ialbert / bio Goto Github PK

I am following along the Biostar Handbook.

I did 'pip install bio --upgrade' (with and without upgrade) and it says requirement already satisfied. But when I try to use the command is doesn't work.

$ bio fetch NC_045512
Command 'bio' not found, did you mean:
command 'bip' from deb bip (0.9.3-1)
command 'gio' from deb libglib2.0-bin (2.72.4-0ubuntu2.2)
command 'fio' from deb fio (3.28-1)
command 'pio' from deb platformio (4.3.4-2)
command 'biom' from deb python3-biom-format (2.1.10-3ubuntu1)
command 'rio' from deb rio (1.07-14ubuntu1)
command 'tio' from deb tio (1.32-1)

Hi!

I wanted to use the fasta2vcf option of bio following the instructions in https://www.bioinfo.help/bio-fasta2vcf.html#bio-fasta2vcf

However, I get the following error: invalid command: fasta2vcf.

I'm using version 1.4.0 of bio. Any help would be appreciated!

Thanks

Hello Albert,

Thanks for this bio package. I wanted to fetch the information for SRR10971381. However when run the command below, I get a HTTP bad reqest error. Would you know why. How should I resolve it?

$ bio fetch SRR10971381
Output
Error for SRR10971381, nuccore, gbwithparts, text: HTTP Error 400: Bad Request

On the other hand bio search SRR10971381 works fine....
akannan@nrnb226 ~/bioinformatics/work/biostar_handbook/covid_analysis
$ bio search SRR10971381
output
[
{
"run_accession": "SRR10971381",
"sample_accession": "SAMN13922059",
"first_public": "2020-02-05",
"country": "China: Wuhan",
"sample_alias": "Human-BALF",
"fastq_bytes": "1160191847;1216048922",
"read_count": "28282964",
"library_name": "1",
"library_strategy": "RNA-Seq",
"library_source": "METATRANSCRIPTOMIC",
"library_layout": "PAIRED",
"instrument_platform": "ILLUMINA",
"instrument_model": "Illumina MiniSeq",
"study_title": "Complete genome of a novel coronavirus associated with severe human respiratory disease in Wuhan, China",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR109/081/SRR10971381/SRR10971381_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR109/081/SRR10971381/SRR10971381_2.fastq.gz"
}
]

Many thanks for your help.

Abhilash Kannan

I am currently going through the biostar handbook to acquire as much knowledge as possible for NGS.
When i try to install "bio" in the environment, which was created to go through this book, it puts out an error:
"
ERROR: Could not find a version that satisfies the requirement biopython>=1.80 (from bio) (from versions: 1.0a3, 1.0a4, 1.10, 1.20, 1.21, 1.22, 1.23, 1.24, 1.30, 1.40b0, 1.41, 1.42, 1.43, 1.44, 1.45, 1.46, 1.47, 1.48, 1.49b0, 1.49, 1.50b0, 1.50, 1.51b0, 1.51, 1.52, 1.53, 1.54b0, 1.54, 1.55b0, 1.55, 1.56, 1.57, 1.58, 1.59, 1.60, 1.61, 1.62b0, 1.62, 1.63b0, 1.63, 1.64, 1.65, 1.66, 1.67, 1.68, 1.69, 1.70, 1.71, 1.72, 1.73, 1.74, 1.75, 1.76, 1.77, 1.78, 1.79)
ERROR: No matching distribution found for biopython>=1.80 (from bio)
"
installing it outside of this environment works though.

any suggestions.
Thank you.

Dear @ialbert,

I managed to install bio in my Windows machine via the command prompt and use some functions (e.g. fasta). But since I could not run 'bio --download', I cannot use all the functionalities of bio.

I printed the error I got below, which is related to a denied permission to one of the temporary files created during the download. I got the same error using the prompt as administrator or not, and I already try to change the access rights of my entire ./Temp folder, but nothing worked so far.

I tried to look online in some possible ideas on the cause of the problem, but it may be that next command line is trying to execute another task before the folder is fully created.

Any ideas? Downloading the 'biodata.tar.gz' directly into my ..bio folder would help?

Thanks!

Having difficulties with install (Mac OS 14.2.1; M1 architecture).

Firstly, could not duplicate the Terminal.app as indicated in instructions as I am using Sonoma, which has removed this function.

