trgn_assignment3b

extract_phonenum.py

Usage

• python3 extract_phonenum.py mytextfile.txt

Description

Extracts every phone numbers from a text file and print them as a list. Use regex re.findall(r'\(?0\d{2,3}[)-]?\d{7,8}').

• #(? represents it could find phonenumber with or without Parenthese "(".
• #0\d{2,3} represents Region number 0XX one to two times.
• #[)-? represents it could or could not follow ")"," ","-" after Region number.
• #\d{7,8} represents 7 or 8 digit number.

It could find phone number in format (0XX) 7 or 8 digit number,0XX- 7 or 8 digit number and 0XX 7 or 8 digit number.

Known issues

None

ensg2hugo.py

Usage

python3 ensg2hugo.py [-f][0-9] [file]

Description

• Read the Homo_sapiens.GRCh37.75.gtf to create a dictionary.
• Convert the Ensembl name to HUGO names in input file.
• "-f[1-9]" means usc the No.n column , in this Unit test file , you should use -f2 to pick the second column.
• git clone the test file expres.anal.csv。

Known Issues

If you want to do this conversion successfully, you should know the right column to use -f[n] and the f-paramter can not be missed.

Histogram.py

Usage

python3 histogram.py [-f][0-9] [file]

Description

• Creates a histogram as a png from a csv file using the specified column in a tab delimited file.
• "-f[n] means you should the nth column to draw this histogram.
• The test file is "addresses.csv" and the histogram obtained is "histogram.png"

Know Issues

• Need to install the python library matplotlib: pip install --user matplotlib
• It is used to handle .csv files.