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"""
Print out which fields of FAST5 files are static or variable for the same experiment.
In a nice hierarchical format.
Given h5dump output of any number of FAST5 files.
Show the constant values with -c flag.
Usage: python3 $0 [h5dump_FAST5_output...] [-c]
"""
from sys import argv
import re
# Class for a hdf5 group
class Group:
def __init__(self, name, prev_group=None):
self.name = name
self.prev_group = prev_group
self.attrs = []
def add_attr(self, attr):
self.attrs.append(attr)
def print_hier(self, prefix=''):
for attr in self.attrs:
if isinstance(attr, Group):
print(f"{prefix}{attr.name}:")
attr.print_hier(prefix + ' ')
else:
print(f"{prefix}{attr}")
def print_hier_if_in(self, arr, show_val=False, prefix=''):
is_dict = type(arr) is dict
for attr in self.attrs:
if isinstance(attr, Group):
print(f"{prefix}{attr.name}:")
attr.print_hier_if_in(arr, show_val, prefix + ' ')
else:
if attr in arr:
if show_val and is_dict:
print(f"{prefix}{attr}: {arr[attr]}")
else:
print(f"{prefix}{attr}")
def __str__(self):
return str(self.attrs)
def __repr__(self):
return str(self.attrs)
args = argv[1:]
if "-c" in args:
args.remove("-c")
show_const = True
else:
show_const = False
attrs = {}
root_group = Group("/")
var = []
const = {}
bracket_pos = 0
group_pos = []
struct_made = False
curr_group = root_group
first_read = True
for fname in args:
f = open(fname)
for line in f:
line = line.split()
# Add group to structure
if not struct_made and line[0] == "GROUP" and line[1] != '"/"':
# Don't repeat the structure for the 'multi' type
if re.match('"read_.+"', line[1]):
if first_read:
first_read = False
else:
struct_made = True
if not struct_made:
group_pos.append(bracket_pos)
new_group = Group(line[1][1:-1])
curr_group.add_attr(new_group)
new_group.prev_group = curr_group
curr_group = new_group
if line[0] == "ATTRIBUTE" or line[0] == "DATASET":
curr_attr = line[1][1:-1]
# Create empty set for attribute if not already there
if curr_attr not in attrs:
attrs[curr_attr] = set()
# Add attribute to structure
if not struct_made:
curr_group.add_attr(curr_attr)
# Data follows a (0)
elif line[0] == "(0):":
# Store attribute's data
data = " ".join(line[1:])
attrs[curr_attr].add(data)
# Closing marker
if not struct_made and "{" in line:
bracket_pos += 1
if not struct_made and "}" in line:
bracket_pos -= 1
# Check if group is finished
if len(group_pos) != 0 and bracket_pos == group_pos[-1]:
group_pos = group_pos[:-1]
curr_group = curr_group.prev_group
if not struct_made:
struct_made = True
# Decide what's constant and variable
for prop in attrs:
if len(attrs[prop]) == 1:
const[prop] = list(attrs[prop])[0]
else:
var.append(prop)
# Print properties which are constant and variable
print("CONSTANT")
root_group.print_hier_if_in(const, show_const)
print("\nVARIABLE")
root_group.print_hier_if_in(var, show_const)
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