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reenble tls warnings #95

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reenble tls warnings #95

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58 changes: 28 additions & 30 deletions ectyper/speciesIdentification.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@
from ectyper import definitions, subprocess_util
import re
import requests
import urllib3
urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
from Bio import SeqIO
import time #for file age calculations

Expand Down Expand Up @@ -164,7 +162,7 @@ def get_species(file, args, cores=1):
"""
LOG.debug(f"Get species prediction for {file}")
top_match="-"; top_match_dist="-"; top_match_hashratio="-"; species="-"
sketch_metadata_file = args.reference+'.txt'
sketch_metadata_file = args.reference+'.txt'
if os.path.exists(sketch_metadata_file) == False:
raise FileNotFoundError(f'Missing required species ID sketch at {sketch_metadata_file} path')

Expand All @@ -181,7 +179,7 @@ def get_species(file, args, cores=1):
]
sort_output = subprocess_util.run_subprocess(sort_cmd,
input_data=mash_output.stdout)


if args.debug:
LOG.debug("Wrote MASH against reference sketch results to {}".format(args.output))
Expand All @@ -198,7 +196,7 @@ def get_species(file, args, cores=1):
head_output = subprocess_util.run_subprocess(head_cmd,
input_data=sort_output.stdout)
top_hit_lines = head_output.stdout.decode("utf-8").split('\n')



if len(top_hit_lines) < 1:
Expand Down Expand Up @@ -229,9 +227,9 @@ def get_species(file, args, cores=1):
LOG.info("MASH dist predicted species name: '{}' based on species ID sketch {}".format(species, args.reference))
else:
LOG.warning(f"Could not determine species based on MASH distance for {file}")
species = "-"
return species, top_match_hashratio, top_match_dist, top_match
species = "-"
return species, top_match_hashratio, top_match_dist, top_match


def getSampleName(file):
# get only the name of the file for use in the fasta header
Expand All @@ -244,13 +242,13 @@ def is_valid_fasta_file(fasta, sampleName):
# try to read the first sequence of FASTA file and make a format validity decision. No reason to check all reads
for contig in SeqIO.parse(fasta, "fasta").records:
if contig.seq != '':
LOG.debug(f'{sampleName}: input file {fasta} is a valid FASTA')
LOG.debug(f'{sampleName}: input file {fasta} is a valid FASTA')
return True
else:
LOG.warning(f'{sampleName}: input FASTA file {fasta} format is invalid FASTA. Skipping further analyses ...')
return False
return False


def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args):
"""
Verifying the E. coli-ness of the genome files and validity of file inputs
Expand All @@ -266,7 +264,7 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
failverifyerrormessage = ''

fasta_files = fasta_fastq_files_dict.keys()

for fasta in fasta_files:
sampleName = getSampleName(fasta)
speciesname = "-"
Expand All @@ -277,48 +275,48 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
)
LOG.error(error_msg)
raise ValueError(error_msg)

if is_valid_fasta_file(fasta, sampleName) == False:
failverifyerrormessage += f"Sample {sampleName} FASTA file ({fasta}) is invalid/empty. This could happen when FASTA file generated from FASTQ input lacks raw reads mapping to O- and H- antigens or input FASTA is corrupted. Please check sequence input file '{sampleName}'."


#do species always regardless of --verify param. Do prediction on fastq files if available for better accuracy
if fasta_fastq_files_dict[fasta]:
fastq_file = fasta_fastq_files_dict[fasta]
speciesname, species_mash_hash_ratio, species_mash_dist, species_top_hit_accession = get_species(fastq_file, args, args.cores)
else:
speciesname, species_mash_hash_ratio, species_mash_dist, species_top_hit_accession = get_species(fasta, args, args.cores)

if args.verify:
failverifyerrormessage += "Sample identified as " + speciesname + ": typing results are only valid for E.coli samples." \
"If sure that sample is E.coli or want results regardless try running without the --verify parameter."
if re.match("Escherichia coli", speciesname):
ecoli_files_dict[sampleName] = {"species":speciesname, "species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
ecoli_files_dict[sampleName] = {"species":speciesname, "species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
"filepath":fasta, "error": ""}
elif is_escherichia_genus(speciesname):
other_files_dict[sampleName] = {"species":speciesname,"filepath":fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
other_files_dict[sampleName] = {"species":speciesname,"filepath":fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
"error":failverifyerrormessage}
else:
other_files_dict[sampleName] = {"species":speciesname, "filepath":fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
other_files_dict[sampleName] = {"species":speciesname, "filepath":fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio,
"species_mash_dist2ref": species_mash_dist, "species_mash_top_reference":species_top_hit_accession,
"error":failverifyerrormessage}
else:
ecoli_files_dict[sampleName] = {"species": speciesname,"filepath": fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio, "species_mash_dist2ref": species_mash_dist,
ecoli_files_dict[sampleName] = {"species": speciesname,"filepath": fasta,
"species_mash_hash_ratio2ref":species_mash_hash_ratio, "species_mash_dist2ref": species_mash_dist,
"species_mash_top_reference":species_top_hit_accession, "error": ""}

for bf in ofiles:
sampleName = getSampleName(bf)
LOG.warning(f"{sampleName} is non fasta / fastq file. Species identification aborted")
other_files_dict[sampleName] = {"error":"Non fasta / fastq file. ","filepath":bf,"species":"-",
other_files_dict[sampleName] = {"error":"Non fasta / fastq file. ","filepath":bf,"species":"-",
"species_mash_hash_ratio2ref":"-", "species_mash_dist2ref":"-", "species_mash_top_reference":"-"}

for file in filesnotfound:
sampleName = getSampleName(file)
filesnotfound_dict[sampleName]={"error":"File {} not found!".format(file), }
return ecoli_files_dict, other_files_dict,filesnotfound_dict

return ecoli_files_dict, other_files_dict,filesnotfound_dict