My method puts reads into a dictionary and will output reads once a pair is found. Usually pairs are near each other so the dictionary shouldn't get that big.

from collections import defaultdict
import pysam


def read_pair_generator(bam, region_string=None):
    """
    Generate read pairs in a BAM file or within a region string.
    Reads are added to read_dict until a pair is found.
    """
    read_dict = defaultdict(lambda: [None, None])
    for read in bam.fetch(region=region_string):
        if not read.is_proper_pair or read.is_secondary or read.is_supplementary:
            continue
        qname = read.query_name
        if qname not in read_dict:
            if read.is_read1:
                read_dict[qname][0] = read
            else:
                read_dict[qname][1] = read
        else:
            if read.is_read1:
                yield read, read_dict[qname][1]
            else:
                yield read_dict[qname][0], read
            del read_dict[qname]

bam = pysam.AlignmentFile(filename, 'rb')
for read1, read2 in read_pair_generator(bam):
    # do stuff

I agree that it should be a bit simpler, given that paired end bam files are so common.

I used the following solution, which is only applicable if the .bam file has been previously sorted by read names samtools sort -n!

samfile = AlignmentFile(filename, 'rb')  # BAM file reader.
# Iterate through reads.
read1 = None
read2 = None

for read in samfile:

    if not read.is_paired or read.mate_is_unmapped or read.is_duplicate:
          continue

    if read.is_read2:
        read2 = read
    else:
        read1 = read
        read2 = None
        continue

     if not read1 is None and not read2 is None and read1.query_name == readf2.query_name:
          print("found a pair!")
          ## do your stuff

This is based on @gizone1's answer.

def read_pair_generator(bam, region_string=None):
"""
Generate read pairs in a BAM file or within a region string.
Reads are added to read_dict until a pair is found.
"""
read_dict = defaultdict(lambda: [None, None])
for align in bam.fetch(until_eof=True, region=region_string):
    if not align.is_paired:
        continue
    qname = align.query_name
    if qname not in read_dict:
        if align.is_read1:
            read_dict[qname][0] = [align]
        else:
            read_dict[qname][1] = [align]
    elif align not in read_dict[qname][0] and align not in read_dict[qname][1]:
        if align.is_read1:
            read_dict[qname][0].extend(align)
        else:
            read_dict[qname][1].extend(align)
    else:
        if align.is_read1:
            yield read_dict[qname][0], read_dict[qname][1]
        else:
            yield read_dict[qname][0], read_dict[qname][1]
        del read_dict[qname]

I change the name from "read" to "align" since each row is an alignment record instead of a read record. Instead of return one pysam.AlignmentSegment object, I returned a list of pysam.AlignmentSegment objects.

And you can call it like this: for read1_aligns, read2_aligns in read_pair_generator(ex_sam):

In this case, read1_aligns will be a python list including all the pysam.AlignmentSegment objects corresponding to this read1. Pls try this out and see if this works.