Python_Parsers

• summarygen.py: This is a script in which works in correlation with specifica output files from RSEQC, STAR mapping, and Splicing Deficiency functions. Developed for use in pipeline which is in development to look at and calculate variables with Splicing Events in dancer patients and cancer data. This script works with files from an individual sample and parses the summarized data and then combines it to generate a two row, or two column (users choice), output file. In theory, each samples output golbal summary file would be combined in an R script (will link to in the future) and generate a TSV global summary file with data from all samples.

• samplecheck.py: This script is used at the end of the pipeline described in the summarygen.py description. After the global summary table is made it will be compared with the starting sample list at the beginning of the pipeline to make sure all the samples put in are accounted for at the end. It will output a PASS or FAIL and let the user know which files are missing from the beginning or added in the end.

• fq_filecheck.py: This script was generated to compar the list of FASTQ files that were suppose to be downloaded with the contents of the folder they were downloaded to. Will let the user know if some files are missing and which ones. It currently uses a user generated list of the files in the FASTQ folder, but I hope to added an OS function that can look in the directory without the user having to generate a list of what is within. This script does require a TXT file of the list of FASTQ sample names (NOT FILE NAMES).