Commit f6409abf authored by Theo Serralta's avatar Theo Serralta

creating new program to isolate aligned sequences

parent c5c6351d
import pysam
samfile = pysam.AlignmentFile("/home/theo/dev/git/cnvCallerGPU/3544.bam", "rb")
align = pysam.AlignmentFile("align.bam", "wb", header = samfile.header)
for read in samfile:
if read.is_mapped:
align.write(read)
samfile.close()
align.close()
total_sequences_alignées = 0
align_file = pysam.AlignmentFile("/home/theo/dev/git/cnvCallerGPU/align.bam", "rb")
reference = align_file.references
reference_dict = {reference: i for i, reference in enumerate(reference)}
print("Index\tChromosome")
for chromosome, index in reference_dict.items():
print(f"{index}\t{chromosome}")
for read in align_file:
print(read)
chr_name = reference[read.reference_id]
position = read.reference_start + 1
print(f"Chromosome: {chr_name}")
print(f"Position: {position}")
print(f"Non aligné: {read.is_unmapped}")
total_sequences_alignées += 1
print(f"Total de sequences alignées : {total_sequences_alignées}")
align_file.close()
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