HTSeqCountCluster package

Subpackages

• HTSeqCountCluster.logger package
  • Submodules
  • HTSeqCountCluster.logger.logger module
    • Logger
      • Logger.custom()
      • Logger.default()
      • Logger.deletelog()
      • Logger.shutdown()
  • Module contents
• HTSeqCountCluster.pbsjob package
  • Submodules
  • HTSeqCountCluster.pbsjob.pbsconfig module
  • HTSeqCountCluster.pbsjob.pbsjob module
    • BasePBSJob
      • BasePBSJob.debug()
    • PBSJob
      • PBSJob.submit_cmd()
      • PBSJob.submit_code()
  • HTSeqCountCluster.pbsjob.pbsutils module
    • basejobids()
    • file_to_str()
    • import_temp()
    • random_id()
    • write_code_file()
  • HTSeqCountCluster.pbsjob.qstat module
    • Qstat
      • Qstat.all_job_ids()
      • Qstat.all_queued_jobs()
      • Qstat.all_running_jobs()
      • Qstat.myjobs()
      • Qstat.qstatinfo()
      • Qstat.watch()
  • Module contents
• HTSeqCountCluster.utils package
  • Module contents
    • csvtolist()

Submodules

HTSeqCountCluster.htseq_count_cluster module

HTSeqCountCluster.htseq_count_cluster.call_htseq(infile, gtf, outfile)

Call the htseq-count script.

Parameters:

• infile (str) – An alignment file of aligned reads in SAM format.

• gtf (str) – The gtf (Gene transfer format) file.

• outfile (str) – The name of the output SAM alignment file.

HTSeqCountCluster.htseq_count_cluster.check_job_status(job_id, email=True)

Use Qstat to monitor your job status.

Parameters:

• job_id (str) – The job’s id.

• email (bool, optional) – A flag to decide whether to send email, defaults to True

HTSeqCountCluster.htseq_count_cluster.htseq_jobber(input_path, inputlist, gtf, outpath, email)

Create multiple pbs jobs based on input list of files.

Parameters:

• input_path ([type]) – [description]

• inputlist ([type]) – [description]

• gtf (str) – The gtf (Gene transfer format) file.

• outpath ([type]) – [description]

• email (str) – An email address to send notifications.

HTSeqCountCluster.htseq_count_cluster.main()

Main CLI entry point with subcommands for run and merge.

HTSeqCountCluster.mergecounts module

HTSeqCountCluster.mergecounts.main()

Run the merge_counts_tables function.

HTSeqCountCluster.mergecounts.merge_counts_tables(files_dir)

Merge multiple counts tables into 1 counts table.

After running htseq-count-cluster, there will be a counts table for each sample in the output directory. This function will use the genes column as the first column and then insert each subsequent sample name as column header with counts data as the column rows.

Parameters:

files_dir (str) – The directory of the individual counts files.

Module contents