labtools.adtools.finder

Module Contents

Functions

pull_AD(read[, barcoded, ad_preceder, bc_preceder, ...])

Find the activation domain tile in a read.

pull_barcode(read[, bc_preceder, bc_anteceder, bclength])

Find the barcode in a read.
labtools.adtools.finder.pull_AD(read, barcoded=False, ad_preceder='GCTAGC', bc_preceder='GGGCCCG', bc_anteceder='GGAGAGAA', ad_length=120, bclength=11, **kwargs)[source]

Find the activation domain tile in a read.

Takes a read sequence and uses customizable anchor sequences to locate a variable sequence (AD/seq of interest) in the read. Includes support for barcodes.

Parameters:

  • read (str) – The biological read of interest.

  • barcoded (bool, default False) – Whether or not the sequence includes a barcode in addition to the AD/seq of interest.

  • ad_preceder (str, default "GCTAGC") – The anchor sequence directly before the AD.

  • bc_preceder (str, default "GGGCCCG") – The anchor sequence directly before the barcode.

  • bc_anteceder (str, default "GGAGAGAA") – The anchor sequence directly after the barcode.

  • ad_length (int, default 120) – The length of the AD/seq of interest.

  • bc_length (int, default 11) – The length of the barcode sequence if used.

Returns:

  • AD (str) – The sequence of interest, if located. Else None.

  • barcode (str) – The barcode, if used and located. Else None.

Examples

>>> pull_AD("ACTTTTATVGCTAGCATGGCTGGTAGATCTTGGTTGATTGATTCTAATAGAATTGCTACTAAGATTATGTCTGCTTCTGCTTCTTCTGATCCAAGACAAGTTGTTTGGAAATCTAATCCATCTAGACATTGTCCAGCTGATCGATGCTAGTAGAGAGAGA")
ATGGCTGGTAGATCTTGGTTGATTGATTCTAATAGAATTGCTACTAAGATTATGTCTGCTTCTGCTTCTTCTGATCCAAGACAAGTTGTTTGGAAATCTAATCCATCTAGACATTGTCCA
labtools.adtools.finder.pull_barcode(read, bc_preceder='GGGCCCG', bc_anteceder='GGAGAGAA', bclength=11, **kwargs)[source]

Find the barcode in a read.

Takes a read sequence and uses customizable anchor sequences to locate a variable sequence (barcode) in the read.

Parameters:

  • read (str) – The biological read of interest.

  • bc_preceder (str, default "GGGCCCG") – The anchor sequence directly before the barcode.

  • bc_anteceder (str, default "GGAGAGAA") – The anchor sequence directly after the barcode.

  • bc_length (int, default 11) – The length of the barcode sequence if used.

Returns:

barcode – The barcode, if used and located. Else None.

Return type:

str

Examples

>>> pull_barcode("ACTTTTATVGCTAGCATGGCTGGTAGATCTTGGTTGATTGATTCTAATAGAATTGCTACTAAGATTATGTCTGCTTCTGCTTCTTCTGATCCAAGACAAGTTGTTTGGAAATCTAATCCATCTAGACATTGTCCAGCTGATCGATGCTAGTAGAGAGAGA")
ATGGCTGGTAGATCTTGGTTGATTGATTCTAATAGAATTGCTACTAAGATTATGTCTGCTTCTGCTTCTTCTGATCCAAGACAAGTTGTTTGGAAATCTAATCCATCTAGACATTGTCCA