Provided by: mirtop_0.4.25-1_all 
NAME
mirtop - mirtop Documentation
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We got a logo: https://github.com/miRTop/mirtop/tree/master/artwork # Installation
## bioconda
conda install mirtop -c bioconda
## pypi
pip install mirtop
## update to develop version from pip
` pip install --upgrade --no-deps git+https://github.com/miRTop/mirtop.git#egg=mirtop `
## install develop version
Thes best solution is to install conda to get an independent environment.
``
` wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$PATH:~/mirtop_env
conda install -c bioconda bioconda bedtools samtools pip nose pysam pandas dateutil pyyaml
pybedtools biopython setuptools
git clone http://github.com/miRTop/mirtop cd mirtop git fetch origin dev git checkout dev
python setup.py develop
``
`
# Quick Start
## Importer
### From Bam files to GFF3
` git clone mirtop cd mirtop/data `
You can use the example data. Here the reads have been mapped to the precursor sequences.
` mirtop gff -sps hsa --hairpin examples/annotate/hairpin.fa --gtf
examples/annotate/hsa.gff3 -o test_out sim_isomir.bam `
### From seqbuster::miraligner files to GFF3
miRNA annotation generated from [miraligner](https://github.com/lpantano/seqbuster) tool:
` mirtop gff --format seqbuster --sps hsa --hairpin examples/annotate/hairpin.fa --gtf
examples/annotate/hsa.gff3 -o test_out examples/seqbuster/reads.mirna `
### From sRNAbench files to GFF3
miRNA annotation generated from [sRNAbench](http://bioinfo2.ugr.es:8080/ceUGR/srnabench/)
tool:
` mirtop gff --format sranbench -sps hsa --hairpin examples/annotate/hairpin.fa --gtf
examples/annotate/hsa.gff3 -o test_out srnabench examples/srnabench `
### From PROST! files to GFF3
miRNA annotation generated from [PROST!]() tool. Export isomiRs tab from excel file to a
tabular text format file.
` mirtop gff --format prost -sps hsa --hairpin examples/annotate/hairpin.fa --gtf
examples/annotate/hsa.gff3 -o test_out examples/prost/prost.example.txt `
### From isomiR-SEA files to GFF3
miRNA annotation generated from [isomiR-SEA]() tool.
` mirtop validate examples/gff/correct_file.gff `
## Operations
### Validator
To validate your mirGFF3 file and make sure if follows the current format:
` mirtop gff --format isomirsea -sps hsa --hairpin examples/annotate/hairpin.fa --gtf
examples/annotate/hsa.gff3 -o test_out examples/isomir-sea/tagMir-all.gff `
### Get statistics from GFF
Get number of isomiRs and miRNAs annotated in the GFF file by isomiR category.
` cd mirtop/data mirtop stats -o test_out example/gff/correct_file.gff `
### Compare GFF file with reference
Compare the sequences from two or more GFF files. The first one will be used as the
reference data.
` cd mirtop/data mirtop compare -o test_out example/gff/correct_file.gff
example/gff/alternative.gff `
### Updates mirGFF3
Updates older versions with the most current one.
` cd mirtop/data mirtop update -o test_out_mirs examples/versions/version1.0.gff `
## Export
### Export file to isomiRs format
To be compatible with [isomiRs](‐
https://bioconductor.org/packages/release/bioc/html/isomiRs.html) bioconductor package
use:
` cd mirtop/data mirtop export -o test_out_mirs --hairpin examples/annotate/hairpin.fa
--gtf examples/annotate/hsa.gff3 examples/gff correct_file.gff `
### Export file to FASTA format
` cd mirtop/data mirtop export -o test_out_mirs --format fasta -d -vd --hairpin
examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3
examples/gff/correct_file.gff `
### Export file to VCF format
` cd mirtop/data mirtop export -o test_out_mirs --format vcf --hairpin
examples/annotate/hairpin.fa --gtf examples/a nnotate/hsa.gff3
examples/gff/correct_file.gff `
### Get count file
This file it is useful to load into R as a matrix. It contains the minimal information
about each sequence and the count data in columns for each samples.
