mglcmdtools

1 Introduction

mglcmdtools is a collection of common cmd tools intended to be used in Python3 scripts. By Guanliang MENG, see https://github.com/linzhi2013/mglcmdtools.

2 Installation

pip install mglcmdtools

3 Usage

from mglcmdtools import rm_and_mkdir, runcmd, longStrings_not_match_shortStrings, read_fastaLike, read_fastaLike2


rm_and_mkdir('Newdirectory')

rm_and_mkdir('Newdirectory', force=True)


cmd = 'ls -lhtr /'
runcmd(cmd)

runcmd(cmd, verbose=True)


Long_strings = ['AABB', 'CCDD', 'EEFF']
Short_strings = ['AA', 'EE']
longStrings_not_match_shortStrings(Long_strings, Short_strings)
# ['CCDD']

seq.fa file has following content:

>scaffold512 Locus_1222_0 8.3 LINEAR length=1717 score=20.785
COX2    2   649 45  643 +   4
COX3    897 1691    18  784 +   4
>C7676 18.0 length=1633 score=19.113
DNA afd
COX1    34  1580    12  1530    -   4
>C7536 14.0 length=1185 score=13.529
CYTB    178 1185    25  1008    +   4
>scaffold619 Locus_1559_0 5.0 LINEAR length=803 score=3.515
ND4 27  764 515 1185    +   2
>scaffold367 Locus_808_0 4.6 LINEAR length=652 score=2.296
ATP6    1   306 324 620 -   4
AAA adfjkaj

Then read each record:

for rec in read_fastaLike('seq.fa'):
    print('seqid line:', rec[0])
    print('sequence line 1:', rec[1])

4 Author

Guanliang MENG

5 Citation

Currently I have no plan to publish mglcmdtools.