generator

sequence generator

usage

SeqBox generator

usage: SeqBox generator [-h] [-out OUT] [-od OUT_DIR] [-gt {random,norepeat,distance}] [-gn GNUMBER] [-gts GTIMES] [-gc GCHAR] [-gd GDISTANCE] [-gl GLEN] 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 -gt {random,norepeat,distance}, --gtype {random,norepeat,distance} -gn GNUMBER, --gnumber GNUMBER sequence number -gts GTIMES, --gtimes GTIMES Number of runs -gc GCHAR, --gchar GCHAR generator charset, like: ATCG -gd GDISTANCE, --gdistance GDISTANCE distance -gl GLEN, --glen GLEN generator sequence length

random

Randomly generated sequence, possible repetitions.

API

from seqbox import SEQ
seq = SEQ(name="test")
seq.name
# 'test'
Grandom = seq.Gseq_random(seq_len=35)
n = 0
while n <= 10:
    seq = next(Grandom)
    print(seq)
    n = n + 1
#2024-05-21 15:16:40.176 | WARNING  | seqbox.seq:Gseq_random:150 - not found params char_set, use 'ATCG' with default
#CATCGTGCATAACTCGGTAGACAGGCAAGGCAACG
#CACTCGGTCTTGCCATGTGTCCTGTAGGTGACTAA
#AGGAACCCCCGTAGTAGCCCGACAGCAAGGTTCAT
#AGTGTGGATAAAAGAGCACCCACAGAGGACCAAAA
#CAAAACGTATGGCACGCTAACCATTTTCTAAACCG
#GATTTAAGCACAAGACCCTTGTTGGAAAGCAATTC
#AGGTCAACGGGCATTTAGTTCAGTTCCAGTGACCC
#ATGACAGGGAGTGTCATCTGAAAGTGCCAACGGGG
#TAGACTCACTATTATGCCTTCCATTCTCGGAGGTG
#CCTCACCGTTTCGCGGAACGTTTCAACCAAACTAA
#TGAGGGTCTACGATAGCTGTCAAGGAAGACCACTT

seq = SEQ(name="test")
Grandom_RNA = seq.Gseq_random(seq_len=35, char_set="AUCG")
n = 0
while n <= 10:
    seq = next(Grandom_RNA)
    print(seq)
    n = n + 1
#UGAGGACGAGGGCGGUGAUAGGCAUUUUAAUUUGG
#UUGUUUAUCUAGUCCUCCAGCCUCGGAACCGGAAC
#GCUACAUUGUCUGCGGGUUUGACAACGACACGGAU
#CACUGAAGGCUGUUCCCUACUGACUUCGAGGCGCA
#CGAGACUCUUGAAUGUAUAAAAGGUAAGAUAUAUC
#GCCUUUUUUCGGGAGUUACUUCGAGUUGUUCAAUC
#AAGUGUUCCGACCUGAUCCUGCCUCCUGAUCACGU
#GGGGUGGAUUCUGGUAUAGGUGAGGCUAAUCAGUU
#CCUAGCACGACCAAGUUCAAUAGAACGAUCAGAGG
#CGAAUGUACGAGAUCGUCAGGCGGGCCGAUGUUGG
#AUCUGACCUAGGCCUUGGGAGGGUACCCACAAAAG

CLI

The main parameters include the length(-gl or --glen) and number(-gn or -gnumber) of generated sequences.

SeqBox generator -gt random -gn 100 -gl 35 -out test_random

output: test_random.tsv

#generator_random:seq_len:35;char_set:ATCG GGTCCGACCTCATCTGGATGCTCCAATGTGGGCTG AGGCATATGGATCGCCGACACCCGTGCTACAGTTA TCAAGCGCGAACCGGGTACCTGCCGAAACCGTATA AACAGTGTTGCGCAGTGCCTGCACTTAAACAAATC GATATAGGGTCTCGTTAGTACGACGATTTCGCGAG CCCACAGGTCGCAGACTCCGCTGTTGCTTGAAGGC CGTTAAAGCTCAATCATCAACCCGATACGTTGTCT GAGAGCCTAGAACAAGGTACACCGAAGACGAGACG GCGCGGCTGTCCTTAGATATAGGTAGCAATACTGA ... CGTACTGATCAAATAACCCCGCAGACGGGTAATGC

norepeat

randomly generate non-repeating sequences.

