sejmodha / miscscripts Goto Github PK

Hi,

I am not sure if this repository is up to date. However, the link

ftp://ftp.ncbi.nih.gov/genomes/refseq/assembly_summary_refseq.txt

needs to be updated.

The output file human_genome.fa is empty.

Thank you for putting this script together! To overcome a KeyError: 'taxid' if you are using a Mac, simply change the subprocess.calls in line 79 and 80 from

subprocess.call("sed -i '1d' assembly_summary_refseq.txt", shell=True) subprocess.call("sed -i 's/^# //' assembly_summary_refseq.txt", shell=True)

to

subprocess.call("sed -i.bu '1d' assembly_summary_refseq.txt", shell=True) subprocess.call("sed -i.bu 's/^# //' assembly_summary_refseq.txt", shell=True)

The addition of the -i.bu creates a backup and operates sed "in place" something that is not standard on a Mac non-GNU version of sed.

Hi sejmodha,

Great work for putting together this script! This might be a noob question, but you mention that this script takes an optional command-line argument which can be specified as the target location where the data should be downloaded and saved.

How do I do that? Can you perhaps give an example?

Cheers,

Sam

Hi @sejmodha . I used your script to successfully setup the kraken database

But when I run I get this error
kraken: database ("/opt/apps/bioinfo/databases/kraken") does not contain necessary file database.kdb

This is the code I used
DB=/opt/apps/bioinfo/databases/kraken
kraken --preload --db $DB sample.trimmed.fa --threads 15 --classified-out sample.classified --unclassified-out sample.unclassified > sample.kraken

Please advice

Hi
I got the following error while trying to convert sequences to kraken input format

Traceback (most recent call last):
File "/home/jason/Documents/Databases/UpdateKrakenDatabases.py", line 118, in
get_fasta_in_kraken_format('human_genome.fa')
File "/home/jason/Documents/Databases/UpdateKrakenDatabases.py", line 107, in get_fasta_in_kraken_format
outseq=">"+seq_id+"|"+taxid+"\n"+str(seq)+"\n"
File "/home/jason/anaconda3/lib/python3.9/site-packages/Bio/Seq.py", line 369, in str
return self._data.decode("ASCII")
File "/home/jason/anaconda3/lib/python3.9/site-packages/Bio/Seq.py", line 156, in decode
return bytes(self).decode(encoding)
File "/home/jason/anaconda3/lib/python3.9/site-packages/Bio/Seq.py", line 2911, in bytes
raise UndefinedSequenceError("Sequence content is undefined")
Bio.Seq.UndefinedSequenceError: Sequence content is undefined

I would apprecciate any help since I'm stuck trying to build the database

Thanks for the script, but getting this error:

updatekrakendb.py
/media/disk1_12TB/tallnut/db/kraken2/refseq
/media/disk1_12TB/tallnut/db/kraken2/refseq
Downloading human genome

--2021-02-18 10:07:12-- ftp://ftp.ncbi.nih.gov/genomes/refseq/assembly_summary_refseq.txt
=> ‘assembly_summary_refseq.txt’
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 165.112.9.228, 2607:f220:41e:250::11, 2607:f220:41e:250::13, ...
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|165.112.9.228|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /genomes/refseq ... done.
==> SIZE assembly_summary_refseq.txt ... 66360144
==> PASV ... done. ==> RETR assembly_summary_refseq.txt ... done.
Length: 66360144 (63M) (unauthoritative)

assembly_summary_refseq.txt 100%[=================================================================================================>] 68.47M 1.13MB/s in 97s

2021-02-18 10:08:54 (724 KB/s) - ‘assembly_summary_refseq.txt’ saved [71801632]

/home/tallnutt/d/scripts/updatekrakendb.py:81: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
assembly_sum = pd.read_table('assembly_summary_refseq.txt',dtype='unicode')
Traceback (most recent call last):
File "/home/tallnutt/d/scripts/updatekrakendb.py", line 116, in
download_refseq_genome(9606,'human_genome_url.txt')
File "/home/tallnutt/d/scripts/updatekrakendb.py", line 81, in download_refseq_genome
assembly_sum = pd.read_table('assembly_summary_refseq.txt',dtype='unicode')
File "/opt/miniconda3/miniconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 702, in parser_f
return _read(filepath_or_buffer, kwds)
File "/opt/miniconda3/miniconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 435, in _read
data = parser.read(nrows)
File "/opt/miniconda3/miniconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 1139, in read
ret = self._engine.read(nrows)
File "/opt/miniconda3/miniconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 1995, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 899, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 914, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 968, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 955, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 2172, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 22 fields in line 141712, saw 36

Hi @sejmodha
I realized the database name is HumanVirusBacteria. Does it mean that only these three are in the database? What about plasmids?