups)
#006
ATOM 1 N SER A 1 67.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 23.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL
#012
ATOM 1 N SER A 1 37.092 83.194 140.076 1.00 0.00 N 
ATOM 2 CA SER A 1 37.216 83.725 138.725 1.00 0.00 C 
TER
ENDMDL

awk '
# All data is assumed to meet the requirements stated below, so this script
# does not perform any data verification.  If any data fails to meet these
# assumptions, results are unspecified.
BEGIN {
    # Initialize variables that do not have default values set by awk.
    cf = "Centre.txt"
    rc = "001"
}
FNR == NR {
    # Process lines from atom.txt.  Assumed format is that each entry in this
    # file is a multiple line value with the final line of each entry matching
    # the ERE "^ENDMDL$".  Entries from this file are stored in array r with
    # the index being the entry number (starting with 001).  The variable rc is
    # the index for the value being accumulated.  I use a 3 digit string with
    # leading zero fill to match the format of the Centre-ID and Branch-ID
    # values that will be found in g.txt.
    r[rc] = r[rc] $0 "\n"
    if($0 == "ENDMDL")
        # End of entry found.  Set rc for the next entry to be processed.
        rc = sprintf("%03d", rc + 1)
    next
}
FNR == 1 {
    # Skip the header line on subsequent file(s).  The file g.txt is assumed to
    # be the first such file.  Any number of other files in the same format can
    # be used in addition to or instead of g.txt.
    next
}
{   # Process lines from subsequent files.  Assumed format is:
    #   Group   Centre      Branches              Id_of_Branches
    #   gid     cid         bcnt         bid[1],bid[2],...,bid[bcnt]
    # where gid is a 1-3 digit Group-ID, cid is a 3 digit (zero filled)
    # Centre-ID, bcnt is a count of the number of Branch-IDs to follow, and
    # each bid field is a 3 digit (zero filled) Branch-ID.  The header line
    # has already been discarded.  Commas will be converted to spaces so bid
    # values can be used directly.  It is assumed that each line contains
    # $3 + 3 fields.
    #
    # Create a file named gx.txt (where x is the Group-ID from this line):
    #   Note that it would seem logical to expand x to a 3 digit zero filled
    #   value so the created g* files would sort into Group-ID order, but that
    #   is not what was requested.
    #   One entry from atom.txt (with the entry number determined by the
    #   Branch-ID) will be written to this file for each Branch-ID on this
    #   line.
    #
    # Also create a file named Centre.txt that will contain one entry from
    #   atom.txt (with the entry number determined by the Centre-ID) for each
    #   line processed.
    #   Note: I assume that a Centre-ID is also a Branch-ID and that the value
    #   given as the cid should also appear as one of the Branch-IDs appearing
    #   on each line.
    #
    # Replace commas on input lines with spaces so the Branch-IDs can be used
    # directly without splitting $4 into another array and processing it in a
    # different loop (besides that some descriptions of this input file say
    # elements are comma separated and other say comma-space separated or
    # terminated; this works either way):
    gsub(/,/, " ")
    # Create the g*.txt file for this line.  Uncomment one of the following two
    # lines.  The 1st line provides requested names, the 2nd line creates names
    # that will sort correctly by Group-ID when looking at output by ls and
    # when having the shell match the patterns g*.txt and g???.txt and groups
    # in the list do not all contain the same number of digits.
    gf = "g" $1 ".txt"
    #gf = sprintf("g%03d.txt", $1)
    for(i = 4; i <= NF; i++) printf("#Id %s\n%s", $i, r[$i]) > gf
    close(gf)
    # Add entry to Centre.txt:
    printf("#Id %s\n%s", $2, r[$2]) > cf
}' atom.txt g.txt