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fixed contig mode filetype detection and implemeted first unit pytests
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@kbessonov1984
kbessonov1984 committed Jan 8, 2025
1 parent 1917934 commit da6a240
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41 changes: 41 additions & 0 deletions .github/workflows/github-actions.yaml
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# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python application

on:
push:
branches: [ "master", "v1.5.0" ]
pull_request:
branches: [ "master", "v1.5.0" ]

permissions:
contents: read

jobs:
build:

runs-on: ubuntu-22.04

steps:
- uses: actions/checkout@v4
- name: Set up Python 3.12
uses: actions/setup-python@v4
with:
python-version: "3.12"
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install ncbi-blast+ clustalw -y
sudo apt-get install python3-pip python3-numpy python3-pandas -y
python3 -m pip install --upgrade pip setuptools
pip3 install pytest "biopython>=>=1.7,<1.78
if [ -f requirements.txt ]; then
pip3 install -r requirements.txt;
else
pip3 install -e .
fi
ectyper_init
- name: Test with pytest
run: |
pytest -o log_cli=true --basetemp=tmp-pytest
74 changes: 39 additions & 35 deletions CryptoGenotyper/gp60.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,9 @@ def readFiles(self, dataFile, forw, output, tabFile, filetype = "abi", customdat
elif filetype == "fasta" or filetype == "fa":
handle=open(dataFile,"r")
record=SeqIO.read(handle, filetype)
#records=list(SeqIO.parse(handle, filetype))
#LOG.info(f"File {handle.name} has {len(records)} sequences {[r.name for r in records]}")
#record = records[0]
raw_seq = list(record.seq)
self.seq = raw_seq
self.phred_qual = [60] * len(raw_seq)
Expand Down Expand Up @@ -793,7 +796,7 @@ def determineRepeats(self):
return False


def determineFamily(self,customdatabsename=None):
def determineFamily(self,customdatabasename=None):
LOG.info(f"Determine family and species of {self.name} of {len(self.seq)}bp sequence ...")
# Filename to write
filename = "query.txt"
Expand All @@ -811,7 +814,7 @@ def determineFamily(self,customdatabsename=None):
# Close the file
myfile.close()

if customdatabsename:
if customdatabasename:
blastn_cline = NcbiblastnCommandline(cmd='blastn', task='blastn', query="query.txt", dust='no',
db="custom_db",
reward=1, penalty=-2, gapopen=5, gapextend=2,evalue=0.00001, outfmt=5, out="gp60result.xml")
Expand Down Expand Up @@ -901,7 +904,7 @@ def determineFamily(self,customdatabsename=None):
#raise Exception()


def blast(self, sequence, contig, filetype, customdatabasename):
def blast(self, sequence, contig, filetype, customdatabasename=None):
if customdatabasename:
blastdbpath="custom_db"
else:
Expand Down Expand Up @@ -1323,7 +1326,7 @@ def blast(self, sequence, contig, filetype, customdatabasename):
#printFasta() prints the results of the alignment and the repeat
# region for each sample. It then prints the fasta sequence for
# each sample that can successfully be analyzed
def printFasta(self, contig, mode, sampleName, filetype="ab1", customdatabsename = None):
def printFasta(self, contig, mode, sampleName, filetype="ab1", customdatabasename = None):
LOG.info(f"Running printFasta() on {self.name} with species '{self.species}' and repeat encoding '{self.repeats}' ...")
#IF WANTING TO PRINT TO SCREEN INSTEAD
if TESTING and contig!="":
Expand All @@ -1347,14 +1350,14 @@ def printFasta(self, contig, mode, sampleName, filetype="ab1", customdatabsename
if contig == "":
sequence=str(self.seq)
if sequence != "Poor Sequence Quality":
bitscore,evalue,query_coverage,query_length,percent_identity, accession, seq = self.blast(sequence,False, filetype, customdatabsename)
bitscore,evalue,query_coverage,query_length,percent_identity, accession, seq = self.blast(sequence,False, filetype, customdatabasename)

