How to find values in string, manipulate and replace them - python

How to find values in string, add specific value to each of them and replace output with fixed string.
import re
def _replace(content):
#x = float(content.group(4))+20
#y = float(content.group(6))+20
return content.group(6)
print re.sub('<g(\s)transform="matrix\((.*)(\s)(.*)(\s)(.*)\)\"', _replace, '<g transform="matrix(0.412445 -0.0982513 0.0982513 0.412445 -5.77618 67.0025)">')


First off, I should repeat the usual warning about not parsing XML with regexes. It's a bad idea, and it will never work for all cases. If you're actually trying to parse the full xml document, use an XML parser.
That having been said, I'm guilty of doing quick and dirty stuff like this all the time. If you really just need a one-off solution, a simple regex can often get the job done. Just be aware that it will come back to haunt you as soon as you run into something more complex!
Next, I confess to not being much of a regex wiz, but here's how I'd modify your code snippet:
import re
def _replace(content):
values = [float(val) for val in content.group(2).split()]
values[3] += 20
values[5] += 100
values = ['{0}'.format(val) for val in values]
return content.group(1) + ' '.join(values) + content.group(3)
test_string = '<g transform="matrix(0.412445 -0.0982513 0.0982513 0.412445 -5.77618 67.0025)">'
pattern = r'(transform=\"matrix\()(.*?)(\))'
print test_string
print re.sub(pattern, _replace, test_string)

Related

Complex string filtering with python

I have a long string that is a phylogenetic tree and I want to do a very specific filtering.
(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;
Basically every x#y is a species#gene_id information. What I am trying to do is trimming this down so that I will only have x instead of x#y.
(Esy, Aar,(Spa,Cpl))...
I tried splitting the string first but the problem is string has different 'split points' for what I want to achieve i.e. some parts x#y is ending with a , and others with a ). I searched for a solution and saw regular expression operations, but I am new to Python and I couldn't be sure if that is what I should be focusing on. I also thought about strip() but it seems like I need to specify the characters to be stripped for this.
Main problem is there is no 'pattern' for me to tell Python to follow. Only thing is that all species ids are 3 letters and they are before an # character.
Is there a method that can do what I want? I will be really glad if you can help me out with my problem. Thanks in advance.

Give this a try:
import re:
pat = re.compile(r'(\w{3})#')
txt = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
pat.findall(t)
Result:
['Esy', 'Aar', 'Spa', 'Cpl', 'Bst', 'Aly', 'Ath', 'Chi', 'Cru', 'Hco', 'Hlo', 'Hla', 'Hse', 'Esa', 'Aal']
If you need the structure intact, we can try to remove the unnecessary parts instead:
pat = re.compile(r'(#|:)[^/),]*')
pat.sub('',t).replace(',', ', ')
Result:
'(Esy, Aar, ((Spa, Cpl), (((Bst, ((Aly, Ath), (Chi, Cru))), (((Hco, Hlo), Hla), Hse)), (Esa, Aal))))'
Regex demo

How about this kind of function:
def parse_string(string):
new_string = ''
skip = False
for char in string:
if char == '#':
skip = True
if char == ',':
skip = False
if not skip or char in ['(', ')']:
new_string += char
return new_string
Calling it on your string:
string = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
parse_string(string)
> '(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hse)),(Esa,Aal))))'

you can use regex:
import re
s = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
p = "...?(?=#)|\(|\)"
result = re.findall(p, s)
and you have your result as a list, so you can make it string or do anything with it
for explaining what is happening :
p is regular expression pattern
so in this pattern:
. means matching any word
...?(?=#) means match any word until I get to a word ? wich ? is #, so this whole pattern means that you get any three words before #
| is or statement, I used it here to find another pattern
and the rest of them is to find ) and (

Try this regex if you need the brackets in the output:
import re
regex = r"#[A-Za-z0-9_\.:]+|[0-9:\.;e-]+"
phylogenetic_tree = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
print(re.sub(regex,"",phylogenetic_tree))
Output:
(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hs)),(Esa,Aal))))

