How to annotate bam/sam file with gtf file through pysam

Question

[anasjamshed]

Is it possible to annotate the bam/sam file by using pysam?

I am using htseq and my code is:

#Importing Libraries
import HTSeq
import itertools
import pysam

#Read Bam file
bamfile = pysam.AlignmentFile("sample_sort.bam")
#Print only importnat cols
for read in bamfile:
    reads = "id",read.qname,"flag",read.flag,"chr no.",read.rname, "position",read.pos
    print(reads)

#Total reads counts in bam file
total = pysam.AlignmentFile("sample_sort.bam").count()
print(total)
#View Features
print(feature.iv)
print(feature.source)
print(feature.type)
print(feature.score)
#View sorted
sorted(feature.attr.items())    

#Declare Exons
exons = HTSeq.GenomicArrayOfSets("auto", stranded=False)

#Fetch Exons from gtf
for feature in gtf_file:
    if feature.type == "exon":
        exons[feature.iv] += feature.name
        iv = HTSeq.GenomicInterval("III", 366085,366700, ".")

 [(st[0], sorted(st[1])) for st in exons[iv].steps()] 


iset = None
for iv2, step_set in exons[iv].steps():
    if iset is None:
        iset = step_set.copy()
    else:
        iset.intersection_update(step_set)
    print(iset)

#Store exons in counts dictionary
counts = {}
for feature in gtf_file:
    if feature.type == "exon":
        counts[feature.name] = 0

#Read Samfile 
sam_file = HTSeq.SAM_Reader("samplesort.sam")

#do alignment
for alnmt in sam_file:
    if alnmt.aligned:
        iset = None
        for iv2, step_set in exons[alnmt.iv].steps():
            if iset is None:
                iset = step_set.copy()
            else:
                iset.intersection_update(step_set)
        if len(iset) == 1:
            counts[list(iset)[0]] += 1

#Print counts with gene names
for name in sorted(counts.keys()):
    print(name, counts[name])

The output is showing 0 in all counts:

I want my result like this:

Can anyone help me, please?

[Ram]

This post is a duplicate of your previous post: Parsing bam file and compare it from gtf file through pysam

I am marking it off-topic - it might be deleted soon.