Code: pylprotpredictor module

CDS class

class pylprotpredictor.cds.CDS(seq_id='', origin_seq=None, origin_seq_id='', start=-1, end=-1, strand='forward', seq=None, alternative_ends=[], alternative_cds=[], alignments=[], conserved_cds=None, rejected_cds=[], status='')

Class to describe a CDS

add_alignment(alignment)

Add an alignment object to the list of alignment

Parameters:alignment – an alignment object

add_alternative_cds(alternative_cds)

Add an alternative CDS to the list of possible alternative CDS

Parameters:alternative_cds – a CDS object

add_id_alignment(seq_id, alignment)

Add alignment to the correct CDS object

Parameters:

• seq_id – id of the CDS
• alignment – alignment object to add

add_rejected_cds(rejected_cds)

Add a rejected CDS to the list of rejected CDS

Parameters:rejected_cds – a CDS object

export_description()

Export the description of the CDS

Returns:string with the description

export_to_dict()

Export the object to CDS

Returns:dict corresponding to CDS object

extract_possible_alternative_seq()

Extract the start, end and sequence of different possible sequences for a CDS identified as potential PYL CDS

find_alternative_ends()

Find alternative ends (on the same ORF) for a CDS until the next found STOP codon on the genome (or its complement if the CDS is on the reverse strand)

get_alignments()

Return the list of alignments

Returns:list of alignment object

get_alternative_cds()

Return the list of possible alternative CDS if the CDS is ending with TAG STOP codon

Returns:list of CDS object

get_alternative_end()

Return the list of alternative CDS end

Returns:list of the end of the alternative CDS

get_alternative_ends()

Return the list of possible alternative ends if the CDS is ending with TAG STOP codon

Returns:list of int corresponding to the alternative ends

get_alternative_start()

Return the list of alternative CDS start

Returns:list of the start of the alternative CDS

get_conserved_cds()

Return the CDS object of the conserved CDS as correct CDS (start, end, sequence)

Returns:CDS object of the conserved CDS

get_end()

Return the end position of the CDS on the origin sequence

Returns:int corresponding to the end position

get_highest_bitscore()

Return the highest bitscore for all alignments

Returns:float

get_id()

Return the id of the CDS

Returns:string corresponding to the id

get_lowest_evalue_alignment()

Return the alignment with the lowest evalue

Returns:alignment

get_origin_seq()

Return the SeqRecord object corresponding to the origin seq of the CDS

Returns:SeqRecord object

get_origin_seq_id()

Return the id of origin seq of the CDS

Returns:string corresponding to the origin seq

get_origin_seq_size()

Return the length of the origin sequence

Returns:int corresponding to the length of the origin sequence

get_origin_seq_string()

Return the string of the origin sequence

Returns:string corresponding to the origin sequence

get_rejected_cds()

Return a list of the rejected CDS objects as correct CDS (start, end, sequence)

Returns:list of CDS objects

get_seq()

Return the sequence of the CDS

Returns:string with the sequence

get_seqrecord()

Return a SeqRecord of the CDS

Returns:SeqRecord

get_start()

Return the start position of the CDS on the origin sequence

Returns:int corresponding to the start position

get_status()

Return the status

Returns:string with the status of the CDS

get_stop_codon()

Return the STOP codon of the CDS

Returns:the STOP codon

get_strand()

Return the strand of the CDS on the origin sequence

Returns:string corresponding to the strand (forward or reverse)

get_translated_alternative_seq()

Return a list of the translated sequences of the alternative sequences

Returns:list of SeqRecord objects

get_translated_seq()

Return the translated sequence of the CDS

Returns:SeqRecord object corresponding to the translated sequence

has_alternative_cds()

Test if the CDS has alternative cds

Returns:boolean

has_alternative_ends()

Test if the list of alternative ends is not empty

Returns:boolean

has_origin_seq()

Test if the CDS has a origin seq

Returns:boolean

identify_cons_rej_cds()

Identify which alternative CDS to converse or reject based on the evalue and the alignment length: Keep the sequence with a lowest evalue and a longer alignment

Returns:better alignment

init_from_dict(in_dict)

Initiate a CDS instance with a dictionary

Parameters:in_dict – dictionary with attribute for a CDS object

init_from_record(record)

Initiate a CDS instance with a SeqRecord object

Parameters:record –

is_potential_pyl()

Test if the sequence has a status for potential pyl

Returns:boolean

is_reverse_strand()

Test if the strand is reverse

Returns:boolean

is_tag_ending()

Test if the sequence has a status for tag-ending

Returns:boolean

is_tag_ending_seq()

Test if the sequence is ending with TAG STOP codon

Returns:boolean

reset_alignments()

Reset the list of alignments

reset_alternative_cds()

