ZSeeker 1.7

ZSeeker is a cli tool to find the propensity of B-DNA to form Z-DNA structures.

ZSeeker

==============

Installation

pip install ZSeeker

CLI Usage

ZSeeker --fasta ./test_GCA_f.fasta --n_jobs 1

Example: In Code usage

from zseeker.zdna_calculator import ZDNACalculatorSeq, Params
# Define parameters
params = Params(
    GC_weight=5.0,
    AT_weight=0.5,
    GT_weight=1.1,
    AC_weight=1.3,
    mismatch_penalty_starting_value=4,
    mismatch_penalty_linear_delta=2,
    mismatch_penalty_type='linear',
    threshold=10,
    consecutive_AT_scoring=[1, 2, 2],
    display_sequence_score=1
    drop_threshold=50,
    total_sequence_scoring=False
)

# Create a ZDNACalculatorSeq instance and nput sequence
zdna_calculator = ZDNACalculatorSeq(data="ACGTACGTACGT", params=params)

# Calculate subarrays above threshold
subarrays = zdna_calculator.subarrays_above_threshold()

# Print results
print(subarrays)

Command-line Help

usage: ZSeeker [-h] [--fasta FASTA] [--GC_weight GC_WEIGHT]
               [--AT_weight AT_WEIGHT] [--GT_weight GT_WEIGHT]
               [--AC_weight AC_WEIGHT]
               [--mismatch_penalty_starting_value MISMATCH_PENALTY_STARTING_VALUE]
               [--mismatch_penalty_linear_delta MISMATCH_PENALTY_LINEAR_DELTA]
               [--mismatch_penalty_type {linear,exponential}]
               [--n_jobs N_JOBS] [--threshold THRESHOLD]
               [--consecutive_AT_scoring CONSECUTIVE_AT_SCORING]
               [--display_sequence_score {0,1}]
               [--output_dir OUTPUT_DIR]
               [--gff_file GFF_FILE]
               [--drop_threshold DROP_THRESHOLD]
               [--total_sequence_scoring]

Given a fasta file and the corresponding parameters it calculates the
ZDNA for each sequence present.

options:
  -h, --help            show this help message and exit
  --fasta FASTA         Path to file analyzed
  --GC_weight GC_WEIGHT
                        Weight given to GC and CG transitions.
                        Default = 7.0
  --AT_weight AT_WEIGHT
                        Weight given to AT and TA transitions.
                        Default = 0.5
  --GT_weight GT_WEIGHT
                        Weight given to GT and TG transitions.
                        Default = 1.25
  --AC_weight AC_WEIGHT
                        Weight given to AC and CA transitions.
                        Default = 1.25
  --mismatch_penalty_starting_value MISMATCH_PENALTY_STARTING_VALUE
                        Penalty applied to the first non
                        purine/pyrimidine transition encountered.
                        Default = 3
  --mismatch_penalty_linear_delta MISMATCH_PENALTY_LINEAR_DELTA
                        Only applies if penalty type is set to
                        linear. Determines the rate of increase of
                        the penalty for every subsequent non
                        purine/pyrimidine transition. Default = 3
  --mismatch_penalty_type {linear,exponential}
                        Method of scaling the penalty for contiguous
                        non purine/pyrimidine transition. Default =
                        linear
  --n_jobs N_JOBS       Number of threads to use. Defaults to -1,
                        which uses the maximum available threads on
                        CPU
  --threshold THRESHOLD
                        Scoring threshold for a for a sequence to be
                        considered potentially Z-DNA forming and
                        returned by the program. This parameter is
                        also used for determining how big the scoring
                        drop within a sequence should be, before it
                        is split into two separate Z-DNA candidate
                        sequences. Default=50
  --consecutive_AT_scoring CONSECUTIVE_AT_SCORING
                        Consecutive AT repeats form a hairpin
                        structure instead of Z-DNA. In order to
                        reflect that, a penalty array is defined,
                        which provides the score adjustment for the
                        first and the subsequent TA appearances. The
                        last element will be applied to every
                        subsequent TA appearance. For more
                        information see documentation. Default =
                        (0.5, 0.5, 0.5, 0.5, 0.0, 0.0, -5.0, -100.0)
  --display_sequence_score {0,1}
  --output_dir OUTPUT_DIR
  --gff_file GFF_FILE Optional GFF file for gene annotation. Only 'gene' features are used.
  --drop_threshold DROP_THRESHOLD
                        Drop threshold used within subarrays
                        detection logic. Default = 50.
  --total_sequence_scoring
                        If set, compute only a single
                        transitions-based total score per
                        sequence (one row each). Skips subarray
                        detection altogether.

Example output file

Chromosome	Start	End	Z-DNA Score	Sequence
Z1	0.0	15.0	87.0	TGCGTGCGCGCGCGCG
Z2	0.0	15.0	87.0	GCGCCCGCGCGCGCGC
Z3	0.0	11.0	71.0	GCGCGCGCGCGT
Z4	0.0	11.0	65.0	GCGCGTGCGCGC
Z5	0.0	10.0	70.0	CGCGCGCGCGC
Z6	0.0	15.0	63.0	GCACGCACACGCGCGT
Z7	0.0	10.0	70.0	GCGCGCGCGCG
Z8	0.0	13.0	61.0	CGCACGCGCACGCA
Z9	0.0	11.0	59.0	CGCGCGCGCACA

Example output file with annotations

Chromosome	Start	End	Z-DNA Score	Sequence	gene_start	gene_end	gene_id	gene_biotype	strand	distance	distance_from_TSS	distance_from_TES
AE004438.1	364	391	63.0	ACGGTGCCGCAGCGGCCGTGTCGCCAGC	362	812	gene-VNG_6001H	protein_coding	-	0	420	2
AE004438.1	2317	2335	51.5	GCGGCGAGTCGCCGTCGCG	1904	3719	gene-VNG_6007H	protein_coding	-	0	1383	413
AE004438.1	3528	3538	52.75	ACGTGCGCGCG	1904	3719	gene-VNG_6007H	protein_coding	-	0	180	1624
AE004438.1	12771	12814	109.25	GCTGTCGCTGTCGGCGGCGGCTGCCGCCGACGCGACAGCGTCGC	12846	13380	gene-VNG_6015H	protein_coding	-	32	565	32
AE004438.1	13178	13195	56.0	ACGGCGCGTCAGCGGCGT	12846	13380	gene-VNG_6015H	protein_coding	-	0	184	332
AE004438.1	13533	13552	52.75	ACGGCGCACCGCCAGCGTGT	12846	13380	gene-VNG_6015H	protein_coding	-	153	154	687
AE004438.1	13853	13872	70.0	CGTCGGCGCACGCGCCGACG	14307	15582	gene-VNG_6016H	protein_coding	+	435	435	1709
AE004438.1	14960	14971	51.25	GCGCGGTCGCGC	14307	15582	gene-VNG_6016H	protein_coding	+	0	653	610
AE004438.1	15105	15126	61.0	CGCGTCGTCGGCGTCCGCGACG	14307	15582	gene-VNG_6016H	protein_coding	+	0	798	455

ZSeeker web application

The web version of ZSeeker can be found at: ZSeeker web application

And a dockerized version of it can be found at this repository for local deployments: ZSeeker web application dockerized