` cd mirtop/data mirtop counts -o test_out_mirs --hairpin examples/annotate/hairpin.fa
--gtf examples/annotate/hsa.gff3 examples/synthetic/let7a-5p.gtf ` # Output
## GFF command
The mirtop gff generates the GFF3 adapter format to capture miRNA variations. The output
is explained [here](https://github.com/miRTop/incubator/blob/master/format/definition.md).
## Stats command
The mirtop stats generates a table with different statistics for each type of isomiRs:
• total counts
• average counts
• total sequences
It generates as well a JSON file with the same information to be integrated easily with QC
tools like [MultiQC](https://multiqc.info/).
## Compare command
The mirtop compare generates a tabular file with information about the difference and
similarities. The first file in the command line will be considered the reference and the
following files will be compared to the reference. Each line of the output has the
following information for each file:
• sample
• idu
• seq
• tag: E if not in reference, D detected in both, M missing in target file
• same_mirna: if the sequence map to the same miRNA in the reference and target file
• one column for each isomiR type with the following tags: FP (variation not in
reference), TP (variation in both), FN (variation not in target file)
## Counts command
The mirtop counts generates a tabular file with the following columns:
• unique identifier
• read sequence
• miRNA name
• Variant attribute from GFF3 column
• One column for each isomiR type showing the exact variation
• One column for each sample with the counts for that sequence
## Export command
The mirtop export generates different files from a mirGFF3 file:
• [isomiRs](https://bioconductor.org/packages/release/bioc/html/isomiRs.html) compatible
files
• [FASTA files](https://en.wikipedia.org/wiki/FASTA_format)
• [VCF files](https://samtools.github.io/hts-specs/VCFv4.2.pdf)
# Structure of the code
• mirtop/bam * __bam.py__
• read_bam: reads BAM files with pysamtools and store in a key - value object
• __filter.py__ * tune: if option --clean is on, filter according generic rules *
clean_hits: get the top hits
• mirtop/gff * __init.py__ wraps the conversion process to GFF3 * __body.py__ create will
create the line according GFF format established.
• read_gff_line: Inside a for loop to read line of the file. It'll return and
structure key:value dictionary for each column.
• __header.py__ generate header and read header section.
• __check.py__ checks header and single lines to be valid according GFF format (NOT
IMPLEMENTED)
• __stats.py__ GFF stats counting number of isomiR, their total and average expression
• __query.py__ accept SQlite queries after option -q ""
• __convert.py__ * create_counts table of counts * allow filtering by attribute * allow
collapse by miRNA/isomiR type
• __filter.py__, parse from query (NOT IMPLEMENTED)
• mirtop/mirna * __fasta.py__:
• read_precursor fasta file: key - value
• __realign.py__: * hits: class that defines hits * isomir: class that defines each
sequence * cigar_correction: function that use CIGAR to make sequence to miRNA
alignemt * read_id and make_id: shorter ID for sequences * make_cigar: giving an
alignment return the CIGAR of it * reverse_complement: return the reverse complement
of a sequence * align: uses biopython to align two sequences of the same size *
expand_cigar: from a 12M to MMMMMMMMMMMM * cigar2snp: from CIGAR code to list of
changes with position and reference and target nts
• __mapper.py__: * read_gtf file: map genomic miRNA position to precursos position, then
it needs genomic position for the miRNA and the precursor. Return would be like
{mirna: [start, end]}
• __annotate.py__: * annotate: read isomiRs and populate all attributes related to
isomiRs
•
mirtop/importer:
• seqbuster.py
• prost.py
• srnabench.py
• isomirsea.py
•
mirtop/exporter:
• isomirs.py: export file to match [isomiRs BioC package](‐
https://github.com/lpantano/isomiRs).
