dib-lab/screed

a simple read-only sequence database, designed for short reads

screed -- short read sequence utils in Python.

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.

screed's Issues

versioneer interactions with khmer: screed installed as 2.0

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

Remove deprecation warning (will stop working in Python 3.8)

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

post demultiplexing script as example

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))

TypeError: Database A_xenica_combined.fastq_screed is not a proper screed database

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
>>>

Screed version?

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

Problems with deepcopy

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

add bgzf/random access code from biopython to screed

also see spacegraphcats

screed docs e-mail address is [email protected]

=> [email protected]

make write_fastx a method on Record, or import at top of screed

remove bz2file dependency!

it's now in the standard library for python >= 3.7, so we don't need to make screed depend on it.

author list in screed docs is wrong.

right now it's just Alex Nolley :)