GSEA.ncbr_huse
GSEA.ncbr_huse
Set of functions supporting the FNL NCBR work
Author: Susan Huse
Created on Mon Aug 6 11:07:30 2018
Functions
| Name | Description |
|---|---|
| con_db | Connect to the database. |
| err_out | Exit with an error message. |
| fasta_count | Count FASTA records in a file. |
| fasta_list | List FASTA record identifiers. |
| pause_for_input | Pause until the user provides a valid response. |
| run_cmd | Run a shell command and capture its output. |
| run_os_cmd | Run an operating-system command. |
| send_update | Send a status update. |
| un_gzip | Decompress a gzipped file. |
con_db
GSEA.ncbr_huse.con_db(host_name, db_name, port_number)Connect to the database.
err_out
GSEA.ncbr_huse.err_out(errMsg, log=None)Exit with an error message.
fasta_count
GSEA.ncbr_huse.fasta_count(fastaFile)Count FASTA records in a file.
fasta_list
GSEA.ncbr_huse.fasta_list(fastaFile)List FASTA record identifiers.
pause_for_input
GSEA.ncbr_huse.pause_for_input(txt, contkey='y', quitkey='q', log=None)Pause until the user provides a valid response.
run_cmd
GSEA.ncbr_huse.run_cmd(theCommand, fn, dorun)Run a shell command and capture its output.
run_os_cmd
GSEA.ncbr_huse.run_os_cmd(theCommand, fn, dorun)Run an operating-system command.
send_update
GSEA.ncbr_huse.send_update(updateStr, log=None, quiet=False)Send a status update.
un_gzip
GSEA.ncbr_huse.un_gzip(fname, logfn)Decompress a gzipped file.