I'm trying to understand some data traffic.
Here are some short packages I captured (Hex string):
Data Checksum
------ ---------
87 0087
7639 7639
7739 7739
DA423030 A25A
DA423031 A25B
DA423130 A35A
DA424030 D25A
DA423040 A22A
DA423032 A258
Can anyone identify how the checksum is made up?
(Note: Adding zero-bytes at the beginning of the data does not change the checksum, but adding them at the end does change it.)
The solution is:
Take the whole string up to the last 2 bytes, perform on it CRC-16/XMODEM.
Perform on the result XOR with the last 2 bytes left.
For example:
Data Checksum
------ ---------
DA423030 A25A
DA42 >> CRC-16/XMODEM >> 926A
926A >> XOR With 3030 >> A25A
I have some basic familiarity with python and have been extracting coding sequences from genbank records. However, I'm unsure how to handle records where the coding sequence has been modified (e.g. owing to correcting internal stop codons). An example of such a sequence is this genbank record (or accession: XM_021385495.1 if the link does not work).
In this example, I can translate the two coding sequences that I can access, but both have internal stop codons - and according to the notes also indels! This is the way I have accessed the CDS:
1 - gb_record.seq
2 - cds.location.extract(gb_record) for where feature == "CDS"
However, I need the sequence that has been corrected. As far as I can tell, I think I need to use the "transl_except" tags in the CDS feature but I am at a loss how to do this.
I wonder if anybody might be able to provide an example or some insight of how to do this?
Thanks
Jo
I've got some demo code written in python3 that should help explain this GenBank record.
import re
aa_convert_codon_di = {
'A':['[GRSK][CYSM].'],
'B':['[ARWM][ARWM][CTYWKSM]', '[GRSK][ARWM][TCYWKSM]'],
'C':['[TYWK][GRSK][TCYWKSM]'],
'D':['[GRSK][ARWM][TCYWKSM]'],
'E':['[GRSK][ARWM][AGRSKWM]'],
'F':['[TYWK][TYWK][CTYWKSM]'],
'G':['[GRSK][GRSK].'],
'H':['[CYSM][ARWM][TCYWKSM]'],
'I':['[ARWM][TYWK][^G]'],
'J':['[ARWM][TYWK][^G]', '[CYSM][TYWK].', '[TYWK][TYWK][AGRSKWM]'],
'K':['[ARWM][ARWM][AGRSKWM]'],
'L':['[CYSM][TYWK].', '[TYWK][TYWK][AGRSKWM]'],
'M':['[ARWM][TYWK][GRSK]'],
'N':['[ARWM][ARWM][CTYWKSM]'],
'O':['[TYWK][ARWM][GRSK]'],
'P':['[CYSM][CYSM].'],
'Q':['[CYSM][ARWM][AGRSKWM]'],
'R':['[CYSM][GRSK].', '[ARWM][GRSK][GARSKWM]'],
