variation

random transformation of sequences, including deletions, additions and mutations.

usage

SeqBox variation

usage: SeqBox variation [-h] [-out OUT] [-od OUT_DIR] [-vi VIN] [-vr VREPLACE] [-vd VDICT] optional arguments: -h, --help show this help message and exit -out OUT, --out_file OUT sequence out file with TSV format -od OUT_DIR, --out_dir OUT_DIR out direction -vi VIN, --vinfile VIN -vr VREPLACE, --vreplace VREPLACE replace base number, like: 1,2,3 -vd VDICT, --vdict VDICT variation dict, like: '1:A-2:T-3:C-4:G'

API

from seqbox import SEQ
seq = SEQ(name="test")
seq.name
#'test'
seq.variation(replaces="1,2,3", seq="ATCGTCGTAGTCGTAGCTAGTCGTAGTAGCTAGT")
#2024-05-21 16:44:48.188 | WARNING  | seqbox.seq:variation:118 - not found params dict_base, use default dict_base
#'ATCGTCGTAGTCGTAGCTAGTCGTAGTAGCTAGT,ACGTCGTAGTCGTACTAGTCGTAGTAGCTAGT,ATCGTCGTAGTGTAGTAGTCGTAGTAGCTAT'

CLI

The main parameters are base variation length(-vr or --vreplace), input file(-vi or --vinfile), and variation encoding(-vd or --vdict).

SeqBox variation -vi test.tsv -out test_variation -vr 1,2,3

input: test.tsv

#seq ACCATTAGCACCAACAGGCAAGCTCCTGCACGGTA GTGCAGGCCCAACTTTCCCCACCTATAGGCTACGG GACCGGGCGGGACTTTCGCCCAATCATCACATACC AACCGGTAGTCGATGAGCGCTCATTAACACGAAGC GTTCTGGTCATTTATCCTCCCTCAGGTACGGATTT TTGCCGCTCAATTGAAAGGTACTGCCAGGAGTGTC AGGCCAGAACGGATATACTAGTTGCTCCAACCTGA ATTGACAGCAGGCGCAAGACATGCCCTAAGCCCTA GTAACTATCCCGAGTCGACGCAGATTGTGCTTCGG CGTAGCCTAGGCGTGGGATTATAACTCTCCGGTAA

output: test_variation.tsv

seq_raw seq_var1 seq_var2 seq_var3 ACCATTAGCACCAACAGGCAAGCTCCTGCACGGTA ACCATAGCACCAACAGGCAAGCTCCTGCACGGTA ACCATTAGCACCTACAGGCAGCTCCTGCACGGTA ACCATTAGCACCAACAGGCAAGCTCCCGCCGGA GTGCAGGCCCAACTTTCCCCACCTATAGGCTACGG GTGCAGGCCCAACTTTCCCCACCTATAGGATACGG GTCAAGGCCCAACTTTCCCCACCTATAGGCTACGG GTGCAGCCAACTTTCCCACCTATAGGCTACGG GACCGGGCGGGACTTTCGCCCAATCATCACATACC GACCGCGGCGGGACTTTCGCCCAATCATCACATACC GACCGGGCGGGACTTTCCCCAATGGATCACATACC GACCGGGCGGGACTTTCGGCCAATCATCACATACA AACCGGTAGTCGATGAGCGCTCATTAACACGAAGC AACCGGTAGTCGATAGCGCTCATTAACACGAAGC AACCGGTAGTATGATGAGCGCTCATTAACACTAAGC AACCGGTGTCGATGAGCGCTTCATTAACACGAAGC GTTCTGGTCATTTATCCTCCCTCAGGTACGGATTT GTTCTGGTCATTTATCCTCCCTCAGGTACGGATTA GTTCTGGTCATTTATCTCCCTCAGGTACGGATT GTTCTGGTCATTATCCTCTTGTTCAGGTACGGATTT TTGCCGCTCAATTGAAAGGTACTGCCAGGAGTGTC TTGCCGCTCAATTGAAAGGTACTGCCAGGAGTGTC TTGCCGCTCAATTAAAGGTACTGCAGGAGTGTC TTGCCGCTCAATTGTGGAAGGTACTGCCAGGCGTGTC AGGCCAGAACGGATATACTAGTTGCTCCAACCTGA AGGCCAGAACGGATATACTAGTTGCTCCAACCTTA AGGCCAGAACGCTATAAAACTAGTTGCTCCAACCTGA AGGCACAACGGATATACTAGTGCTCCAACCTGA ATTGACAGCAGGCGCAAGACATGCCCTAAGCCCTA ATTGACAGCAGGCGCAAACACATGCCCTAAGCCCTA ATTGACAGCAGGCGCAAAACATGCCCTAAGCCTA ATTGATGAGCAGGCGCAATACATGCCCTAGCCCTA GTAACTATCCCGAGTCGACGCAGATTGTGCTTCGG GTAACTATCCCGAGTCGACGCAGATTGTGCTCGG GTAACTATCCCGAGTCACGCAGATTGGAGCTTCGG GTAACTATCCCGATCGACGCAGATTGTCCCTTCGG CGTAGCCTAGGCGTGGGATTATAACTCTCCGGTAA CGTAGCCTAGGCGTGGGATATAACTCTCCGGTAA CGTAAGCCTAGGCGTGGGATATAACTCTCCGGTAA CGTAGCCGAAGCGTGGGATATAACTCTCCGGTAA

vdict

default variation dict: deletions, mutations, and additions, the ratio of the three mutation types is 1:1:1. Customize using parameters(-vd or -vdict), like: 0- ;00- ;1-A;2-T.

dict_var = {"0":"", "00":"","000":"","0000":"","00000":"","00001":"","00002":"","00003":"","00004":"","00005":"","00006":"","00007":"","00008":"","00009":"","000010":"","000011":"",
"0001":"A","001":"A","01":"A","1":"A","0002":"T","002":"T","02":"T","2":"T","0003":"C","003":"C","03":"C","3":"C","04":"G","004":"G","0004":"G","4":"G",
"5":"AA","6":"AT","7":"AC","8":"AG","9":"TA","10":"TT","11":"TC","12":"TG","13":"CA","14":"CT","15":"CC","16":"CG","17":"GA","18":"GT","19":"GC","20":"GG"}