Because you are trying to parse a phylogenetic tree, I highly suggest to let BioPython do the heavy lifting for you.
You can easily parse and display a phylogenetic with Bio.Phylo. Then it is just iterating over all tree elements and splitting the names at the 'at'-sign.
Because Phylo expects the input to be in a file, we create an in-memory file-like object with io.StringIO. Getting the complete tree is then as easy as
Phylo.read(io.StringIO(s), 'newick')
In order to check if the parsed tree looks sane, I print it once with print(tree).
Now we want to change all node names that contain a '#'. With tree.find_elements we get access to all nodes. Some nodes don't have a name and some might not contain a '#'. So to be extra careful, we first check if n.name and '#' in n.name. Only then do we split each node's name at the '#' and take just the first part (index 0) of it:
n.name = n.name.split('#')[0]
In order to recreate the initial string representation, we use Phylo.write:
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Again, write wants to get a file argument - if we just want to get a string, we can use a StringIO object again.
Full code:
import io
from Bio import Phylo
if __name__ == '__main__':
s = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
tree = Phylo.read(io.StringIO(s), 'newick')
print(' before '.center(20, '='))
print(tree)
for n in tree.find_elements():
if n.name and '#' in n.name:
n.name = n.name.split('#')[0]
print(' result '.center(20, '='))
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Output:
====== before ======
Tree(rooted=False, weight=1.0)
Clade(branch_length=0.0129090235079)
Clade(branch_length=0.0726396855636, name='Esy#ESY15_g64743_DN3_SP7_c0')
Clade(branch_length=0.137507902808, name='Aar#AA_maker7399_1')
Clade(branch_length=0.0129090235079)
Clade(branch_length=9.05326020871e-05)
Clade(branch_length=0.0318934795022, name='Spa#Tp2g18720')
Clade(branch_length=0.0273465005242, name='Cpl#CP2_g48793_DN3_SP8_c')
Clade(branch_length=0.00328120860999)
Clade(branch_length=0.00859075940423)
Clade(branch_length=0.0340484449097)
Clade(branch_length=0.0332592496158, name='Bst#Bostr_13083s0053_1')
Clade(branch_length=0.0150356382287)
Clade(branch_length=0.0205924636564)
Clade(branch_length=0.0328569260951, name='Aly#AL8G21130_t1')
Clade(branch_length=0.0391706378372, name='Ath#AT5G48370_1')
Clade(branch_length=0.00998579652059)
Clade(branch_length=0.0954469923893, name='Chi#CARHR183840_1')
Clade(branch_length=0.0570981548016, name='Cru#Carubv10026342m')
Clade(branch_length=0.0372829371381)
Clade(branch_length=0.0206478928557)
Clade(branch_length=0.0144626717872)
Clade(branch_length=0.00823215335663, name='Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100')
Clade(branch_length=0.0085462978729, name='Hlo#DN13684_c0_g1_i1_p1')
Clade(branch_length=0.0225079453622, name='Hla#DN22821_c0_g1_i1_p1')
Clade(branch_length=0.048590776459, name='Hse#DN23412_c0_g1_i3_p1')
Clade(branch_length=1.00000050003e-06)
Clade(branch_length=0.0378509854703, name='Esa#Thhalv10004228m')
Clade(branch_length=0.0712272454125, name='Aal#Aa_G102140_t1')
==== result =====
(Esy:0.07264,Aar:0.13751,((Spa:0.03189,Cpl:0.02735):0.00009,(((Bst:0.03326,((Aly:0.03286,Ath:0.03917):0.02059,(Chi:0.09545,Cru:0.05710):0.00999):0.01504):0.03405,(((Hco:0.00823,Hlo:0.00855):0.01446,Hla:0.02251):0.02065,Hse:0.04859):0.03728):0.00859,(Esa:0.03785,Aal:0.07123):0.00000):0.00328):0.01291):0.01291;
The default format of Phylo uses less digits than in your original tree. In order to keep the numbers unchanged, just override the branch length format string with a '%s':
Phylo.write(tree, out, "newick", format_branch_length="%s")