'S':['[TYWK][CYSM].', '[ARWM][GRSK][CTYWKSM]'],
'T':['[ARWM][CYSM].'],
'U':['[TYWK][GRSK][ARWM]'],
'V':['[GRSK][TYWK].'],
'W':['[TYWK][GRSK][GRSK]'],
'X':['...'],
'Y':['[TYWK][ARWM][CTYWKSM]'],
'Z':['[CYSM][ARWM][AGRSKWM]','[GRSK][ARWM][AGRSKWM]'],
'_':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]'],
'*':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]'],
'x':['[TYWK][ARWM][AGRSKWM]', '[TYWK][GRSK][ARWM]']}
dna_convert_aa_di = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'*', 'TAG':'*',
'TGC':'C', 'TGT':'C', 'TGA':'*', 'TGG':'W'}
dna_str = "ATGACCGAGGTGCAAGACCTTGCACTTGGATTTGTTGAACCTCATGAGGTTCCCCTGGGCCCCTGGACATCGCCTTTTTCCAGCGTTCCACCAGAGACTTCACCCAACTGCTGTGACTTTTCAAACATCATTGAGAGCGGCTTGATACAGTTAGGCCACTCTCGCAGCTGTGAAGTTGTGAAGGCAAACTCCAGCGACCCATTCCTTCTTCCTTCAGAAAAGCAACTCGAGGAGCAGCGGGAGGAAACCCAGCTCTATCCTGCAGCGAGCGGGGCTGCGCAAGAGGCAGGTGCTGCTCTCACGGCCCGAAGGCAGCTCCGAGCTGCCGGGTGCGGTCACGTCAGCGGCCGAGCTGCCCGGCGGGGTGTGCATAAGAGCGAGCTATATGTGCTGCGTGTCATCACGGAGCCTTTCAAGTCCCTCCCTCCTTCTCCACTGCTGGGGCTGCAGTGGGCACCGGGCAGGAGGAGCGGCCGCAGCCCCGCGGGGGTGGGACGAGTCTCTGGGGGCTGCGCCACTTGGAAGATTTGCATTGGGTACATTGATAGCATTGTGATTGATGGCCTATTTAATACCATAATGTGTTCTTTAGATTTCTTTTTGGAGAACTCAGAAGAAAATTTGAAGCCAGCTCCACTTTTTCCAGCACAAATGACCCTTACTGGCACAGAAATTCATTTTAAACTTTCTCTAGATAAAGAGGCTGATGATGGCTTTTATGACCTTATGGATGAACTACTGGGTGATATTTTCCGAATGTCTGCCCAAGTGAAGAGACTAGAAGCCCACCTGGAATCAGAACATTAGGAGGACTATATGAACAGTGTGTTTGATCTGTCTGAACTCAGGCAGGAGAGTATGGAGAGAGTAATAAACGTCACCAACAAGGCCTTGAAGTACAGAAGATCTCATGATAGCTATGCTTATCTCTGACTAGAGGATCAGCTTGAGTTTATGAGGCAATTTCTTCCTTGTGCTCGTGGTTTAATGTCCACACAGATATCTCTTACTGGCATCCCACTACTAAACTGTGTAAAAAGCAGGCAAGAAAGAAACTAGTTTAAATAACTTCCTATTTATGAAAATCTCTGTGTTCAGATGAGTAAGTTTGAAGACCCAAGAATTTTTGAAAGCTGGTTTAAGGTGATTATGAAGCCTTTCAAAATGACACTTCTAAACATTACTAAGAAGTGGAGCTGGATGTTTAAGTAGTACACTATAGAAATAATAAGATTGAGTCTGAATGACTTCAAAGACTTTATAAAAGTGACAGATGCTGGACTTCAAAGAGGGAGGCATTATTGTGCACTGGCAGAAATCACCGGTCACCTCTTGGCTGTGAAAGAGAGGCAGACAGCTGCTGGTGAATCCTTTGAACCTTTAAAAGAANTTGTTGCATTGTTGGAAAGCTACAGACAGAAGATGCCAGATCAAGTTTGCATCCAGTGTCAAATCAGTTGTATCCTGGGAGCCTTTAAGGGTTATGTACTTCTGGTTGGAGTAGGTGGTAGTGATAAATGAAGCTTGTCAAGGCTGGCAGCATGCATCTCTTCCCTGGAGGTCTTTTAAATCATATGGAAGAAAGACCATGAGAGCAAGAACCTGAAGGTAGATGTTGCCAGTTTGTGCATCAAGACTGGTGCCAAGAACATGCCCACAGTGTTTTTGCTGACAGATGCCCAGGTTCCAGATGAACGCTTTCTTGTGCTGATTAATGACTTGTTGGCATCAAGAGATCTTCCTGATCTGTTCAGTGGTGAAGATGAGGAGGGCAAAGTTGCAGGAGTCAGAAAAGAAGTCNNCCTGGGCTTGATGGACACCACAGAAAGCTGCTGGAGGTGGTTCTTTGGTAGAGCGCAGCAGCTGTTAAAAGTGTATGGTGAAGTAGAGTCGAAATGTTGTGCACTGGTCCAGGCAAATACAAAATTAGCAACAGCTAAAGAGAATCTAGAAACAATCTTGAAAAAGCTTATTTCTGAAAATGTGCATTGGAGCCAATCTGTTGAAAACCTCAAAGCATAAAAGAAAACTGTACTCAAGGATGTTACATCAGCAGCAGCGTTTGCATCTTTCTTTGGAGCCTTCACAAAACCATATAGTCAAGAACAGATGGAACATTTCTGGATTCTTTCTCTAAAGTCACAGGAGTGTCCTGTTCCTGTGATAGAGGGGCCAGACTCTGCCATCCTGATGAATGATGCTCCAAGAGCAGCACAGAGTAACAAGAGTCTGCTTGCTGATAGGGTGTCAGCAGAAAATGCCACTGCTCTGACACACTGTGAGCAGGGCCCTCTGATGATAGATCCCCAGAAACAGGGAATTGAATGGACACAGAATAAATACAGAACTGACTTTAAAGTCATGCATCTAGGAGAGAATGGTTATGTGTGTACTATTGATACAGCTTTGGCTTGTGGAGAGATTATACTAATTGAAAACATGGCTGAATCTATCGATCTCTTACTTGATCCCCTAACTGGAAGACATACAGGTAAAAGGGGAAGGAATACTTGCGCAATCAGAATTTCTTGAAGACAAAAAAAAAAAAAGTGTGAATTCTACAGGAATTTCCATCTCATCCTTCACACTAAGCTGGCTAACCCTCCCTGCAAGCCAGAGCTTNAGGCTCAGACCACTCTCATTATTTTCACAGATACCAGGGGCAGGCTGGAAGAACAGCTGTTGGCTGAGGTGGTGAGTGCTGAAAGGCCTGACTTGGAAAACCATACGTCAGCACTGGCGAAACAGAAGAGTGTCTCTGAAATCAAGCCCAAGCAGCTTGAGGACAACATGCTGCTCAGTCTGTCAGCTGCCCAGAGCACTTTTGTAGGTGACAGTGAACTTGAAGAGAAATTCAAGTCAACTGCAGGAGAAATGATTGTCCGCCCACATGTTCACAGCTTCTTATTTTGGCAAAAAGCTTCCACTGTAGACTCTGGAAGATTTCATATCTCTTTAGGACAAGGGCAGGAGATGGTTGTGGAGNGACAACTTGAGAAGGCTGCCAAGCCTGGCCACTGGCTTCTTCTCCAAAATATTAATGTGGTAGCCAAGTGGCTAGGAACCTTGGAAAAACTCCTCGAGCAATAGAGTGAAGAAAGTCACTGGTATTTCCGTGTCTTCACTAGTGCTGAACCAGCTCCAGCCCCAGAAGAGCACATCATTCTTCAAGGAGTACTTGAAAACTGAATTAAAATTACCAGACTATCAATAACACTGCCAGTTGTTAAGTGGATAAATGTATTCCTTTTTTTCCTTTGGCAGGATACCCTTGAACTGTGTGGCAAAGAACAGGAATTTAAGAGCATTCTTTTCTCCCTTCGTTATTTTCACACCCGTGTTGCCAGCAGACTCATTTGGCCTTCCAGGCTGCAATTAAGATACCCATACAATACTAGAGATCTCACTGTTTGCATCAGTGTGCCCTGCAACTATTTAGACACTTACACAGAGGTCAGACGCAGTGGTCAGAAAAACAAGTCTATAAAATCAGCTGATTCCAACCCTTAG"
aa_str = "MTEVQDLALGFVEPHEVPLGPWTSPFSSVPPETSPNCCDFSNIIESGLIQLGHSRSCEVVKANSSDPFLLPSEKQLEEQREETQLYPAASGAAQEAGAALTARRQLRAAGCGHVSGRAARRGVHKSELYVLRVITEPFKSLPPSPLLGLQWAPGRRSGRSPAGVGRVSGGCATWKICIGYIDSIVIDGLFNTIMCSLDFFLENSEENLKPAPLFPAQMTLTGTEIHFKLSLDKEADDGFYDLMDELLGDIFRMSAQVKRLEAHLESEHXEDYMNSVFDLSELRQESMERVINVTNKALKYRRSHDSYAYLXLEDQLEFMRQFLPCARGLMSTQISLTGIPLLNCVKSRQERNXFKXLPIYENLCVQMSKFEDPRIFESWFKVIMKPFKMTLLNITKKWSWMFKXYTIEIIRLSLNDFKDFIKVTDAGLQRGRHYCALAEITGHLLAVKERQTAAGESFEPLKEXVALLESYRQKMPDQVCIQCQISCILGAFKGYVLLVGVGGSDKXSLSRLAACISSLEVFXIIWKKDHESKNLKVDVASLCIKTGAKNMPTVFLLTDAQVPDERFLVLINDLLASRDLPDLFSGEDEEGKVAGVRKEVXLGLMDTTESCWRWFFGRAQQLLKVYGEVESKCCALVQANTKLATAKENLETILKKLISENVHWSQSVENLKAXKKTVLKDVTSAAAFASFFGAFTKPYSQEQMEHFWILSLKSQECPVPVIEGPDSAILMNDAPRAAQSNKSLLADRVSAENATALTHCEQGPLMIDPQKQGIEWTQNKYRTDFKVMHLGENGYVCTIDTALACGEIILIENMAESIDLLLDPLTGRHTGKRGRNTCAIRISXRQKKKKCEFYRNFHLILHTKLANPPCKPELXAQTTLIIFTDTRGRLEEQLLAEVVSAERPDLENHTSALAKQKSVSEIKPKQLEDNMLLSLSAAQSTFVGDSELEEKFKSTAGEMIVRPHVHSFLFWQKASTVDSGRFHISLGQGQEMVVEXQLEKAAKPGHWLLLQNINVVAKWLGTLEKLLEQXSEESHWYFRVFTSAEPAPAPEEHIILQGVLENXIKITRLSITLPVVKWINVFLFFLWQDTLELCGKEQEFKSILFSLRYFHTRVASRLIWPSRLQLRYPYNTRDLTVCISVPCNYLDTYTEVRRSGQKNKSIKSADSN"
mod_dna_str = ""
mod_aa_str = aa_str[:]
start = 0
for index in range(start, len(dna_str), 3):
codon = dna_str[index:index+3]
if len(mod_aa_str) == 0:
break
if codon in dna_convert_aa_di and dna_convert_aa_di[codon] == mod_aa_str[0]:
mod_aa_str = mod_aa_str[1:]
else:
codon_match = "|".join(aa_convert_codon_di[mod_aa_str[0]])
if len(re.findall(codon_match, codon)) > 0:
print(index, codon_match, codon)
mod_aa_str = mod_aa_str[1:]
Code output:
804 ... TAG
930 ... TGA
1056 ... TAG
1065 ... TAA
1209 ... TAG
1389 ... NTT
1518 ... TGA
1566 ... TAA
1800 ... NNC
2019 ... TAA
2529 ... TGA
2622 ... NAG
2985 ... NGA
3087 ... TAG
3186 ... TGA
From the note section of the CDS, we have: inserted 5 bases in 4 codons; deleted 2 bases in 2 codons; substituted 11 bases at 11 genomic stop codons".
How does this relate to our output? The reading frame never changes, suggesting that the 2 deleted bases are absent from the given nucleotide sequence. Five unknown nucleotides (N) exist in 4 codons (unknown amino acid, X). The authors of the sequence have accounted for indels. Eleven premature stop codons are present, which are simply translated as unknown amino acids. The "transl_except" tags match the locations of the premature stop codons. The nucleotides at these sites have not been altered. The authors provide XP_021241170 as a possible corrected translation product, but it's still very bad.
I have been trying to produce a checksum based on a file header and am receiving conflicting results. In the slave devices manual, it states the following to produce the checksum:
"A simple eight-bit calculation is used for the header checksum. The steps required are as follows:
Calculate the sum of the header bytes in a single byte. Alternatively calculate
the sum and then AND the result with FFhex.
