if the scripts start with pytricks, it is from the book pytricks, it shows some python skills.

pytricks_dict_if.py 

pytricks_merge_dicts.py

if the scripts start with "smart", it is mostly a wraper of some tools, for example:

smart_git.py : is a wraper for git, it will submit and push your code with one step.
smart_split.py : split a file with a integer  number. quick split files.

each file ...

Brute_Force_zip.py is a script that can brute force zip file while using the passwords.txt as a known passwords database.

• related refs: passwords.txt

example:

zip -q -r  -P 19910319 G17E2L1_R1_10pct_R1.fq.zip G17E2L1_R1_10pct_R1.fq.gz

python Brute_Force_zip.py -f <your_file.zip> -d <password.txt>
$ python Brute_Force_zip.py -f G17E2L1_R1_10pct_R1.fq.zip -d password.txt
('Found Passwd : ', '19910319')

With this tool you can calculate the intersection(s) of list of elements. It will generate a textual output indicating which elements are in each intersection or are unique to a certain list. Currently you are able to calculate the intersections of at maximum 30 lists.

The graphical output is produced in JPG format.

• related refs: compare.py compare.list_a.txt compare.list_b.txt

example:

python compare.py -a compare.list_a.txt -al 1 -b compare.list_b.txt -bl 1

This script was used to parser html info that aimed for Fastqc result.
example: 
python fastqc_html_parser.py /path/to/html/

# just type:
python print_MCUC.py

all scripts are in Fastx dir.

1. complement and reverse a Fastq file: python complement_reverse_Fastq_2_Fastq.py xxx.fq >xxx.complement.reverse.fq
2. extract.FastX.py

#support read id list file
python extract.FastX.py test.fq test.list
# support gzip file and specific read id
python extract.FastX.py test.fastq.gz M04261:27:000000000-C7J75:1:1101:11401:1775
# support specific region 
python extract.FastX.py test.fa chr1 2 5
# support specific chrome.
python extract.FastX.py test.fa chr1

more detail see: "https://www.jianshu.com/p/22051fc6e0a3" 3. simulate_fasta2fastq.py simulate_fasta2fastq.py

normally, use md5sum -c MD5.txt
sh smart_md5sum_check.sh # this script is a tricks of use md5sum in patch way.

this is the raster2matrix converting

merge two or more batch of sequening data automatically. see: https://www.jianshu.com/p/9c4f398eb33d

this folder contains some scripts that can convert data format from one type to another. for example:

1. gene2ensembl
2. matrix2raster

• convert matrix to raster format. see:

3. raster2matrix

• convert raster to matrix format. see:

4. featureCounts2TPM.py

• convert featuresCounts txt to TPM, calculate TPM. see:https://www.jianshu.com/p/

5. dna sequencing to complementory and reverse.
6. nuclear tide to aminoacid.