The official repository for screed is:
https://github.com/dib-lab/screed
See http://readthedocs.org/docs/screed/en/latest/ for docs.
Issues are tracked at https://github.com/dib-lab/khmer/issues.
a simple read-only sequence database, designed for short reads
The official repository for screed is:
https://github.com/dib-lab/screed
See http://readthedocs.org/docs/screed/en/latest/ for docs.
Issues are tracked at https://github.com/dib-lab/khmer/issues.
Using eelpond instructions, screed ends up installed as 2.0:
cd ~/
python2.7 -m virtualenv pondenv
source pondenv/bin/activate
cd pondenv
pip install -U setuptools
git clone --branch v2.0 https://github.com/dib-lab/khmer.git
cd khmer
make install
Seems to be related to python-versioneer/python-versioneer#101
screed/openscreed.py:12: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import MutableMapping
see below:
#! /usr/bin/env python
from __future__ import print_function
import screed
import sys
import argparse
p = argparse.ArgumentParser()
p.add_argument('r1_file')
p.add_argument('r2_file')
p.add_argument('code_r1')
p.add_argument('code_r2')
args = p.parse_args()
for record1, record2 in zip(screed.open(args.r1_file),
screed.open(args.r2_file)):
if record1.sequence[8:].startswith(args.code_r1) and \
record2.sequence[0:].startswith(args.code_r2):
print('@{}\n{}\n+\n{}'.format(record1.name, record1.sequence,
record1.quality))
print('@{}\n{}\n+\n{}'.format(record2.name, record2.sequence,
record2.quality))
I'm using screed 1.0 to convert a fastq file to a fasta file, but it appears that the db file is being written over in the second step.
First:
screed db A_xenica_combined.fastq
With this result:
-rw-r--r-- 1 ljcohen ljcohen 86451998720 Aug 15 20:17 A_xenica_combined.fastq_screed
Second, this command:
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ python -m screed dump_fasta A_xenica_combined.fastq_screed A_xenica_combined.fasta
With this result:
Traceback (most recent call last):
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/openscreed.py", line 147, in __init__
admin_table, = res.fetchone()
TypeError: 'NoneType' object is not iterable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 52, in <module>
main()
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 48, in main
ScreedCommands()
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 44, in __init__
cmd(sys.argv[2:])
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/dump_fasta.py", line 27, in main
n = ToFasta(args.dbfile, args.outputfile)
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/conversion.py", line 75, in ToFasta
db = ScreedDB(dbFile)
File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/openscreed.py", line 157, in __init__
% self._filepath)
TypeError: Database A_xenica_combined.fastq_screed is not a proper screed database
And now my file is only 8K:
-rw-r--r-- 1 ljcohen ljcohen 8192 Aug 16 09:25 A_xenica_combined.fastq_screed
Contents of file:
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ cat A_xenica_combined.fastq_screed
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ LE SCREEDADMIN (id INTEGER PRIMARY KEY, FIELDNAME TEXT, ROLE TEXT)
Screed was installed with khmer 3.0.0a1 from the bioconda channel in a Python 3 conda 4.5.4 environment running on Ubuntu 16.04.4 LTS on the UCD farm cluster.
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 16.04.4 LTS
Release: 16.04
Codename: xenial
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ python
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
>>>
I was writing up a separate issue, and trying to find the screed version. It appears that there is not a version -v
or --version
flag? I found the version with the help of @luizirber via conda list
:
screed 1.0 py_1 bioconda
via @standage:
There is a maximum recursion depth exception when using deepcopy with screed records. This triggers the bug:
import screed
from copy import deepcopy
record = screed.screedRecord.Record()
deepcopy(record)
output
screed/screedRecord.py in __getattr__(self, name)
39 def __getattr__(self, name):
40 try:
---> 41 return self.d[name]
42 except KeyError:
43 raise AttributeError(name)
RuntimeError: maximum recursion depth exceeded while calling a Python object
also see spacegraphcats
it's now in the standard library for python >= 3.7, so we don't need to make screed depend on it.
right now it's just Alex Nolley :)
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