However, I was able to install Homebrew and XCode etc. and after this command:

curl http://data.biostarhandbook.com/install.sh | bash

install progressed and received #The Biostar Handbook software installation has completed!"

but upon this command:

source ~/.bash_profile

received this error:

/Users/cbishop/.bash_profile:1: not a directory: /opt/homebrew/bin/brew/brew
/Users/cbishop/.biostar.sh:12: = not found

and cannot activate bioinfo environment.

verified that packages had installed under ~/micromamba/pkgs

I also get that same error: -bash: /opt/homebrew/bin/brew/brew: Not a directory

when I open the terminal

any clues?

Hi, I am using Bio 1.3.7 version to retrieve documents from the pubmed db. I observed a mismatch in the number of search results from the Pubmed search and Bio api.

Entrez.email = "[email protected]"
Entrez.api_key = <API_KEY>
handle = Entrez.esearch(db=DB, term=QUERY, rettype="medline")
record = Entrez.read(handle)

count = int(record['Count'])
handle = Entrez.esearch(db=DB, term=QUERY, retmax=count, rettype="medline")
record = Entrez.read(handle)

id_list = record["IdList"]

query = ((cSCC) OR (Cutaneous squamous cell carcinoma)) AND ((relapse) OR (relapse rate) OR (treatment progression))

No. of results from Bio api = 1552
No. of results from Pubmed search = 1749

For a few other queries, I observed this difference to be quite large. Can you please look into this. Thanks.

Whenever I run the following command (tried with multiple different genomes including NC_001474.2, MN996532 NC_045512, NC_048217.1), I get the following error: AttributeError: 'SeqFeature' object has no attribute 'strand'
Command:

bio fetch NC_048217.1 > MHV_genomes.gb
bio gff MHV_genomes.gb | head -5

I installed bio using pip inside a new conda environment, and it installed versions: bio-1.6.0 biopython-1.82 biothings-client-0.3.1

Error:
Traceback (most recent call last):
File "/home/leah.dorman/.conda/envs/gff/bin/bio", line 8, in
sys.exit(run())
^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/main.py", line 14, in run
router()
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/main.py", line 130, in wrapper
func(args, **kwargs)
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/main.py", line 202, in router
plac.call(func)
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/libs/placlib.py", line 440, in call
cmd, result = parser.consume(arglist)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/libs/placlib.py", line 291, in consume
return cmd, self.func((args + varargs + extraopts), **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/gff.py", line 17, in run
convert.run(start=start, end=end, type_=type_, match=match, id_=id_, gene=gene, rename=rename, olap=olap, fasta=False, fnames=fnames)
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/convert.py", line 406, in run
recs = parser.get_records(fnames)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/parser.py", line 426, in get_records
recs = flatten(recs)
^^^^^^^^^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/parser.py", line 215, in flatten
return functools.reduce(operator.iconcat, nested, [])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/leah.dorman/.conda/envs/gff/lib/python3.11/site-packages/biorun/parser.py", line 396, in record_generator
brec.strand = feat.strand
^^^^^^^^^^^
AttributeError: 'SeqFeature' object has no attribute 'strand'

I tried to run bio gff to convert a genbank file to gff and got the following error:
$ bio gff MHV_genomes.gb --type CDS
Traceback (most recent call last):
File "/home/hhao/mambaforge-pypy3/bin/bio", line 8, in
sys.exit(run())
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/main.py", line 14, in run
router()
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/main.py", line 130, in wrapper
func(args, **kwargs)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/main.py", line 202, in router
plac.call(func)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/libs/placlib.py", line 440, in call
cmd, result = parser.consume(arglist)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/libs/placlib.py", line 291, in consume
return cmd, self.func((args + varargs + extraopts), **kwargs)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/gff.py", line 17, in run
convert.run(start=start, end=end, type_=type_, match=match, id_=id_, gene=gene, rename=rename, olap=olap, fasta=False, fnames=fnames)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/convert.py", line 406, in run
recs = parser.get_records(fnames)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/parser.py", line 422, in get_records
recs = flatten(reader)
File "/home/hhao/mambaforge-pypy3/lib/pypy3.9/site-packages/biorun/parser.py", line 215, in flatten
return functools.reduce(operator.iconcat, nested, [])
TypeError

Hi,

I have made your neat tool available on our software module system, however, I wondered if there was a way to point the program at a centrally downloaded set of data (the data procured by --download), rather than each user downloading it themselves?

Thanks!