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fix: repair pyfoldtree corecut pipeline #38

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fix: repair pyfoldtree corecut pipeline #38

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f577022
fixed arguments
AthinaGav Aug 19, 2026
abd33dc
tried minimal fixes for pyfoldtree
AthinaGav Aug 20, 2026
dbdeda8
fixed correction and Tajima_dist call
AthinaGav Aug 20, 2026
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6 changes: 3 additions & 3 deletions src/foldtree/corecut.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ def extract_core(resdf , outfile, hitthresh = .8 ,minthresh = .6, corefolder =

"""

#read all results
folder =''.join([ sub + '/' for sub in resdf.split('/')[:-1] ])
# read all results
folder = os.path.dirname(resdf)
print(folder)
resdf = pd.read_table(resdf, header = None)
resdf.columns = 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,lddt,lddtfull,alntmscore'.split(',')
Expand Down Expand Up @@ -75,7 +75,7 @@ def extract_core(resdf , outfile, hitthresh = .8 ,minthresh = .6, corefolder =
if '/' in q:
qfile = qfile.split('/')[-1]

struct = parser.get_structure(q.split('.')[0], folder+structfolder+qfile )
struct = parser.get_structure(q.split('.')[0], os.path.join(structfolder, qfile))

#zero based indexing...
struct_core = Bio.PDB.Dice.extract( struct ,'A' , hits[q]['min']+1 , hits[q]['max']+1 ,folder+corefolder+qfile )
Expand Down
54 changes: 32 additions & 22 deletions src/foldtree/pyfoldtree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,13 @@
import numpy as np
import pandas as pd
import os
import shutil

def structblob2tree(input_folder, outfolder, overwrite = False,
fastmepath = 'fastme', quicktreepath = 'quicktree' ,
foldseekpath = 'foldseek' , delta = 0.0001 ,
correction = False , kernel = 'fident' , core = False
, hittresh = .8 , minthresh = .6):
, hitthresh = .8 , minthresh = .6):
'''
run fold tree pipeline for a folder of pdb files

Expand All @@ -41,20 +42,28 @@ def structblob2tree(input_folder, outfolder, overwrite = False,
kernel to use, either 'fident', 'lddt' or 'alntmscore'

'''
if shutil.which(fastmepath) is None:
raise RuntimeError(
f"FastME executable '{fastmepath}' was not found. "
"FastME is required to run pyfoldtree. "
"Install it or provide its location with --fastmepath."
)
os.makedirs(outfolder, exist_ok=True)

#check if the foldseek output is already there
if os.path.exists(outfolder + 'res.m8') and overwrite == False:
if os.path.exists(os.path.join(outfolder, 'res.m8')) and overwrite == False:
print('found foldseek output, skipping foldseek')
alnres = outfolder + 'res.m8'
alnres = os.path.join(outfolder, 'res.m8')
else:
alnres = foldseek2tree.runFoldseek_allvall_EZsearch(input_folder , outfolder + 'res.m8', foldseekpath = foldseekpath)
alnres = foldseek2tree.runFoldseek_allvall_EZsearch(input_folder , os.path.join(outfolder, 'res.m8'), foldseekpath = foldseekpath)

if core == True:
corecut.extract_core( alnres , resdf+'.core.csv', hitthresh = .8 ,minthresh = .6, corefolder = input_folder+'core_structs/' , structfolder = input_folder )
if os.path.exists(outfolder + 'res.m8') and overwrite == False:
corecut.extract_core( alnres , outfolder+'.core.csv', hitthresh = hitthresh ,minthresh = minthresh, corefolder = input_folder+'core_structs/' , structfolder = input_folder )
if os.path.exists(os.path.join(outfolder, 'core.res.m8')) and overwrite == False:
print('found foldseek core output, skipping foldseek')
alnres = outfolder + 'core.res.m8'
alnres = os.path.join(outfolder, 'core.res.m8')
else:
alnres = foldseek2tree.runFoldseek_allvall_EZsearch(input_folder , outfolder + 'core.res.m8', foldseekpath = foldseekpath)
alnres = foldseek2tree.runFoldseek_allvall_EZsearch(input_folder , os.path.join(outfolder, 'core.res.m8'), foldseekpath = foldseekpath)