• data/examples/ * check gff files: example of correct, invalid, warning GFF files *
check BAM file * check mapping from genome position to precursor position, example of
+/- strand. Using mirtop/mirna/map.read_gtf. * check clean option: sequence mapping
to multiple precursors/mirna, get the best score. Using mirtop/bam/filter.clean_hits.
To add new sub-commands, modify the following:
• mirtop/lib/parse.py * query: TODO * transform: TODO * create: TODO * check: TODO
# Examples of contributions
## How to add a new sub-command
You need first to clone and install the tool in [develop mode](installation.html)
Let's say that you want to add a new operation to mirtop, for instance, similar to the
stats command to work with sGFF3 files. Assume a test function for this example to just
read the file and print Hello GFF3.
• Create the folder inside mirtop/test. The create to empty files named:
• test.py
• __init__.py
• Modify the test.py file with this content:
``
` from mirtop.gff.body import read_gff_line
import mirtop.libs.logger as mylog logger = mylog.getLogger(__name__)
def test(args):
for fn in args.files:
_test(fn) logger.info("Hello GFF3: %s" % fn)
def _test(fn):
logger.debug("I am going to read this file: %s" % fn) for line in fn:
read_gff_line(line)
``
`
• Choose a sub_command name, in this case: test.
• Add the arguments function at the end of this file:
https://github.com/miRTop/mirtop/blob/dev/mirtop/libs/parse.py, using a naming following
add_subparser_test.
``
` def add_subparser_test(subparsers):
parser = subparsers.add_parser("test", help="test function")
parser.add_argument("files", nargs="*", help="GFF/GTF files.") parser =
_add_debug_option(parser) return parser
``
`
• Add the function name to parse_cl function, at the end of the sub_cmds array.
``
`
sub_cmds = {"gff": add_subparser_gff,
"stats": add_subparser_stats, "compare": add_subparser_compare, "target":
add_subparser_target, "simulator": add_subparser_simulator, "counts":
add_subparser_counts, "export": add_subparser_export, "test":
add_subparser_test }
``
`
• To get the function re-directed from the command line when you use the sub_cmd name, add
a line to the command_line.py file, adding another else statement:
``
`
elif "test" in kwargs: logger.info("Run test.") test(kwargs["args"])
``
`
• The function you use to link to the operation added need to be imported at the
beginning. Let's say that the test function is at mirtop/test/test.py:
` from mirtop.test import test `
Try the new operation:
` mirtop test data/examples/correct_file.gff `
## Add a unit test
## for the internal function
Add to the end of test/test_functions.py, but inside class
FunctionsTest(unittest.TestCase): this code:
``
`
@attr(fn_test=True) def test_function_test(self):
from mirtop import test test._test("data/examples/gff/correct_file.gff")
``
`
## for the sub-command
Add to the end of test/test_function.py, but inside class
AutomatedAnalysisTest(unittest.TestCase): this code:
``
`
@attr(cmd_test=True) def test_srnaseq_annotation_bam(self):
"""Run test analysis """ with make_workdir():
clcode = ["mirtop",
"test", "../../data/examples/gff/correct_file.gff"]
print("") print(" ".join(clcode)) subprocess.check_call(clcode)
``
`
## test the unit
nose is needed: pip install nose
Run the function test from the top parent folder:
` ./run_test.sh fn_test `
Run the command test from the top parent folder:
` ./run_test.sh cmd_test `
DOCUMENTATION FOR THE CODE
bam
Read bam files
mirtop.bam.bam.read_bam(bam_fn, args, clean=True)
Read bam file and perform realignment of hits
Args: bam_fn: a BAM file with alignments to the precursor
precursors: dict with keys being precursor names and values
being sequences. Come from mirtop.mirna.fasta.read_precursor().
clean: Use mirtop.filter.clean_hits() to remove lower score hits.
Returns:
reads (dict):
keys are read_id and values are mirtop.realign.hits
mirtop.bam.filter.clean_hits(reads)
Select only best matches from a list of hits from the same read.