The checksum = FFhex - the sum from step 1."
Here, I have created the following code in Lua:
function header_checksum(string)
local sum = 0
for i = 1, #string do
sum = sum + string.byte(i)
end
local chksum = 255 - (sum & 255)
return chksum
end
If I send the following (4x byte) string down print(header_checksum("0181B81800")) I get the following result:
241 (string sent as you see it)
0 (each byte is changed to hex and then sent to function)
In the example given, it states that the byte should be AD, which is 173(dec) or \255.
Can someone please tell me what is wrong with what I am doing; either the code written, my approach, or both?
function header_checksum(header)
local sum = -1
for i = 1, #header do
sum = sum - header:byte(i)
end
return sum % 256
end
print(header_checksum(string.char(0x01,0x81,0xB8,0x18,0x00))) --> 173
I have a variable named A in SPSS database.
A
--
102102
23453212
142378
2367890654
2345
45
I want to split this variable by 2 lengths and create multiple variables as follows.
A_1 A_2 A_3 A_4 A_5
--- --- --- --- ---
10 21 02
23 45 32 12
14 23 78
23 67 89 06 54
23 45
45
Can anyone write SPSS macro to compute this operation?
Using STRING manipulations (after converting the NUMERIC field to STRING, if necessary), specifically SUBSTR you can extract out pairs of digits as you wish.
/* Simulate data */.
data list list / x (f8.0).
begin data.
102102
23453212
142378
2367890654
2345
45
end data.
dataset name dsSim.
If you have a known maximum value, in your example a value of 10 digits long then you'll need 5 variables to store the pairs of digits, which the follow does:
preserve.
set mxwarns 0 /* temporarily supress warning messages */ .
string #xstr (a10).
compute #xstr=ltrim(string(x,f18.0)).
compute A_1=number(substr(#xstr,1,2), f8.0).
compute A_2=number(substr(#xstr,3,2), f8.0).
compute A_3=number(substr(#xstr,5,2), f8.0).
compute A_4=number(substr(#xstr,7,2), f8.0).
compute A_5=number(substr(#xstr,9,2), f8.0).
exe.
restore.
However, you may prefer to code something like this more dynamically (using python) where the code itself would read the maximum value in the data and create as many variables as needed.
begin program.
import spssdata, math
spss.Submit("set mprint on.")
# get maximum value
spss.Submit("""
dataset declare dsAgg.
aggregate outfile=dsAgg /MaxX=max(x).
dataset activate dsAgg.
""")
maxvalue = spssdata.Spssdata().fetchone()[0]
ndigits=math.floor(math.log(maxvalue,10))+1
cmd="""
dataset close dsAgg.
dataset activate dsSim.
preserve.
set mxwarns 0.
string #xstr (a10).
compute #xstr=ltrim(string(x,f18.0)).
"""
for i in range(1,int(math.ceil(ndigits/2))+1):
j=(i-1)*2+1
cmd+="\ncompute B_%(i)s=number(substr(#xstr,%(j)s,2), f8.0)." % locals()
cmd+="\nexe.\nrestore."
spss.Submit(cmd)
spss.Submit("set mprint off.")
end program.
You would need to weigh up the pros on cons of each method to asses which suits you best, for how you anticipate your data to arrive and how you then go onto work with in later. I haven't attempted to wrap either of these up in a macro but that could just as easily be done.
I've just ran
$ sha1sum myfile
out of boredom.
myfile is an empty file which I created with
$ touch myfile
I was surprised that sha1sum actually returned a checksum. Aren't these checksums supposed to be computed from some non-empty content? Is the checksum for an empty file just a hardcoded "magic" constant?
There's nothing fundamentally different with an empty message from a message with say a byte of data. The algorithm is described here http://en.wikipedia.org/wiki/SHA-1#Examples_and_pseudocode and it's fine with zero data.
Eg.
Pre-processing:
append the bit '1' to the message append 0 ≤ k < 512 bits '0', so that the resulting message length (in bits) is
congruent to 448 (mod 512)