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53 lines
2.5 KiB
Python
53 lines
2.5 KiB
Python
'''
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#Author, date: ?
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#Uploaded: updated by Adri Grow, Aug 2025
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#Intent: map a group of trimmed reads to a reference
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#Dependencies: Python3, hisat2, samtools, sambamba
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#EDIT LINES: 18 & 33
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#Inputs: Folder named 'TrimmedReads' containing all the trimmed reads
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#Outputs: Folders with the names of the LKHs containing the sam/bam files
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#Example: python ReadMapping.py
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'''
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import os
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from Bio import SeqIO
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#this first command builds your reference with HISAT
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#If you've already done this, DON'T run this command! Instead, comment it out (use a # in front of it)
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#It will output several files. Don't worry about them, HISAT will know what to do
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os.system("hisat2-build Foram_reference.fasta Foram_Index") #change to your reference.fasta and (optionally) rename the index
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folder = os.listdir("TrimmedReads") #Insert the name of the folder which has your trimmed reads inside the quotes
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folder.sort() #This sorts the folder so that all the LKHs are in order
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for x in folder:
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if "LKH" in x and "FPE" in x: #assigning a variable to forward reads. Make sure you have both forward and reverse reads for each cell!
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FPE = x
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sample_id = FPE.split("_FPE")[0]
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if "LKH" in x and "RPE" in x: #assigning a variable to reverse reads
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RPE = x
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if FPE.split("_FPE")[0] == RPE.split("_RPE")[0]: # Match sample IDs dynamically
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#The next few lines are several HISAT commands that will create new files
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#EDIT the name of the index and the name of the trimmed reads folder in the first command below (line 33) if necessary
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os.system("hisat2 -x Foram_Index -1 TrimmedReads/" +FPE+ " -2 TrimmedReads/" +RPE+ " -S sample.sam")
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os.system("samtools view -bS sample.sam > sample.bam")
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os.system("samtools fixmate -O bam sample.bam fixmate_sample.bam")
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os.system("samtools sort -O bam -o sorted_sample.bam fixmate_sample.bam")
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os.system("sambamba markdup -r sorted_sample.bam sorted_sample.dedup.bam")
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os.system("samtools view -h -b -q 40 sorted_sample.dedup.bam > sorted_sample.q40.bam")
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os.system("samtools view -h -b -q 20 sorted_sample.dedup.bam > sorted_sample.q20.bam")
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os.system("samtools view -h -F 4 -b sorted_sample.dedup.bam > defaultparameters_sample.bam")
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if not os.path.isdir(sample_id):
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os.mkdir(sample_id) #making folders with the names of the LKHs
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for file in os.listdir('.'): #These lines move the sam/bam files that Hisat creates into the new LKH folders.
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if(file.endswith('.sam') or file.endswith('.bam')):
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os.rename(file, f"{sample_id}/{file}")
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print("~~~~~~~~~~~:>~") #When the snake appears in terminal, your script has finished running!
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