else:
sequence = contig

if sequence != "Poor Sequence Quality":
LOG.info("Running BLAST on contig of acceptable quality and getting top hit accession ...")
bitscore,evalue,query_coverage,query_length,percent_identity, accession, seq = self.blast(sequence, True, customdatabsename)
bitscore,evalue,query_coverage,query_length,percent_identity, accession, seq = self.blast(sequence, True, customdatabasename)

if self.seq == "Poor Sequence Quality":
self.tabfile.write("\t\t\tPoor Sequence Quality. Check manually.\t" + str(self.averagePhredQuality) + "\t\t\t\t\t\t\n")
Expand All @@ -1370,7 +1373,7 @@ def printFasta(self, contig, mode, sampleName, filetype="ab1", customdatabsename

else:
self.seq = seq
self.determineFamily(customdatabsename)
self.determineFamily(customdatabasename)


#Output Species and Subfamily(ex. C.parvum\tIIa)
Expand Down Expand Up @@ -1410,7 +1413,7 @@ def printFasta(self, contig, mode, sampleName, filetype="ab1", customdatabsename
#Still outputting repeats if there's a subfamily
if len(speciesName.split("|")) == 3 and foundRepeat == True:
subfamily = speciesName.split("|")[2]
LOG.debug(f"Appending family subtype {subfamily} to {speciesName.split("|")[1]}{self.repeats}")
LOG.debug(f'Appending family subtype {subfamily} to {speciesName.split("|")[1]}{self.repeats}')
self.file.write(subfamily)
self.tabfile.write(subfamily)

Expand Down Expand Up @@ -1519,7 +1522,7 @@ def getFileType(path):
return None


def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdatabsename, noheader, verbose):
def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdatabasename, noheader, verbose):
if verbose:
LOG.setLevel(logging.DEBUG)

Expand Down Expand Up @@ -1574,8 +1577,8 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat
#Write output fasta with comments
file.write("\n;>****************************************************************************")
file.write("\n;>gp60 SEQUENCE ANALYSIS INPUT PARAMETERS:")
if customdatabsename:
file.write("\n ;>Reference File: " + customdatabsename)
if customdatabasename:
file.write("\n ;>Reference File: " + customdatabasename)
else:
file.write("\n ;>Reference File: " + "gp60_ref.fa (default)") #debug this might not be always true, actually it is blast_gp60.fa as default
file.write("\n ;>Program mode: " + typeSeq)
Expand All @@ -1599,11 +1602,12 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat
reverse = analyzingGp60() #reverse read object



filetypeF = getFileType(path)
filetypeR = getFileType(pathlist[idx+1])
#for i in range(0, len(fPrimers)):
#if fPrimer in path:
forwSeqbool = forward.readFiles(path, True, file, tabfile, customdatabsename)
revSeqbool = reverse.readFiles(pathlist[idx+1], False, file, tabfile, customdatabsename)
forwSeqbool = forward.readFiles(path, True, file, tabfile, filetypeF,customdatabasename)
revSeqbool = reverse.readFiles(pathlist[idx+1], False, file, tabfile,filetypeR, customdatabasename)
pathlist.remove(pathlist[idx+1])

forwardPhred = forward.averagePhredQuality
Expand All @@ -1616,7 +1620,7 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat
if forwSeqbool and revSeqbool:
goodTrimF = forward.trimSeq()
goodTrimR = reverse.trimSeq()
#print(dir(forward),dir(reverse),customdatabsename)
#print(dir(forward),dir(reverse),customdatabasename)
#print(f"forward seq top hit blast {forward.species} reverse {reverse.species}")

if not goodTrimF and not goodTrimR:
Expand All @@ -1625,9 +1629,9 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat

else:

if customdatabsename:
forward.determineFamily(customdatabsename)
reverse.determineFamily(customdatabsename)
if customdatabasename:
forward.determineFamily(customdatabasename)
reverse.determineFamily(customdatabasename)


if forward.species == reverse.species and forward.species!= "":
Expand All @@ -1638,21 +1642,21 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat

#if the crypto subfamily was found, find repeat region
if forward.species == reverse.species and forward.species != "" and forward.repeats == reverse.repeats and forward.repeats != "":
#forward.determineFamily(customdatabsename)
#reverse.determineFamily(customdatabsename)