Parsing code can be hard to follow. Tatsu lets you write readable parsing code by combining grammars and python:
text = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
import sys
import tatsu
grammar = """
start = things ';'
;
things = thing [ ',' things ]
;
thing = x '#' y ':' number
| '(' things ')' ':' number
;
x = /\w+/
;
y = /\w+/
;
number = /[+-]?\d+\.?\d*(e?[+-]?\d*)/
;
"""
class Semantics:
def x(self, ast):
# the method name matches the rule name
print('X =', ast)
parser = tatsu.compile(grammar, semantics=Semantics())
parser.parse(text)

Python - Extract text from string

What are the most efficient ways to extract text from a string? Are there some available functions or regex expressions, or some other way?
For example, my string is below and I want to extract the IDs as well
as the ScreenNames, separately.
[User(ID=1234567890, ScreenName=RandomNameHere), User(ID=233323490, ScreenName=AnotherRandomName), User(ID=4459284, ScreenName=YetAnotherName)]
Thank you!
Edit: These are the text strings that I want to pull. I want them to be in a list.
Target_IDs = 1234567890, 233323490, 4459284
Target_ScreenNames = RandomNameHere, AnotherRandomName, YetAnotherName

import re
str = '[User(ID=1234567890, ScreenName=RandomNameHere), User(ID=233323490, ScreenName=AnotherRandomName), User(ID=4459284, ScreenName=YetAnotherName)]'
print 'Target IDs = ' + ','.join( re.findall(r'ID=(\d+)', str) )
print 'Target ScreenNames = ' + ','.join( re.findall(r' ScreenName=(\w+)', str) )
Output :
Target IDs = 1234567890,233323490,4459284
Target ScreenNames = RandomNameHere,AnotherRandomName,YetAnotherName

It depends. Assuming that all your text comes in the form of
TagName = TagValue1, TagValue2, ...
You need just two calls to split.
tag, value_string = string.split('=')
values = value_string.split(',')
Remove the excess space (probably a couple of rstrip()/lstrip() calls will suffice) and you are done. Or you can take regex. They are slightly more powerful, but in this case I think it's a matter of personal taste.
If you want more complex syntax with nonterminals, terminals and all that, you'll need lex/yacc, which will require some background in parsers. A rather interesting thing to play with, but not something you'll want to use for storing program options and such.

The regex I'd use would be:
(?:ID=|ScreenName=)+(\d+|[\w\d]+)
However, this assumes that ID is only digits (\d) and usernames are only letters or numbers ([\w\d]).
This regex (when combined with re.findall) would return a list of matches that could be iterated through and sorted in some fashion like so:
import re
s = "[User(ID=1234567890, ScreenName=RandomNameHere), User(ID=233323490, ScreenName=AnotherRandomName), User(ID=4459284, ScreenName=YetAnotherName)]"
pattern = re.compile(r'(?:ID=|ScreenName=)+(\d+|[\w\d]+)');
ids = []
names = []
for p in re.findall(pattern, s):
if p.isnumeric():
ids.append(p)
else:
names.append(p)
print(ids, names)

How to split a string and keeping the pattern

This is how the string splitting works for me right now:
output = string.encode('UTF8').split('}/n}')[0]
output += '}\n}'
But I am wondering if there is a more pythonic way to do it.
The goal is to get everything before this '}/n}' including '}/n}'.

This might be a good use of str.partition.
string = '012za}/n}ddfsdfk'
parts = string.partition('}/n}')
# ('012za', '}/n}', 'ddfsdfk')
''.join(parts[:-1])
# 012za}/n}
Or, you can find it explicitly with str.index.
repl = '}/n}'
string[:string.index(repl) + len(repl)]
# 012za}/n}
This is probably better than using str.find since an exception will be raised if the substring isn't found, rather than producing nonsensical results.
It seems like anything "more elegant" would require regular expressions.
import re
re.search('(.*?}/n})', string).group(0)
# 012za}/n}

It can be done with with re.split() -- the key is putting parens around the split pattern to preserve what you split on:
import re
output = "".join(re.split(r'(}/n})', string.encode('UTF8'))[:2])
However, I doubt that this is either the most efficient nor most Pythonic way to achieve what you want. I.e. I don't think this is naturally a split sort of problem. For example:
tag = '}/n}'
encoded = string.encode('UTF8')
output = encoded[:encoded.index(tag)] + tag
or if you insist on a one-liner:
output = (lambda string, tag: string[:string.index(tag)] + tag)(string.encode('UTF8'), '}/n}')
or returning to regex:
output = re.match(r".*}/n}", string.encode('UTF8')).group(0)