Reset the list of alternative cds

reset_rejected_cds()

Reset the list of rejected cds

set_alternative_ends(alternative_ends)

Change the list of alternative ends

Parameters:alternative_ends – list of int corresponding to the new alternative ends

set_conserved_cds(conserved_cds)

Change the conserved CDS

Parameters:conserved_cds – CDS object of the conserved CDS

set_end(end)

Change the end position of the CDS

Parameters:end – new end value (int)

set_evalue(evalue)

Change the evalue

Parameters:evalue – new evalue

set_id(seq_id)

Change the id of the CDS

Parameters:seq_id – new seq id value

set_origin_seq(origin_seq)

Change the SeqRecord object corresponding to the origin seq of the CDS

Parameters:origin_seq – SeqRecord object

set_origin_seq_id(origin_seq_id)

Change the id of the origin sequence of the CDS

Parameters:origin_seq_id – new origin seq id value

set_seq(seq)

Change the sequence object of the CDS

Parameters:seq – new Seq object with the sequence of the CDS

set_start(start)

Change the start position of the CDS

Parameters:start – new start value (int)

set_status(status)

Change the status

Parameters:status – new status

set_strand(strand)

Change the strand value of the CDS

Parameters:end – new strand (forward or reverse)

pylprotpredictor.cds.extract_seq_desc(desc)

Extract from description the seq id, the origin sequence, start, end and strand from a predicted CDS

Parameters:desc – description of a prediced CDS with Prodigal Returns:id of predicted CDS Returns:id of the origin sequence Returns:start position of the predicted CDS Returns:end position of the predicted CDS Returns:strand of the predicted CDS

pylprotpredictor.cds.find_stop_codon_pos_in_seq(seq)

Find position of STOP codon inside a sequence (not the last position)

Parameters:seq – string sequence of amino acids Returns:list of position for possible STOP codons in a sequence

pylprotpredictor.cds.test_to_continue(end, origin_seq_size)

Test if possible to extract next codon: position still in the genome

Parameters:

• end – int corresponding to the current end
• origin_seq_size – size of the origin sequence

Returns:

boolean

pylprotpredictor.cds.transform_strand(strand_id)

Transform strand from numerical value to string value

Parameters:strand_id – numerical value to represent a strand (1 or -1) Returns:string value (forward or reverse) for the strand

pylprotpredictor.cds.translate(seq)

Translate a sequence into amino acids while replacing any possible STOP codon encoded by TAG by a Pyl amino acid

Parameters:seq – a Seq object Returns:string with the corresponding amino acid sequence with the TAG encoded STOP are replaced by Pyl amino acid

Alignment class

class pylprotpredictor.alignment.Alignment(sseqid='', pident=0, length=0, mismatch=0, gapopen=0, qstart=0, qend=0, sstart=0, send=0, evalue=10, bitscore=0)

Class to describe a DIAMOND alignment

get_bitscore()

Return bit score

Returns:query sequence id

get_evalue()

Return expect value

Returns:float

get_gapopen()

Return number of gap openings

Returns:int

get_length()

Return alignment length

Returns:int

get_mismatch()

Return number of mismatches

Returns:int

get_pident()

Return percentage of identical matches

Returns:float

get_qend()

Return end of alignment in query

Returns:int

get_qstart()

Return query sequence id

Returns:query sequence id

get_send()

Return end of alignment in subject

Returns:int

get_sseqid()

Return query sequence id

Returns:string

get_sstart()

Return start of alignment in subject

Returns:int

init_from_search_report_row(row)

Initiate an Alignment instance with a row extracted from a BLAST/DIAMOND table

Parameters:row – a pandas row

set_bitscore(bitscore)

Modify bit score

Parameters:bitscore – int

set_evalue(evalue)

Modify evalue

Parameters:evalue – float

set_gapopen(gapopen)

Modify number of gap openings

Parameters:gapopen – string

set_length(length)

Modify alignment length

Parameters:length – int

set_mismatch(mismatch)

Modify number of mismatches

Parameters:mismatch – int

set_pident(pident)

Modify percentage of identical matches

Parameters:pident – float

set_qend(qend)

Modify end of alignment in query

Parameters:qend – string

set_qstart(qstart)

Modify start of alignment in query

Parameters:qstart – string

set_send(send)

Modify end of alignment in subject

Parameters:send – int

set_sseqid(sseqid)

Modify query Seq-id

Parameters:sseqid – string

set_sstart(sstart)

Modify start of alignment in subject

Parameters:sstart – int

Predict

pylprotpredictor.predict.extract_potential_pyl_cds(pred_cds, pot_pyl_cds_filepath, pot_pyl_cds_info_filepath, pred_cds_obj_filepath)

Extract potential PYL CDS from TAG-ending CDS

Parameters:

