Tophat.py - working with tophat/cufflinks output files

Author:Andreas Heger Release:$Id$ Date:December 09, 2013 Tags:Python

Code

Tophat.parseTranscriptComparison(infile)

read cufflinks 1.0.3 output in infile stream.

returns a two-level dictionary mapping with levels track and contig.

class Tophat.Locus

Bases: tuple

Locus(locus_id, contig, strand, start, end, transcript_ids, transcripts)

contig

Alias for field number 1

count(value) → integer -- return number of occurrences of value

end

Alias for field number 4

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

locus_id

Alias for field number 0

start

Alias for field number 3

strand

Alias for field number 2

transcript_ids

Alias for field number 5

transcripts

Alias for field number 6

class Tophat.Tracking

Bases: tuple

Tracking(transfrag_id, locus_id, ref_gene_id, ref_transcript_id, code, transcripts)

code

Alias for field number 4

count(value) → integer -- return number of occurrences of value

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

locus_id

Alias for field number 1

ref_gene_id

Alias for field number 2

ref_transcript_id

Alias for field number 3

transcripts

Alias for field number 5

transfrag_id

Alias for field number 0

Tophat.TranscriptInfo

alias of Transfrag

Tophat.iterate_tracking(infile)

parse .tracking output file from cuffcompare

returns iterator with list of loci.

Tophat.iterate_locus(infile)

parse .loci output file from cuffcompare

returns iterator with list of loci.