Args: reads: dictionary as:
>>> {'read_id': mirtop.realign.hits, ...}
Returns:
reads: same than input but with best hits only.
mirtop.bam.filter.tune(seq, precursor, start, cigar)
The actual fn that will realign the sequence to find the nt changes at 5', 3'
sequence and nt variations.
Args: seq (str): sequence of the read.
precursor (str): sequence of the precursor.
start (int): start position of sequence on the precursor, +1.
cigar (str): similar to SAM CIGAR attribute.
Returns:
list with:
subs (list): substitutions
add (list): nt added to the end
cigar (str): updated cigar
exporter
Read GFF files and output isomiRs compatible format
mirtop.exporter.isomirs.convert(args)
Main function to convert from GFF3 to isomiRs Bioc Package.
Reads a GFF file to produces output file containing Expression counts
Args:
args(namedtuple): arguments parsed from command line with
mirtop.libs.parse.add_subparser_counts().
Returns:
file (file): with columns like:
UID miRNA Variant Sample1 Sample2 ... Sample N
Read GFF files and output FASTA format
mirtop.exporter.fasta.convert(args)
Main function to convert from GFF3 to FASTA format.
Args:
args: supported options for this sub-command.
See mirtop.libs.parse.add_subparser_export().
mirtop.exporter.vcf.cigar_2_key(cigar, readseq, refseq, pos, var5p, var3p, parent_ini_pos,
parent_end_pos, hairpin)
Args: 'cigar(str)': CIGAR standard of a compressed alignment representation, this
CIGAR omits the '1' integer. 'readseq(str)': the read sequence
'refseq(str)': the reference sequence 'pos(str)': the start current position
'var5p(int)': extra nucleotides not in the reference miRNA (5p strand)
'var3p(int)': extra nucleotides not in the reference miRNA (3p strand)
'parent_ini_pos(int)': the start position of the parent miRNA
'parent_end_pos(int)': the last position of the parent miRNA 'hairpin(str)':
the string of the hairpin for all the miRNA
Returns:
'key_pos(str list)': a list with the positions of the variants.
'key_var(str list)': a list with the variant keys found. 'ref(str)':
reference base(s). 'alt(str)': altered base(s).
mirtop.exporter.vcf.convert(args)
Main function to convert from GFF3 to VCF.
Args:
args: supported options for this sub-command.
See mirtop.libs.parse.add_subparser_export().
mirtop.exporter.vcf.create_vcf(mirgff3, precursor, gtf, vcffile)
Args: 'mirgff3(str)': File with mirGFF3 format that will be converted
'precursor(str)': Fasta format sequences of all miRNA hairpins 'gtf(str)':
Genome coordinates 'vcffile': name of the file to be saved
Returns:
Nothing is returned, instead, a VCF file is generated
gff
GFF reader and creator helpers
mirtop.gff.body.create(reads, database, sample, args, quiet=False)
Read https://github.com/miRTop/mirtop/issues/9
mirtop.gff.body.lift_to_genome(line, mapper)
Function to get a class of type feature from classgff.py
and map the precursors coordinates to the genomic coordinates
Args: line(str): string GFF line. mapper(dict): dict with mirna-precursor-genomic
coordinas from
mirna.mapper.read_gtf_to_mirna function.
Returns:
(line): string with GFF line with updated chr, star, end, strand
mirtop.gff.body.paste_columns(line, sep=' ')
Create GFF/GTF line from read_gff_line
mirtop.gff.body.read(fn, args)
Read GTF/GFF file and load into annotate, chrom counts, sample, line
mirtop.gff.body.read_gff_line(line)
Read GFF/GTF line and return dictionary with fields
mirtop.gff.body.read_variant(attrb, sep=' ')
Read string in variants attribute.
Args: attrb(str): string in Variant attribute.
Returns:
(gff_dict): dictionary with:
>>> {'iso_3p': -3, ...}
mirtop.gff.body.variant_with_nt(line, precursors, matures)
Return nucleotides changes for each variant type using Variant attribute, precursor
sequences and mature position.
