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python and NGS data

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  • python and NGS data

    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!

  • #2
    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.

    Comment


    • #3
      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/
      In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
      --Stephen Jay Gould

      Comment


      • #6
        Originally posted by crazyhottommy View Post
        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
        In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
        --Stephen Jay Gould

        Comment


        • #7
          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.

          Comment


          • #8
            Originally posted by csmatyi View Post
            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/2014/03/0...s-with-docker/

            Comment


            • #9
              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?

              Comment


              • #10
                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.

                Comment

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