I send some samples for Sanger sequencing to a commercial facility. I'm able to read the files they send using the command
from Bio import SeqIO
from Bio import Seq
rec = SeqIO.read("isolation-round4/3dr23_Forward.ab1",'abi-trim').seq
But recently, due to a move, we had to send the samples elsewhere for sequencing. Now, if I try to run the same command on the output I get an error:
UnboundLocalError: local variable 'qual' referenced before assignment in
File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\AbiIO.py", line 462, in AbiIterator letter_annotations={"phred_quality": qual}
I would appreciate any help in dealing with this. Here are two files, one that works and one that does not, if you would like to have a look.
Thanks in advance for your help!
Bug should have already been fixed in Biopython 1.77
Update: See https://github.com/biopython/biopython/issues/3221 - turned out to be a new unexpected configuration of the ABI software producing files with no quality scores.
Related
When I trying to install nltk and download the file punket using nltk.download('punkt').
I am getting the following errors. Have tried many alternative codes and changing networks.
error
Please help with this error.
Post applying :-
= df['num_words'] = df['text'].apply(lambda x:len(nltk.word_tokenize(x)))
I am gettring the error:-
**Resource punkt not found.
Please use the NLTK Downloader to obtain the resource:
import nltk
nltk.download('punkt')
For more information see: https://www.nltk.org/data.html
Attempted to load tokenizers/punkt/english.pickle**
I tried some alternative codes like
import nltk
import ssl
try:
_create_unverified_https_context = ssl._create_unverified_context
except AttributeError:
pass
else:
ssl._create_default_https_context = _create_unverified_https_context
nltk.download()
Also tried changing the networks as at some places I found it is saying server issue.
Try to launch the jupyter notebooks session as administrator (open the command or anaconda prompt as administrator).
The last option would be to download the corpus manually. You may find this, helpful in your case.
ValueError: "MosekSolver cannot Solve because MosekSolver::available() is false, i.e., MosekSolver has not been compiled as part of this binary. Refer to the MosekSolver class overview documentation for how to compile it."
Hi, I got the above error when trying to use the Mosek solver in Drake. It is not clear to me how to enable Mosek in Deepnote with Drake. Do I need to include something in the Dockerfile or the init file? Any tips would be appreciated.
Links I looked at:
https://drake.mit.edu/pydrake/pydrake.solvers.mosek.html
https://drake.mit.edu/bazel.html#mosek
Mosek+Drake does work on Deepnote. The workflow is like this:
Obtain a Mosek license file (from the Mosek website), and upload it to Deepnote.
Set an environment variable to tell Drake where to find the license file. For instance, you can add the following at the top of your notebook:
import os
os["MOSEKLM_LICENSE_FILE"] = "mosek.lic"
Now MosekSolver.available() should be True, and Mosek will even be chosen as the default preferred solver for if you simply call Solve(prog).
Note: Please be very careful not to share the Deepnote notebook with your mosek.lic uploaded.
I've been experimenting with PyCharm in conjunction with LO and UNO for some time (win10).
What I don't understand:
Why do I get the error Unresolved reference 'com' from PyCharm when I enter the code in editor, but everything seems to be OK, when I run the script with PyCharm or entered in console?
Example:
import uno
from com.sun.star.awt import Point
p = Point(100, 200)
print(p)
=> (com.sun.star.awt.Point){ X = (long)0x64, Y = (long)0xc8 }
What I would expect would be a relationship between the UNO interfaces com.sun.star.awt and Python so that I can use Intellisense/autocomplete (for example) when entering the code from com.sun.star.awt import Point in PyCharm'.
What I know is that all interfaces are described in the IDL files (SDK). I thought it must be possible to define a so-called stub/mock "package" that enables me to do this. Unfortunately, this request is beyond my capabilities at the moment. The attempt to integrate the idl structure from sdk is only inadequate (path structure only).
Are there any ready-made solutions? (which I doubt - intensively searched all sources)
Do I have to live with it now, or which approach would go in the right direction (I love intellisense)? - Maybe I think too complicated?
