API reference

class seqreport.SeqCollection(records, cost_per_base=0.25, cost_per_seq=0, currency_symbol='£', projectname='', comments='', min_length=100, max_length=3000, name_length=15, assembly_plan='', fasta_name='')

Class to store basic properties of a collection of sequences.

Parameters:

  • records (list) – A list of Biopython SeqRecords.

  • cost_per_base (float) – Cost per nucleotide base.

  • cost_per_seq (float) – Fix overhead cost for each sequence part (cloning, delivery costs etc).

  • currency_symbol (str) – The currency symbol (or string) to display in the report.

  • projectname (str) – The name of the project.

  • comments (str) – Any comments to be included in the report.

  • min_length (int) – Check that all sequences are at least this long.

  • max_length (int) – Check that all sequences are at most this long.

  • name_length (int) – Check which sequence IDs are longer than this cutoff. Genbank has a character limit.

  • assembly_plan (str, optional) – Optional assembly plan CSV path for calculating savings by re-using DNA parts.

  • fasta_name (str, optional) – Optional name of the FASTA file for easy identification.

class seqreport.read_fasta(fasta)

Read a FASTA sequence file into a list of records.

Parameters:

fasta (str) – The FASTA filepath.

class seqreport.seqcollection_from_csv(csv_file, records=None, param_dict={})

Create a SeqCollection, using parameters in a CSV file.

The CSV file parameters override the default class parameters, and this function’s parameters override the CSV file parameters. Either a FASTA file (in the CSV or in param_dict) or a list of SeqRecords must be specified. For the parameter descriptions, see parameters in the docstring of SeqCollection, except records and fasta_name.

class seqreport.write_pdf_report(target, seqcollection)

Write a sequence collection report with a PDF summary.

Parameters:

  • target (str) – Path for PDF file.

  • seqcollection (SeqCollection) – A SeqCollection instance.