Compare multiple GFF files to a reference
mirtop.gff.compare.compare(args)
From a list of GFF files produce comparison with a reference set.
Args:
args(namedtuple): arguments parsed from command line with
mirtop.libs.parse.add_subparser_compare(). First file will be
considered the reference set.
Returns:
(out_file): comparison of the GFF files with the reference.
mirtop.gff.compare.read_reference(fn)
Read GFF into UID:Variant
Args: fn (str): GFF file.
Returns:
srna (dict): dict with >>> {'UID': 'iso_snp:-2,...'}
Helpers to define the header fo the GFF file
mirtop.gff.header.create(samples, database, custom, filter=None)
Create header for GFF file.
Args: samples (list): character list with names for samples
database (str): name of the database.
custom (str): extra lines.
filter (list): character list with filter definition.
Returns:
header (str): header string.
mirtop.gff.header.read_samples(fn)
Read samples from the header of a GFF file.
Args: fn(str): GFF file to read.
Returns:
(list): character list with sample names.
mirtop.gff.header.read_version(fn)
Extract mirGFF3 version
mirtop.gff.merge.merge(dts, samples)
For dictionary with sample as keys and values as lines merge them into one GFF
file.
Args: dts(dict): dictionary as >>> {'file': {'mirna': {start: gff_list}}}.
gff_list has the format as defined in mirtop.gff.body.read().
samples(list): character list with sample names.
Returns:
merged_lines (nested dicts):gff_list has the format as defined in
mirtop.gff.body.read().
Produce stats from GFF3 format
mirtop.gff.stats.stats(args)
From a list of GFF files produce general isomiRs stats.
Args:
args (namedtupled): arguments parsed from command line with
mirtop.libs.parse.add_subparser_stats().
Returns:
(stdout) or (out_file): GFF general stats.
Update gff3 files to newest version
mirtop.gff.update.convert(args)
Update previous GFF3 versions.
Args:
args (namedtupled): arguments parsed from command line with
mirtop.libs.parse.add_subparser_update().
Returns:
(out_file): most updated GFF3 file.
mirtop.gff.update.update_file(gff_file, new_gff_file)
Update file from file version to current version
mirtop.gff.validator.check_multiple(args)
Check GFF3 format.
Args:
args (namedtupled): arguments parsed from command line with
mirtop.libs.parse.add_subparser_validator().
Returns:
(std_out): warnings or errors of the files showing issues with the format.
importer
Read isomiR GFF files
mirtop.importer.isomirsea.cigar2variants(cigar, sequence, tag)
From cigar to Variants in GFF format
mirtop.importer.isomirsea.header(fn)
Custom header for isomiR-SEA importer.
Args: fn (str): file name with isomiR-SEA GFF output
Returns:
(str): isomiR-SEA header string.
mirtop.importer.isomirsea.read_file(fn, args)
Read isomiR-SEA file and convert to mirtop GFF format.
Args: fn(str): file name with isomiR-SEA output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads (nested dicts):gff_list has the format as
defined in mirtop.gff.body.read().
Read prost! files
mirtop.importer.prost.header()
Custom header for PROST! importer.
Returns:
(str): PROST! header string.
mirtop.importer.prost.read_file(fn, hairpins, database, mirna_gtf)
Read PROST! file and convert to mirtop GFF format.
Args: fn(str): file name with PROST output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads: dictionary where keys are read_id and values are mirtop.realign.hits
Read seqbuster files
mirtop.importer.seqbuster.header()
Custom header for seqbuster importer.
Returns:
(str): seqbuster header string.
mirtop.importer.seqbuster.read_file(fn, args)
Read seqbuster file and convert to mirtop GFF format.
Args: fn(str): file name with seqbuster output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads: dictionary where keys are read_id and values are mirtop.realign.hits
Read sRNAbench files
mirtop.importer.srnabench.read_file(folder, args)
Read sRNAbench file and convert to mirtop GFF format.