>>> string_to_split = 'first item{\n{second item'
>>> sep = '{\n{'
>>> output = [item + sep for item in string_to_split.split(sep)]
NOTE: output = ['first item{\n{', 'second item{\n{']
then you can use the result:
for item_with_delimiter in output:
...
It might be useful to look up os.linesep if you're not sure what the line ending will be. os.linesep is whatever the line ending is under your current OS, so '\r\n' under Windows or '\n' under Linux or Mac. It depends where input data is from, and how flexible your code needs to be across environments.

Adapted from Slice a string after a certain phrase?, you can combine find and slice to get the first part of the string and retain }/n}.
str = "012za}/n}ddfsdfk"
str[:str.find("}/n}")+4]
Will result in 012za}/n}

Python: Dividing a string into substrings

I have a bunch of mathematical expressions stored as strings. Here's a short one:
stringy = "((2+2)-(3+5)-6)"
I want to break this string up into a list that contains ONLY the information in each "sub-parenthetical phrase" (I'm sure there's a better way to phrase that.) So my yield would be:
['2+2','3+5']
I have a couple of ideas about how to do this, but I keep running into a "okay, now what" issue.
For example:
for x in stringy:
substring = stringy[stringy.find('('+1 : stringy.find(')')+1]
stringlist.append(substring)
Works just peachy to return 2+2, but that's about as far as it goes, and I am completely blanking on how to move through the remainder...

One way using regex:
import re
stringy = "((2+2)-(3+5)-6)"
for exp in re.findall("\(([\s\d+*/-]+)\)", stringy):
print exp
Output
2+2
3+5

You could use regular expressions like the following:
import re
x = "((2+2)-(3+5)-6)"
re.findall(r"(?<=\()[0-9+/*-]+(?=\))", x)
Result:
['2+2', '3+5']

Replacing variable length items in a list using regex in python

I am trying to replace variable length items in a list using regex. For example this item "HD479659" should be replaced by "HD0000000479659". I need just to insert 7 0s in between.I have made the following program but every time I run it I got the following error:"TypeError: object of type '_sre.SRE_Pattern' has no len()". Can you please help me how to solve this error.
thank you very much
Here is the program
import xlrd
import re
import string
wb = xlrd.open_workbook("3_1.xls")
sh = wb.sheet_by_index(0)
outfile=open('out.txt','w')
s_pat=r"HD[1-9]{1}[0-9]{5}"
s_pat1=r"HD[0]{7}[0-9]{6}"
pat = re.compile(s_pat)
pat1 = re.compile(s_pat1)
for rownum1 in range(sh.nrows):
str1= str(sh.row_values(rownum1))
m1=[]
m1 = pat.findall(str1)
m1=list(set(m1))
for a in m1:
a=re.sub(pat,pat1,a)
print >> outfile, m1

I think your solution is quite to complicated. This one should do the job and is much simpler:
import re
def repl(match):
return match.group(1) + ("0"*7) + match.group(2)
print re.sub(r"(HD)([1-9]{1}[0-9]{5})", repl, "HD479659")
See also: http://docs.python.org/library/re.html#re.sub
Update:
To transform a list of values, you have to iterate over all values. You don't have to search the matching values first:
import re
values_to_transform = [
'HD479659',
'HD477899',
'HD423455',
'does not match',
'but does not matter'
]
def repl(match):
return match.group(1) + ("0"*7) + match.group(2)
for value in values_to_transform:
print re.sub(r"(HD)([1-9]{1}[0-9]{5})", repl, value)
The result is:
HD0000000479659
HD0000000477899
HD0000000423455
does not match
but does not matter

What you need to do is extract the variable length portion of the ID explicitly, then pad with 0's based on the desired length - matched length.
If I understand the pattern correctly you want to use the regex
r"HD(?P<zeroes>0*)(?P<num>\d+)"
At that point you can do
results = re.search(...bla...).groupdict()
Which returns the dict {'zeroes': '', 'num':'479659'} in this case. From there you can pad as necessary.
It's 5am at the moment or I'd have a better solution for you, but I hope this helps.

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