Module DIGEST_functions

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Module DIGEST_functions

source code

Class and functions use by the DIGEST workflow

Requires:

jobArrayLSFlauncher_modif.sh
mpirun-genoscope-modif.sh

Classes

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MyDialect
csv class use to read csv files

jobLauncher
Create class able to launch a list of jobs on SLURM or LSF on a Job Scheduler

sequence
New sequence object

ORF
New ORF object from MetaGene output

ContigORF
New contig ORF object from MetaGene output

Cigar
New alignment CIGAR object

alignmentSAM
New alignmentSAM object from a line of a SAM file, see SAM format for more informations

cluster
New cluster object

clusterSequence
New sequence in a cluster object

Functions

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integer

exist(fname)
Check the existence of a file.

source code

list

clstrParser(file)
parse .clstr file from cd hit

source code

dictionary

fastaReader(file)
Fasta parser

source code

booleen

geneExtended(orfSTART, orfEND, alignSTART, alignEND, orfSTATUT)
Check if a gene has been extended

source code

booleen

geneSeen(orfSTART, orfEND, alignSTART, alignEND)
Check if a gene has been seen

source code

string

reverseComplement(sequen)
make the reverse complement of a sequence

source code

dictionary

metageneParser(file)
Sotck ORFs of metagene file

source code

list

subjectStartStop(alignment, subjectLength)
From an alignment and a length, compute the start and stop alignment position

source code

integer

fileLineNumber(file)
Compute the int number of lines from a file

source code

integer

nbSequenceFasta(file)
Compute the number of sequences in a FASTA file

source code

writeORF(ORFlist, prefix, ID, sequence, n)
write ORFs in PREFIX_complete.fasta file or PREFIX_partial.fasta file

source code

Variables

[hide private]

__doc__ = ...

__package__ = None

Function Details

[hide private]

exist(fname)

source code

Check the existence of a file.

Parameters:

fname (string) - file name

Returns: integer

1 if the file is present, 0 otherwise

clstrParser(file)

source code

parse .clstr file from cd hit

Parameters:

file (string) - file name

Returns: list

list of cluster object

fastaReader(file)

source code

Fasta parser

Parameters:

file (string) - file name

Returns: dictionary

dictionnary of sequence object with sequence ID as key

geneExtended(orfSTART, orfEND, alignSTART, alignEND, orfSTATUT)

source code

Check if a gene has been extended

Parameters:

orfSTART (integer) - ORF start position in sequence extended
orfEND (integer) - ORF end position in sequence extended
alignSTART (integer) - alignement start position of sequence on contig
alignEND (integer) - alignement end position of sequence on contig
orfSTATUT (string) - ORF complete or partial

Returns: booleen

True if the gene is completed, Fasle otherwise

geneSeen(orfSTART, orfEND, alignSTART, alignEND)

source code

Check if a gene has been seen

Parameters:

orfSTART (integer) - ORF start position in sequence extended
orfEND (integer) - ORF end position in sequence extended
alignSTART (integer) - alignement start position of sequence on contig
alignEND (integer) - alignement end position of sequence on contig

Returns: booleen

True if the gene is seen, Fasle otherwise

reverseComplement(sequen)

source code

make the reverse complement of a sequence

Parameters:

sequen (string) - nucleotide sequence

Returns: string

reverse complement of sequence

metageneParser(file)

source code

Sotck ORFs of metagene file

Parameters:

file (string) - file name

Returns: dictionary

a a dictionnary with contigs IDs as key and contig object as value

subjectStartStop(alignment, subjectLength)

source code

From an alignment and a length, compute the start and stop alignment position

Parameters:

alignment (alignmentSAM) - alignmentSAM object
subjectLength (integer) - subject sequence length

Returns: list

a list with the position start and stop of the alignment (if start = -1 --> alignment start befor the subject sequence ; if stop = -2 --> alignment stop after the subject sequence)

fileLineNumber(file)

source code

Compute the int number of lines from a file

Parameters:

file (string) - file name

Returns: integer

number of lines

nbSequenceFasta(file)

source code

Compute the number of sequences in a FASTA file

Parameters:

file (string) - file name

Returns: integer

number of sequences

writeORF(ORFlist, prefix, ID, sequence, n)

source code

write ORFs in PREFIX_complete.fasta file or PREFIX_partial.fasta file

Parameters:

ORFlist (list) - list of ORF object
prefix (string) - prefix of output file name
ID (string) - sequence ID
sequence (string) - nucleotide sequence
n (integer) - limte length for partial ORF

Variables Details

[hide private]

doc

Value:

"""
Class and functions use by the DIGEST workflow

@requires: jobArrayLSFlauncher_modif.sh
@requires: mpirun-genoscope-modif.sh
"""