res = pd.read_table(alnres , header = None )
res[0] = res[0].map(lambda x :x.replace('.pdb', ''))
Expand Down Expand Up @@ -84,38 +93,38 @@ def structblob2tree(input_folder, outfolder, overwrite = False,
factor = .93
else:
factor = 1
matrices[k] = Tajima_dist(matrices[k], factor = factor)
np.save( input_folder + k + '_distmat.npy' , matrices[k])
distmat_txt = foldseek2tree.distmat_to_txt( ids , matrices[k] , outfolder + k + '_distmat.txt' )
matrices[k] = foldseek2tree.Tajima_dist(matrices[k], bfactor = factor)
np.save(os.path.join(input_folder, k + '_distmat.npy'), matrices[k])
distmat_txt = foldseek2tree.distmat_to_txt( ids , matrices[k] , os.path.join(outfolder, k + '_distmat.txt'))
out_tree = foldseek2tree.runFastme( fastmepath = fastmepath , clusterfile = distmat_txt )
out_tree = foldseek2tree.postprocess(out_tree, input_folder + 'structblob_tree.nwk' , delta = delta)
out_tree = foldseek2tree.postprocess(out_tree, os.path.join(input_folder, 'structblob_tree.nwk') , delta = delta)
trees[k] = out_tree
return alnres, trees

if __name__ == '__main__':
def main():
parser = argparse.ArgumentParser(description='run foldtree pipeline for a folder of pdb files')
parser.add_argument('struct_dir', help='path to folder with pdb files')
parser.add_argument('output_dir', help='output directory')
parser.add_argument('--corecut', help='cut the core of the proteins and realign')
parser.add_argument('--corecut', action='store_true', help='cut the core of the proteins and realign')
parser.add_argument('--kernel', choices = ['lddt', 'fident', 'tmalign' ] ,
default = 'fident',
help='this is the comparison metric used to build the tree')
parser.add_argument('--fastmepath', default='fastme', help='path to fastme binary')
parser.add_argument('--quicktreepath', default='quicktree', help='path to quicktree binary')
parser.add_argument('--foldseekpath', default='../foldseek/foldseek', help='path to foldseek binary')
parser.add_argument('--foldseekpath', default='foldseek', help='path to foldseek binary')
parser.add_argument('--delta', default=0.0001, help='small number to replace negative branch lengths with')
parser.add_argument('--correction', help='use the -ln correction for the distance matrix')
parser.add_argument('--correction', action='store_true', help='use the -ln correction for the distance matrix')
parser.add_argument('--overwrite', help='overwrite existing foldseek output')
parser.add_argument( 'hittresh', default = .8, help='threshold for finding the boundaries of the core')
parser.add_argument( 'minthresh', default = .6, help='threshold if the core is not found')
parser.add_argument( '--hitthresh', default = .8, help='threshold for finding the boundaries of the core')
parser.add_argument( '--minthresh', default = .6, help='threshold if the core is not found')

args = parser.parse_args()

if not all([args.positional1, args.positional2]):
if not all([args.struct_dir, args.output_dir]):
parser.error("Positional arguments are required.")
flag_dict = {}
flag_dict['corecut'] = True if args.corecut else False
flag_dict['hittresh'] = args.hittresh
flag_dict['core'] = args.corecut
flag_dict['hitthresh'] = args.hitthresh
flag_dict['minthresh'] = args.minthresh
flag_dict['correction'] = True if args.correction else False
flag_dict['overwrite'] = True if args.overwrite else False
Expand All @@ -129,4 +138,5 @@ def structblob2tree(input_folder, outfolder, overwrite = False,
print('Done!')



if __name__ == '__main__':
main()
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