common cmd tools to be used in Python3 scripts. By Guanliang MENG, see https://github.com/linzhi2013/mglcmdtools.
Project description
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
.
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