API

from seqbox import SEQ
seq = SEQ(name="test")
seq.name
#'test'
Gnorepeat = seq.Gseq_norepeat(seq_len=35)
n = 0
while n <= 10:
    seq = next(Gnorepeat)
    print(seq)
    n = n + 1
#2024-05-21 16:08:06.289 | WARNING  | seqbox.seq:Gseq_norepeat:177 - not found params char_set, use 'ATCG' with default
#GGTTGTAACAGCGATAACACGGTTTAACGGACCAG
#GTTAACTCTAACATATACCTCCTTTCTTCGCCACA
#GCGTCGGATATAGAAGCTTGCGCCCTAATGTTATA
#AATGCCTTGCTCGATTCAATTAGCTCCCAAACTTT
#TTGAGAGAGGTCCTGTCGTTCTTATCCTTTCCTAA
#CGTAACATATAGGATACTTACACGCAGGAGAGTAT
#CCCACCCTACGCATCCGCCGTCGGTCTGTCGCTAT
#AACGCGATGTCTAGAAGACCATGTTTCACCTAACT
#CGGCGGTGGTTATGGGATATGGGGCTCTGAGTGAG
#GTGCAGCCACGTGAATTTACGTCCTTCGCCGATCC
#CGGCAAATACTCTTGGATAGAGATTAGCAGCGAGC

seq = SEQ(name="test")
Gnorepeat_RNA = seq.Gseq_random(seq_len=35, char_set="AUCG")
n = 0
while n <= 10:
    seq = next(Gnorepeat_RNA)
    print(seq)
    n = n + 1
#CGUCUUAAUUAAACCUCGAAUUGGGAGUUGGCUUG
#CCCAAUCUUCCACUUCUAUAGCGGUAACAUUAAAU
#UCACAUGCAACUCCACGGAACCAAUUAAACCAGGA
#GUGGAAAACCACUUCCAGACUGUAAAGCCAAUGGU
#CUGGACCUACGAUCGCAAAGAUAUAGCUCCUGUAG
#GAGUUUGGCUAGCAGUAUGAGGAGAUUGCAAAUCU
#UCGCUCACGGCGAAACAAUUCUGUAUUUGAGAAGG
#UUAUUCACGAUAUCGGCGGACAGCGAAGGAGUUAU
#AGGACCCUACAUGACGCACAGAGACCAGGUAUCGG
#AGUGUGGGCGUCUCCCGAAACGAAUCGCAUUGUUC
#UUCGUACCGAAGGUUUAGUGGAAUAGGUGGAGAGU

CLI

The main parameters include the length(-gl or --glen) and number(-gn or -gnumber) of generated sequences.

SeqBox generator -gt norepeat -gn 100 -gl 35 -out test_norepeat

output: test_norepeat.tsv

#generator_norepeat:seq_len:35;char_set:ATCG ACTAGATTTTGATTTGGTCCGGAGTTAGAGATCGT GGGATCGAAAGGGGTCGCCTCTCTTGAGAGCATTG GCTATTTATTCAAATAGACTATATACAACAGTACA GGACCTGTAGCGGCGTAGAATGTGCTGTGATACGA CCTTGGACAGTGGGGTATAACCTATGGTGTGAGTA TCACCTTTATTCAGGCGTATCTACGGTACTATCAA GTAGGGTTTCTACCGTTTGAGCATGTAGATGCCAT GCTTAAGTGATGTAAGGTGGCTTACCATCATCGAA ... CATACCACGTAACAACCCGTAGGTTCGCGTTAGGT

distance

randomly generate sequences with edit distances between sequences greater than a fixed value.