I am attempting to send a file from IFS to an outq on our AS/400 system. Whenever I do, I get exactly what I send, as well as a line of "#" symbols of varying lengths appended to the end.
Here's the command I'm using:
qsh cmd('cat -c /path/test.txt | Rfile -wbQ -c "ovrprtf file(qprint)
outq(*LIBL/ABCD) devtype(*USERASCII) rplunprt(*no) splfname(test) hold(*no)"
qprint')
The contents of test.txt is just Hello World!
The output I get when I send the command is
Hello World!####################################################################
I have not found any posts online about a similar problem, and have tried changing values and looking for additional switches to get it to work. Nothing I'm doing seems to fix the issue.
Is there a command or switch that I am missing, or is something I have in there already causing this?
EDIT:
I found this documentation which is the first time I've seen this issue mentioned, but it's not very helpful:
“Messages for a Take Action command might consist of a long string of "at" symbols (#) in a pop-up message. (The Reflex automation Take Action command, which is configured in situations, does not have this problem.) A resolution for this problem is under construction. This problem might be resolved by the time of the product release. If you see this problem, contact IBM Software Support.”
The only differences are: 1) this is not a pop-up message, it's printed. 2) I don't believe we use Tivoli Monitoring, although I could be wrong.
Assuming we do use Tivoli Monitoring, what would the solution be? There's no additional documentation past that, and I am not a system administrator, so I can't really make the call to IBM Software Support myself. And assuming we DON'T use it, what else could cause this issue?
I get different results, yet similar. I created a test.txt with Windows Explorer, put in Hello, world!, saved it and tried the script. I got gibberish for the 'Hello, world!' and then the line of # symbols.
My system is 7.3 TR5, CCSID 37 (US English) and my IFS file is CCSID 1252 (Windows English). Results did not change if I used a stream file of CCSID 819 (US ASCII).
I didn't have any luck modifying Rfile switches.
I found that removing devtype(*userascii) produced printed output in plain English without the # symbols. Do you really need *USERASCII? I would think that would be more for a pre-formatted 'print-ready' file like Postscript or the like.
EDIT: some more things to try
I don't understand why *USERASCII is adding those # symbols; it looks like a translation issue.
I tried this and still got the extra ###... You might have to play with the TOCCSID() parameter. Although a failure, it did give me an idea: what if those # symbols are EBCDIC spaces being sent as-is to the *USERASCII print stream? All we'd need is a way to send only the number of bytes in the stream file, without any padding.
CRTPF FILE(QTEMP/PRTSTMF) RCDLEN(132)
CPY OBJ('/path/test.txt') TOOBJ('/qsys.lib/qtemp.lib/prtstmf.file/prtstmf.mbr') replace(*yes)
ovrprtf file(qprint) outq(*LIBL/prt3812) devtype(*USERASCII) rplunprt(*no) splfname(test) hold(*no)
cpyf prtstmf qprint
The data in QTEMP/PRTSTMF is in ASCII; DSPPFM shows that much. It also shows a bunch of spaces: after all, it is a fixed length file. My next step was to write an RPG program to read the stream file and print it, but Scott Klement already did that: http://www.scottklement.com/PrtStmf.zip
This works on my system:
ovrprtf file(qsysprt) outq(*LIBL/abcd) devtype(*USERASCII) rplunprt(*no) splfname(test) hold(*no)
prtstmf stmf('/path/test.txt') outq(abcd)
I have an neo4j-admin import script set up with --bad-tolerance=100000 (note, also tried --bad-tolerance 100000) as a flag. My script fails during import during the collect dense nodes step with the following message: unexpected error: Too many bad entries 1001, where last one was: InputRelationship:...
I thought bad tolerance was supposed to address that flag so that it would fail at the (in this case) 100,001st bad entry?
bin/neo4j-admin import is feature wise not yet on par with the good old bin/neo4j-import tool - which is marked deprecated in 3.1.1.
To use --bad-tolerance you need to go back to use bin/neo4j-import.