Args: fn(str): file name with sRNAbench output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads (nested dicts):gff_list has the format as
defined in mirtop.gff.body.read().
Read isomiR GFF files from optimir tool
mirtop.importer.optimir.read_file(fn, args)
Read OptimiR file and convert to mirtop GFF format.
Args: fn(str): file name with isomiR-SEA output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads (nested dicts):gff_list has the format as
defined in mirtop.gff.body.read().
Read Manatee files
mirtop.importer.manatee.read_file(fn, database, args)
Read Manatee file and convert to mirtop GFF format.
Args: fn(str): file name with Manatee output information.
database(str): database name.
args(namedtuple): arguments from command line.
See mirtop.libs.parse.add_subparser_gff().
Returns:
reads (nested dicts):gff_list has the format as
defined in mirtop.gff.body.read().
libs
Centralize running of external commands, providing logging and tracking. Integrated from
bcbio package with some changes.
mirtop.libs.do.find_bash()
Find bash full path
mirtop.libs.do.find_cmd(cmd)
Find command in session
mirtop.libs.do.run(cmd, data=None, checks=None, region=None, log_error=True,
log_stdout=False)
Run the provided command, logging details and checking for errors.
Helpers to work with fastq files
mirtop.libs.fastq.is_fastq(in_file)
Check whether file is fastq accepting
txt, fq and fastq extensions understanding compression with gzip: .gzip and
.gz (copy from bcbio)
Args: in_file(str): file name.
Returns:
(boolean): Yes or Not.
mirtop.libs.fastq.open_fastq(in_file)
open a fastq file, using gzip if it is gzipped
(from bcbio package)
Args: in_file(str): file name.
Returns:
(File): file handler.
mirtop.libs.fastq.splitext_plus(fn)
Split on file extensions, allowing for zipped extensions.
(copy from bcbio)
Args: fn(str): file name.
Returns:
base, ext(str, str): basename and extension.
mirtop.libs.parse.parse_cl(in_args)
Function to parse the subcommands arguments.
utils from http://www.github.com/chapmanb/bcbio-nextgen.git
mirtop.libs.utils.chdir(p)
Change dir temporaly using with:
>>> with chdir(temporal):
do_something()
mirtop.libs.utils.file_exists(fname)
Check if a file exists and is non-empty.
mirtop.libs.utils.safe_dirs(dirs)
Create folder if not exitsts
mirtop.libs.utils.safe_remove(fn)
Remove file skipping
mirna
Read bam files
mirtop.mirna.annotate.annotate(reads, mature_ref, precursors, quiet=False)
Using coordinates, mismatches and realign to annotate isomiRs
Args:
reads(dicts of hits):
dict object that comes from mirotp.bam.bam.read_bam()
mirbase_ref (dict of mirna positions):
dict object that comers from mirtop.mirna.read_mature()
precursors dict object (key : fasta):
that comes from mirtop.mirna.fasta.read_precursor()
quiet(boolean):
verbosity state
Return:
reads (dict):
dictionary where keys are read_id and values are mirtop.realign.hits
Read precursor fasta file
mirtop.mirna.fasta.read_precursor(precursor, sps=None)
Load precursor file for that species
Args: precursor(str): file name with fasta sequences
sps(str): if any, select species to keep.
It'll do a header_sequence.find(sps).
Returns:
hairpin(dict): keys are precursor names and
values are precursor sequences.