API

from seqbox import SEQ
seq = SEQ(name="test")
seq.name
#'test'
Gdistance = seq.Gseq_distance(seq_len=35, distance=5)
n = 0
while n <= 10:
    seq = next(Gdistance)
    print(seq)
    n = n + 1
#2024-05-21 16:13:45.385 | WARNING  | seqbox.seq:Gseq_random:150 - not found params char_set, use 'ATCG' with default
#CCGAGATAAGATACCGCCGCGGGCAACAGCAACCT
#TGAACGTACTTTTCGTCCTGGCGTCATGGGCTAGC
#ACTTAATCTTTGTTTCGACTGTGAGTCACCTATGT
#ACTGTTTCTCCGAGCACTGTCCAATCGTCTTCCCT
#CCTTACGTCCCGTTGTGCGTGTCCATTCGGCAACG
#TAGATTAACTAGCTTGCCGATCGATCAGTTAATTC
#GGAGACCTCAGCAAAGTTCCGCCTCTAAACAGGTA
#CCTCTTTAACATATTGCCTAATCACCGTGGGATAT
#TCGTTAGGAATGTGGACATTTTGAATGGCCAACCT
#TGAAGTAATATTAATCGAAGTTTATTGAGCTAACC
#AGTTGACATTAGCACGTGTGGGATGCGGTCCGAAT

seq = SEQ(name="test")
Gdistance_RNA = seq.Gseq_distance(seq_len=35, char_set="AUCG", distance=5)
n = 0
while n <= 10:
    seq = next(Gdistance_RNA)
    print(seq)
    n = n + 1
#UGUGGCUCCGCACACUGGGCGCUGCCGUGAUGAGA
#ACUAGCAACGACGUAAUAGGUGCUAAUUUACAGUU
#CCUCAACGUAGUAGGGAUUCCAGCUCUACGCAUGA
#CCGCAGACCCAUAGUUAUAUAGCUUCCACUUUUUA
#CAGAGGUUCUUGCGUCUAAUCUCAUUGCAAGUAAU
#GCCCAUGGGGUACUCUUGCCCGAUGUUUGACUGUG
#UCUCCUUCGGGUAGGUGCCACACCGAGCCUUGAGU
#AACCAGAGAGUGACCAUUUGACAACGCACUACCUU
#UCACGUCAAGUUAAGCGAGCAAGAGGGCGCGUCGU
#UAACCUAUGUUCUACUCUUCACUUCUAAGUUAAGG
#CUUCGACCUCUACAUGAAGGCAAGCUUUGAAGUAU


seq = SEQ(name="test")
# When the distance is relatively large, it takes too long to obtain a sufficient number of entries. 
# At this time, set the times parameter to control the number of attempts and avoid too long loops.
Gdistance = seq.Gseq_distance(seq_len=35, distance=35, times=10)
n = 0
while n < 10:
    seq = next(Gdistance)
    print(seq)
    n = n + 1
#2024-05-21 16:31:31.828 | WARNING  | seqbox.seq:Gseq_random:150 - not found params char_set, use 'ATCG' with default
#GGAATATAGCGTTATTCAGACCTAGTAGACAATTC
#---------------------------------------------------------------------------
#StopIteration                             Traceback (most recent call last)
#Cell In[14], line 3
#      1 n = 0
#      2 while n < 10:
#----> 3     seq = next(Gdistance)
#      4     print(seq)
#      5     n = n + 1
#
#StopIteration: 

CLI

The main parameters include the length(-gl or --glen), number(-gn or -gnumber), distance(-gd or --gdistance) and try_times(-gts or gtimes) of generated sequences.

SeqBox generator -gt distance -gn 100 -gl 35 -gd 5 -out test_distance

output: test_norepeat.tsv

#generator_distance:seq_len:35;char_set:ATCG;distance:5 ACCATTAGCACCAACAGGCAAGCTCCTGCACGGTA GTGCAGGCCCAACTTTCCCCACCTATAGGCTACGG GACCGGGCGGGACTTTCGCCCAATCATCACATACC AACCGGTAGTCGATGAGCGCTCATTAACACGAAGC GTTCTGGTCATTTATCCTCCCTCAGGTACGGATTT TTGCCGCTCAATTGAAAGGTACTGCCAGGAGTGTC AGGCCAGAACGGATATACTAGTTGCTCCAACCTGA ATTGACAGCAGGCGCAAGACATGCCCTAAGCCCTA GTAACTATCCCGAGTCGACGCAGATTGTGCTTCGG