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#!/usr/bin/env python
import sys
#---
# Add items to dictionary
#---
def addToDict(vals, key, val):
out = ''
if key == 'MOL_ID':
out = show(vals) # Show old values
vals.clear() # Reset
init = 1
# Add key or append to previous key (line continuation)
if key in vals:
vals[key] += val
else:
vals[key] = val
return out
#---
# Parse compound sub fields
#---
def parseKeyVal(keyPrev, line):
field = line[10:].strip()
if ':' in field:
(key, val) = field.split(':', 1)
key = key.strip()
else:
key = keyPrev
val = field
val = val.strip()
if val.endswith(';'):
val = val[:-1]
return (key, val)
#---
# Show dict entries as one string
#---
def show(vals):
ret = ''
if 'MOL_ID' not in vals:
return ret
for key in ['MOL_ID', 'MOLECULE', 'SYNONYM', 'CHAIN']:
if key in vals:
ret += vals[key]
ret += '\t'
return ret[:-1]
#-------------------------------------------------------------------------------
# Main
#-------------------------------------------------------------------------------
# Parse name from command line
name = sys.argv[1]
# Initialize
done = False
vals = dict()
compounds = list()
orgs = list()
key = ''
for l in sys.stdin:
l = l.rstrip()
if l.startswith('COMPND'):
done = True
(key, val) = parseKeyVal(key, l) # Parse compound sub fields
outStr = addToDict(vals, key, val)
if outStr: compounds.append(outStr)
elif l.startswith('SOURCE'):
(key, val) = parseKeyVal(key, l) # Parse compound sub fields
if key == 'ORGANISM_COMMON' or key == 'ORGANISM_SCIENTIFIC':
orgs.append( val )
else:
if done: break;
# Add last element
compounds.append( show(vals) )
# Show results
out = [i for tup in zip(compounds, orgs) for i in tup] # Merge lists and create string
out = '\t'.join( out )
count = len(compounds)
if count > 1:
organisms = ','.join(orgs)
print(f"{name}\t{organisms}\t{count}\t{out}")
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