#forward.determineFamily(customdatabasename)
#reverse.determineFamily(customdatabasename)
print(customdatabasename)
Fbitscore,Fevalue,Fquery_coverage,Fquery_length,Fpercent_identity, Faccession, Fnewseq = forward.blast(str(forward.seq), False, customdatabasename)
Rbitscore,Revalue,Rquery_coverage,Rquery_length,Rpercent_identity, Raccession, Rnewseq = reverse.blast(str(reverse.seq), False, customdatabasename)
LOG.info(f"Build contig from forward and reverse extracted sequences of {len(Fnewseq)}bp and {len(Rnewseq)}bp")
contig = buildContig(Fnewseq, Rnewseq)

sampleName = forward.name.split(".ab1")[0] + ", " + reverse.name.split(".ab1")[0]

forward.printFasta(contig, "contig", sampleName, customdatabsename)
forward.printFasta(contig, "contig", sampleName, customdatabasename)

else:
#forward.determineFamily(customdatabsename)
#reverse.determineFamily(customdatabsename)
#forward.determineFamily(customdatabasename)
#reverse.determineFamily(customdatabasename)
forward.printFasta("", "forward", forward.name.split(".ab1")[0])
reverse.printFasta("", "reverse", reverse.name.split(".ab1")[0])

Expand All @@ -1663,25 +1667,25 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat
forward.repeats="Could not classify repeat region. Check manually."

else:
forward.determineFamily(customdatabsename)
forward.determineFamily(customdatabasename)

forward.printFasta("", "forward", forward.name.split(".ab1")[0], customdatabsename)
forward.printFasta("", "forward", forward.name.split(".ab1")[0], customdatabasename)


reverse.seq = "Poor Sequence Quality"
reverse.printFasta("", "reverse", reverse.name.split(".ab1")[0], customdatabsename)
reverse.printFasta("", "reverse", reverse.name.split(".ab1")[0], customdatabasename)

elif revSeqbool and not forwSeqbool:
forward.seq = "Poor Sequence Quality"
forward.printFasta("", "forward", forward.name.split(".ab1")[0], customdatabsename)
forward.printFasta("", "forward", forward.name.split(".ab1")[0], customdatabasename)

goodTrim = reverse.trimSeq()

if not goodTrim:
reverse.repeats="Could not classify repeat region. Check manually."

else:
reverse.determineFamily(customdatabsename)
reverse.determineFamily(customdatabasename)

reverse.printFasta("", "reverse", reverse.name.split(".ab1")[0])

Expand All @@ -1696,29 +1700,29 @@ def gp60_main(pathlist_unfiltered, fPrimer, rPrimer, typeSeq, expName, customdat
file.write("\nCannot find all paired forward and reverse files. Make sure all files are included to produce the contig.")

else:
LOG.info("Forward/Reverse read input only mode started ...")
LOG.info("Forward or Reverse read input only mode started ...")
for path in pathlist:
filetype = getFileType(path)
LOG.info(f"Running {path} as {filetype} file type")
forward = analyzingGp60()

if onlyForwards:
read_ok = forward.readFiles(path, True, file, tabfile, filetype, customdatabsename)
read_ok = forward.readFiles(path, True, file, tabfile, filetype, customdatabasename)
elif onlyReverse:
read_ok = forward.readFiles(path, False, file, tabfile, filetype, customdatabsename)
read_ok = forward.readFiles(path, False, file, tabfile, filetype, customdatabasename)

if read_ok == False:
forward.seq = "Poor Sequence Quality"
forward.printFasta("", typeSeq, forward.name.split(f".{filetype}")[0], customdatabsename)
forward.printFasta("", typeSeq, forward.name.split(f".{filetype}")[0], customdatabasename)
else:
goodTrim = forward.trimSeq(filetype)
if goodTrim == False:
forward.repeats="Could not classify repeat region. Check manually."
else:
forward.determineFamily(customdatabsename)
forward.determineFamily(customdatabasename)
forward.determineRepeats()

forward.printFasta("", typeSeq, forward.name.split(f".{filetype}")[0], filetype, customdatabsename)
forward.printFasta("", typeSeq, forward.name.split(f".{filetype}")[0], filetype, customdatabasename)
LOG.info(f"Finished analyzing sequence {path} ...")

experimentName = expName + "_"
Expand Down
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