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variation.md

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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"}