Read database information
mirtop.mirna.mapper.get_primary_transcript(database)
Get the ID to identify the primary transcript in the
GTF file with the miRNA and precursor coordinates to be able to parse BAM
files with genomic coordinates.
mirtop.mirna.mapper.guess_database(args)
Guess database name from GFF file.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
database(str): name of the database
TODO: this needs to be generic to other databases.
mirtop.mirna.mapper.read_gtf_chr2mirna(gtf)
Load GTF file with precursor positions on genome.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
db_mir(dict): dictionary with keys being chr and values
mirna and genomic positions.
mirtop.mirna.mapper.read_gtf_to_mirna(gtf)
Load GTF file with precursor positions on genome.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
db_mir(dict): dictionary with keys being mirnas and values
genomic positions.
mirtop.mirna.mapper.read_gtf_to_precursor(gtf)
Load GTF file with precursor positions on genome Return dict with key being
precursor name and value a dict of mature miRNA with relative position to
precursor.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
map_dict(dict):
>>> {'parent': {mirna: [start, end]}}
mirtop.mirna.mapper.read_gtf_to_precursor_mirbase(gtf, format='precursor')
Load GTF file with precursor positions on genome Return dict with key being
precursor name and value a dict of mature miRNA with relative position to
precursor. For miRBase and similar GFF3 files.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
map_dict(dict):
>>> {'parent': {mirna: [start, end]}}
mirtop.mirna.mapper.read_gtf_to_precursor_mirgenedb(gtf, format='precursor')
Load GTF file with precursor positions on genome Return dict with key being
precursor name and value a dict of mature miRNA with relative position to
precursor. For MirGeneDB and similar GFF3 files.
Args:
gtf(str): file name with GFF miRNA genomic positions and
header lines.
Returns:
map_dict(dict):
>>> {'parent': {mirna: [start, end]}}
mirtop.mirna.realign.align(x, y, local=False)
Pairwise alignments between two sequenes.
https://medium.com/towards-data-science/pairwise-sequence-alignment-using-biopython-d1a9d0ba861f
Args: x(str): short sequence.
y(str): long sequence.
local(boolean): local or global alignment.
Returns:
aligned_x(hit): alignment information, socre and positions.
mirtop.mirna.realign.align_from_variants(sequence, mature, variants)
Giving the sequence read,
the mature from get_mature_sequence, and the variant GFF annotation: get a
list of substitutions
Args: sequence(str): read sequence.
mature(str): mature sequence from
mirtop.mirna.realing.get_mature_sequence().
variants(str): string from Variant attribute in GFF file.
Returns:
snp(list): [[pos, target, reference]]
mirtop.mirna.realign.cigar2snp(cigar, reference)
From a CIGAR string and reference sequence detect mistmatches positions and
reference and target nucleotides.
Args: cigar(str): CIGAR string.
reference(str): reference sequence.
Returns:
snp(list): position of mismatches (indels included) as:
>>> [pos, seq_nt, ref_nt]
mirtop.mirna.realign.cigar_correction(cigarLine, query, target)
Read from CIGAR in BAM file to define mismatches.
Args: cirgarLine(str): CIGAR string from BAM file.
query(str): read sequence.
target(str): target sequence.
Returns:
(list): [query_nts, target_nts]
mirtop.mirna.realign.expand_cigar(cigar)
From short CIGAR version to long CIGAR version where each character is each nts in
the sequence.
Args: cigar(str): CIGAR string.
>>> 10MA3M
Returns:
cigar_long(str): CIGAR long.
>>> MMMMMMMMMMAMMM
mirtop.mirna.realign.get_mature_sequence(precursor, mature, exact=False, nt=5)
From precursor and mature positions
get mature sequence with +/- 4 flanking nts.
Args: precursor(str): long sequence.
mature(list): [start, end].
exact(boolean): not add 4+/- flanking nts.
nt(int): number of nts to get.
Returns:
(str): mature sequence.
class mirtop.mirna.realign.hits
"Class with alignment information.
mirtop.mirna.realign.is_sequence(seq)
This function check whether the sequence is valid or not.
Args: seq(str): string acting as a sequence.
Returns:
boolean: whether is or not a valid nucleotide sequence.
class mirtop.mirna.realign.isomir
Class to represent isomiRs information.
format(sep='\t')
Create tabular line from variant fields.
formatGFF()
Create Variant attribute.
format_id(sep='\t')
Create simple identifier from variant fields.
get_score(sc)
Get score from variant fields.
is_iso()
Define whether element is isomiR or not.
set_pos(start, l, strand='+')
Set end position
mirtop.mirna.realign.make_cigar(seq, mature)
Function that will create CIGAR string from aligment between read and reference
sequence.
