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resume
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@Cantalapiedra
Cantalapiedra committed Feb 16, 2022
1 parent 53aff97 commit cc03707
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Showing 2 changed files with 34 additions and 31 deletions.
6 changes: 3 additions & 3 deletions eggnogmapper/search/diamond/diamond.py
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 135,7 @@ def clear(self):
return

##
def search(self, in_file, seed_orthologs_file, hits_file, gff_outfile):
def search(self, in_file, seed_orthologs_file, hits_file):
hits_generator = None

if not DIAMOND:
Expand All @@ -157,11 157,11 @@ def search(self, in_file, seed_orthologs_file, hits_file, gff_outfile):

# 2) parse search hits to seeds orthologs
if self.itype == ITYPE_CDS or self.itype == ITYPE_PROTS:
hits_generator = self._parse_diamond(raw_dmnd_file)
hits_generator = self._parse_diamond(hits_file)

else: #self.itype == ITYPE_GENOME or self.itype == ITYPE_META:
# parse_genepred (without coordinate change)
hits_generator = self._parse_genepred(raw_dmnd_file)
hits_generator = self._parse_genepred(hits_file)


# 3) output seeds
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59 changes: 31 additions & 28 deletions eggnogmapper/search/mmseqs/mmseqs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 16,7 @@

from ..hmmer.hmmer_seqio import iter_fasta_seqs

from ..hits_io import parse_hits, output_hits, change_hits_coordinates
from ..hits_io import output_seeds, change_seeds_coordinates
from ..diamond.diamond import hit_does_overlap, ALLOW_OVERLAPS_ALL

def create_mmseqs_db(dbprefix, in_fasta):
Expand Down Expand Up @@ -117,7 117,7 @@ def clear(self):
return

##
def search(self, in_file, seed_orthologs_file, hits_file, gff_outfile):
def search(self, in_file, seed_orthologs_file, hits_file):
hits_generator = None

if not MMSEQS2:
Expand All @@ -127,12 127,11 @@ def search(self, in_file, seed_orthologs_file, hits_file, gff_outfile):

try:
cmds = None
hits_parser = None

# 1) either resume from previous hits or run diamond to generate the hits
if self.resume == True:
if pisfile(hits_file):
if self.itype == ITYPE_CDS or self.itype == ITYPE_PROTS:
if pisfile(seed_orthologs_file):
hits_parser = parse_hits(seed_orthologs_file)
pass
else:
raise EmapperException(f"Couldn't find hits file {hits_file} to resume.")
else:
Expand All @@ -146,17 145,39 @@ def search(self, in_file, seed_orthologs_file, hits_file, gff_outfile):
alignmentsdb, cmds = self.run_mmseqs(in_file, querydb,
self.targetdb, resultdb, bestresultdb)
shutil.copyfile(f'{alignmentsdb}.m8', hits_file)


hits_generator = self.parse_mmseqs(hits_file, hits_parser, gff_outfile)
hits_generator = output_hits(cmds, hits_generator,
seed_orthologs_file, self.resume,
self.no_file_comments, False)
# 2) parse search hits to seeds orthologs
if self.itype == ITYPE_CDS or self.itype == ITYPE_PROTS:
hits_generator = self._parse_mmseqs(hits_file)

else: #self.itype == ITYPE_GENOME or self.itype == ITYPE_META:
# parse_genepred (without coordinate change)
hits_generator = self._parse_genepred(hits_file)

# 3) output seeds
if self.itype == ITYPE_CDS or self.itype == ITYPE_PROTS:
hits_generator = output_seeds(cmds, hits_generator,
seed_orthologs_file, self.resume,
self.no_file_comments, False)

else: #self.itype == ITYPE_GENOME or self.itype == ITYPE_META:

# change seeds coordinates relative to the ORF, not to the contig (to use them for the .seed_orthologs file)
hits_generator = change_seeds_coordinates(hits_generator)

hits_generator = output_seeds(cmds, hits_generator,
seed_orthologs_file, self.resume,
self.no_file_comments, False)

hits_generator = recover_seeds_coordinates(hits_generator)

except Exception as e:
raise e

return hits_generator


def run_mmseqs(self, fasta_file, querydb, targetdb, resultdb, bestresultdb):
cmds = []

Expand Down Expand Up @@ -257,24 278,6 @@ def convertalis_step(self, querydb, targetdb, resultdb):
except subprocess.CalledProcessError as cpe:
raise EmapperException("Error running 'mmseqs convertalis': " cpe.stderr.decode("utf-8").strip().split("\n")[-1])
return cmd


##
def parse_mmseqs(self, raw_mmseqs_file, hits_parser, gff_outfile):
if self.itype == ITYPE_CDS or self.itype == ITYPE_PROTS:
hits_generator = self._parse_mmseqs(raw_mmseqs_file, hits_parser)
# False parameter means only wrap but don't compute new coordinates
hits_generator = change_hits_coordinates(hits_generator, False)

else: #self.itype == ITYPE_GENOME or self.itype == ITYPE_META:
# parse_genepred (without coordinate change)
hits_generator = self._parse_genepred(raw_mmseqs_file)
# generate gff (with original coordinates)
hits_generator = create_blastx_hits_gff(hits_generator, gff_outfile, self.name, self.gff_ID_field)
# change_hits_coordinates (to use them for the .seed_orthologs file)
hits_generator = change_hits_coordinates(hits_generator, True)

return hits_generator

##
def _parse_mmseqs(self, raw_mmseqs_file, hits_parser):
Expand Down

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