python and NGS data

[markero]

Hi all,
I am wondering how many python packages are available for NGS data analysis.
As far as I know, HTSeq and Erange are written in python.
Any others?
Thanks a lot!

[maubp]

Biopython has support for SFF, FASTQ, FASTA + QUAL - handy for simple manipulation of input data. Also has an ACE parser if you are getting those from your assemblies.

[Gus]

You may want to check out my blacktie pipeline. It combines all data and commands to automate running the tuxedo protocol: tophat/cufflinks/cummerbund.

http://blacktie.readthedocs.org/en/latest/

[crazyhottommy]

some of my collections:
cruzdb https://github.com/chapmanb/bcbio-nextgen
pygr http://code.google.com/p/pygr/
pycogent http://pycogent.org/

https://github.com/chapmanb/bcbio-nextgen

bx-python https://bitbucket.org/james_taylor/b...pts?at=default
metaseq http://pythonhosted.org/metaseq/
MISO http://genes.mit.edu/burgelab/miso/docs/index.html
Nesoni http://www.vicbioinformatics.com/nesoni-cookbook/#
reditools https://code.google.com/p/reditools/

btw; blacktie is also one of my collections

[crazyhottommy]

some of my collections:
cruzdb https://github.com/chapmanb/bcbio-nextgen
pygr http://code.google.com/p/pygr/
pycogent http://pycogent.org/

https://github.com/chapmanb/bcbio-nextgen

bx-python https://bitbucket.org/james_taylor/b...pts?at=default
metaseq http://pythonhosted.org/metaseq/
MISO http://genes.mit.edu/burgelab/miso/docs/index.html
Nesoni http://www.vicbioinformatics.com/nesoni-cookbook/#
reditools https://code.google.com/p/reditools/

btw; blacktie is also one of my collections

[Gus]

some of my collections:
btw; blacktie is also one of my collections

Thats great! If you find anything that needs attention or even just want to request a new feature, PLEASE file an issue at https://github.com/xguse/blacktie/issues!

I am eager to improve blacktie but I need user input!

Thanks,

Gus

[csmatyi]

some of my collections:
cruzdb https://github.com/chapmanb/bcbio-nextgen
pygr http://code.google.com/p/pygr/
pycogent http://pycogent.org/

https://github.com/chapmanb/bcbio-nextgen

bx-python https://bitbucket.org/james_taylor/b...pts?at=default
metaseq http://pythonhosted.org/metaseq/
MISO http://genes.mit.edu/burgelab/miso/docs/index.html
Nesoni http://www.vicbioinformatics.com/nesoni-cookbook/#
reditools https://code.google.com/p/reditools/

btw; blacktie is also one of my collections

Hi, maybe you can help me with an installation problem I have with bcbio-nextgen. I want to install it on linux, but I get this error:

-----

Error: Cannot install tabix because conflicting formulae are installed.

htslib: because tabix and bgzip binaries are now part of the HTSlib project

Please `brew unlink htslib` before continuing.

Unlinking removes a formula's symlinks from /home/unmc_cbsb/matt/bin/bcbio. You can
link the formula again after the install finishes. You can --force this
install, but the build may fail or cause obscure side-effects in the
resulting software.

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/home/unmc_cbsb/matt/bin/bcbio/lib/perl5:${PERL5LIB} && /home/unmc_cbsb/matt/bin/bcbio/bin/brew install --env=inherit tabix'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 253, in <module>
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 41, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/lustre/work/unmc_cbsb/matt/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/home/unmc_cbsb/matt/bin/bcbio', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1

-----

the command I use at installation is:

python bcbio_nextgen_install.py /lustre/work/unmc_cbsb/matt/bcbio-nextgen --tooldir=/home/unmc_cbsb/matt/bin/bcbio --nosudo --isolate

Thanks in advance for any help.

[crazyhottommy]

Hi, maybe you can help me with an installation problem I have with bcbio-nextgen. I want to install it on linux, but I get this error:

-----

Error: Cannot install tabix because conflicting formulae are installed.

htslib: because tabix and bgzip binaries are now part of the HTSlib project

Please `brew unlink htslib` before continuing.

Unlinking removes a formula's symlinks from /home/unmc_cbsb/matt/bin/bcbio. You can
link the formula again after the install finishes. You can --force this
install, but the build may fail or cause obscure side-effects in the
resulting software.

Fatal error: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/home/unmc_cbsb/matt/bin/bcbio/lib/perl5:${PERL5LIB} && /home/unmc_cbsb/matt/bin/bcbio/bin/brew install --env=inherit tabix'

Aborting.
Traceback (most recent call last):
File "bcbio_nextgen_install.py", line 253, in <module>
main(parser.parse_args(), sys.argv[1:])
File "bcbio_nextgen_install.py", line 41, in main
subprocess.check_call([bcbio["bcbio_nextgen.py"], "upgrade"] + _clean_args(sys_argv, args, bcbio))
File "/usr/lib64/python2.6/subprocess.py", line 505, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/lustre/work/unmc_cbsb/matt/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/home/unmc_cbsb/matt/bin/bcbio', '--nosudo', '--isolate', '--data']' returned non-zero exit status 1

-----

the command I use at installation is:

python bcbio_nextgen_install.py /lustre/work/unmc_cbsb/matt/bcbio-nextgen --tooldir=/home/unmc_cbsb/matt/bin/bcbio --nosudo --isolate

Thanks in advance for any help.

see a post here

http://bcbio.wordpress.com/2014/03/06/improving-reproducibility-and-installation-of-genomic-analysis-pipelines-with-docker/

[csmatyi]

Hi crazyhottommy,

I have no sudo privilege on the server I'm on.
Basically, how do I install it in a simple way without any special necessary privileges needed?

[Anna16]

Hey Markero, I have a solution for you, you I can refer a website community where you can find all your queries resolved or you can join their python certification training which is high in demand.