Args: seq(str): read sequence.
mature(str): short sequence.
Return:
short(str): CIGAR string.
mirtop.mirna.realign.make_id(seq)
Create a unique identifier for the sequence from the nucleotides, replacing 5 nts
for a unique sequence.
It uses the code from mirtop.mirna.keys().
Inspired by MINTplate: https://cm.jefferson.edu/MINTbase
https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates
Args: seq(str): nucleotides sequences.
Returns:
idName(str): unique identifier for the sequence.
mirtop.mirna.realign.read_id(idu)
Read a unique identifier for the sequence and convert it to the nucleotides,
replacing an unique code for 5 nts.
It uses the code from mirtop.mirna.keys().
Inspired by MINTplate: https://cm.jefferson.edu/MINTbase
https://github.com/TJU-CMC-Org/MINTmap/tree/master/MINTplates
Args: idu(str): unique identifier for the sequence.
Returns:
seq(str): nucleotides sequences.
mirtop.mirna.realign.reverse_complement(seq)
Get reverse complement of a sequences
Args: seq(str): sequence.
>>> GCAT
Returns:
(str): reverse complemente sequence:
>>> ATGC
mirtop.mirna.realign.variant_to_3p(hairpin, pos, variant)
From a sequence and a start position get the nts
+/- indicated by iso_3p. Pos option is 0-base-index
Args:
hairpin(str): long sequence:
>>> AAATTTT
position(int): >>> 3
variant(int): number of nts involved in the variant:
>>> -1
Returns:
(str): nucleotide involved in the variant:
>>> A
mirtop.mirna.realign.variant_to_5p(hairpin, pos, variant)
From a sequence and a start position get the nts
+/- indicated by iso_5p. Pos option is 0-base-index
Args:
hairpin(str): long sequence:
>>> AAATTTT
position(int): >>> 3
variant(int): number of nts involved in the variant:
>>> -1
Returns:
(str): nucleotide involved in the variant:
>>> T
mirtop.mirna.realign.variant_to_add(read, variant)
From a sequence and a start position get the nts
+/- indicated by iso_3p. Pos option is 0-base-index
Args:
hairpin(str): long sequence:
>>> AAATTTT
position(int): >>> 3
variant(int): number of nts involved in the variant:
>>> 2
Returns:
(str): nucleotide involved in the variant:
>>> TT
mirtop.mirna.snps.create_vcf(isomirs, matures, gtf, vcf_file=None)
Create vcf file of changes for all samples. PASS will be ones with > 3 isomiRs
supporting the position and > 30% of reads, otherwise LOW
mirtop.mirna.snps.liftover(pass_pos, matures)
Make position at precursor scale
mirtop.mirna.snps.liftover_to_genome(pass_pos, gtf)
Liftover from precursor to genome
mirtop.mirna.snps.print_vcf(data)
Print vcf line following rules.
classes
class mirtop.mirna.realign.hits
"Class with alignment information.
class mirtop.mirna.realign.isomir
Class to represent isomiRs information.
format(sep='\t')
Create tabular line from variant fields.
formatGFF()
Create Variant attribute.
format_id(sep='\t')
Create simple identifier from variant fields.
get_score(sc)
Get score from variant fields.
is_iso()
Define whether element is isomiR or not.
set_pos(start, l, strand='+')
Set end position
AUTHOR
Lorena Pantano, Thomas Desvignes, Karen EIlbeck, Ioannis Vlachos, Bastian Fromm, Marc K.
Halushka, Michael Hackenberg, Gianvito Urgese
COPYRIGHT
2022, Lorena Pantano, Thomas Desvignes, Karen EIlbeck, Ioannis Vlachos, Bastian Fromm,
Marc K. Halushka, Michael Hackenberg, Gianvito Urgese