5. seq_qual.py

5.1. Description

This program generates heatmap from a FASTQ file to visualize the sequencing quality.

5.2. Options

--version	show program’s version number and exit
-h, --help	show this help message and exit
-i IN_FILE, --infile=IN_FILE
	Input file in FASTQ (https://en.wikipedia.org/wiki/FASTQ_format#) format.
-o OUT_FILE, --outfile=OUT_FILE
	The prefix of output files.
-n MAX_SEQ, --nseq-limit=MAX_SEQ
	Only process this many sequences and stop. default=none (generate logo from ALL sequences).
--cell-width=CELL_WIDTH
	Cell width (in points) of the heatmap. default=12
--cell-height=CELL_HEIGHT
	Cell height (in points) of the heatmap. default=10
--font-size=FONT_SIZE
	Font size in points. If –display-num was set, fontsize_number = 0.8 * font_size. default=6
--angle=COL_ANGLE
	The angle (must be 0, 45, 90, 270, 315) of column text lables under the heatmap. default=45
--text-color=TEXT_COLOR
	The color of numbers in each cell. default=black
--file-type=FILE_TYPE
	The file type of heatmap. Choose one of ‘pdf’, ‘png’, ‘tiff’, ‘bmp’, ‘jpeg’. default=pdf
--no-num	if set, will not print numerical values to cells. default=False
--verbose	If set, will produce detailed information for debugging.

5.3. Example

$ python3 seq_qual.py -i  ../normal_dat/indepth_C05_MissingLibrary_1_HL5G3BBXX/bamtofastq_S1_L004_R1_001.fastq.gz -n  5000000 -o R1_qual

2020-09-29 04:34:40 [INFO]  Reading FASTQ file "../normal_dat/indepth_C05_MissingLibrary_1_HL5G3BBXX/bamtofastq_S1_L004_R1_001.fastq.gz" ...
2020-09-29 04:35:30 [INFO]  5000000 quality sequences finished
2020-09-29 04:35:30 [INFO]  Make data frame from dict of dict ...
2020-09-29 04:35:30 [INFO]  Filling NA as zero ...
2020-09-29 04:35:30 [INFO]  Writing R code to "R1_qual.qual_heatmap.r"
2020-09-29 04:35:30 [INFO]  Displayed numerical values on heatmap
2020-09-29 04:35:30 [INFO]  Running R script file "R1_qual.qual_heatmap.r"
Loading required package: Matrix
Loading required package: SPAtest
Loading required package: pheatmap

5.4. Output files

• R1_qual.qual_count.csv
• R1_qual.qual_heatmap.pdf
• R1_qual.qual_heatmap.r
• R1_qual.qual_percent.csv

R1_qual.qual_heatmap.pdf