• pred_cds – a dictionary with the predicted CDS represented as CDS objects
• pot_pyl_cds_filepath – path to fasta file in which the protein sequences of the potential PYL CDS are saved
• pot_pyl_cds_info_filepath – path to a cvs file to get information about potential PYL CDS
• pred_cds_obj_filepath – path to generated JSON file to store the list of predicted CDS objects

pylprotpredictor.predict.extract_predicted_cds(pred_cds_path, pred_cds_info_path, tag_ending_cds_info_path, genome_filepath)

Extract the list of predicted CDS and identify the CDS ending with TAG STOP codon

Parameters:

• pred_cds_path – path to the output of CDS prediction (Prodigal)
• pred_cds_info_path – path to a CSV file in which the information (start, end, strand, origin) are collected for each predicted CDS
• tag_ending_cds_info_path – path to CSV file to export the information about the TAG ending CDS
• genome_filepath – path to reference genome

Returns:

a dictionary with the predicted CDS represented by CDS object

pylprotpredictor.predict.extract_seqs(seq_filepath)

Extract the sequences in a fasta file

Parameters:seq_filepath – path to a fasta file Returns:a dictionary with all sequences indexed by their id, their length and their complement sequence

pylprotpredictor.predict.predict_pyl_proteins(genome_filepath, pred_cds_filepath, pot_pyl_seq_filepath, log_filepath, pred_cds_info_filepath, tag_ending_cds_info_filepath, pot_pyl_seq_info_filepath, pred_cds_obj_filepath)

Run prediction of potentila PYL CDS:

• Extraction of predicted CDS into a dictionary
• Identification of TAG-ending proteins
• Extraction of potential PYL sequences

Parameters:

• genome_filepath – path to file with genome sequence
• pred_cds_filepath – path to the output of CDS prediction (Prodigal)
• pot_pyl_seq_filepath – path to fasta file with potential PYL CDS sequence
• log_filepath – path to log file
• pred_cds_info_filepath – path to CSV file with predicted CDS info
• tag_ending_cds_info_filepath – path to CSV file with TAG-ending CDS info
• pot_pyl_seq_info_filepath – path to CSV file with potential PYL CDS info
• pred_cds_obj_filepath – path to generated JSON file to store the list of predicted CDS objects

Check

pylprotpredictor.check.check_pyl_proteins(pot_pyl_similarity_search, pred_cds_obj_filepath, cons_pred_cds_seq, info_filepath)

Check predicted PYL CDS:

• Get the potential PYL CDS
• Parse the similarity search report
• Identify and extract the correct CDS sequence (the one with the lowest evalue and longest alignment for potential PYL)

Parameters:

• pot_pyl_similarity_search – path to similarity search report of potential PYL CDS against a reference database
• pred_cds_obj_filepath – path to generated JSON file to store the list of predicted CDS objects
• cons_pred_cds_seq – path to a FASTA file for the conserved CDS sequences
• info_filepath – path to a CSV file with final information about the CDS

pylprotpredictor.check.extract_correct_cds(pred_cds, cons_pred_cds_seq, info_filepath)

Identify and extract the correct CDS sequence

Parameters:

• pred_cds – dictionary of the predicted CDS
• cons_pred_cds_seq – path to a FASTA file for the conserved CDS sequences
• info_filepath – path to a CSV file with final information about the CDS

pylprotpredictor.check.get_cds_obj(cds_id, pred_cds)

Find the CDS object given an id

Parameters:

• cds_id – id of the CDS to find
• pred_cds – dictionary of the predicted CDS

Returns:

a CDS object

pylprotpredictor.check.import_cds(cds_obj_filepath)

Parameters:cds_obj_filepath – path to JSON file with collection of CDS objects Returns:dictionary of the CDS objects

pylprotpredictor.check.parse_similarity_search_report(pot_pyl_similarity_search, pred_cds)

Parse the similarity search report and add information to the list of potential PYL CDS

Parameters:

• pot_pyl_similarity_search – path to similarity search report of potential PYL CDS against a reference database
• pred_cds – dictionary of the predicted CDS

Write report

pylprotpredictor.write_report.extract_row_number(csv_filepath)

Extract row number of a CSV file

Parameters:csv_filepath – path to a CSV file Returns:an integer corresponding to the number of lines in the CSV file

pylprotpredictor.write_report.write_report(pred_cds, tag_ending_cds, pot_pyl_cds, final_cds, report_filepath)

Write HTML report to summarize the full analysis

Parameters:

• pred_cds – path to CSV file with predicted CDS info
• tag_ending_cds – path to CSV file with TAG-ending CDS info
• pot_pyl_cds – path to CSV file with potential PYL CDS info
• final_cds_info – path to a CSV file with final information about the CDS
• report_filepath – path to HTML file in which writing the report