This is README. Welcome to read my code and join me review my code.

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 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')

Compared two files:

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

parse Fastqc's html

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

print Most commonly used commands in Linux

# just type:
python print_MCUC.py

deal Fastx file

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

md5sum check

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

raster2matrix

this is the raster2matrix converting

data merge

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

for Format converting.

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.