seriesoftubes.converters

conversion/discover tools for file formats most of these can be run as scripts

seriesoftubes.converters.discover

seriesoftubes.converters.discover.discover_file_format(filename)

discover the format of a file returns a tuple (open_function, ‘FORMAT’)

open_function will either be open, gzip.GzipFile, bz2.BZ2File, or None FORMAT can be ‘BAM’, ‘SAM’, ‘FASTQ’, ‘FASTA’, or None

seriesoftubes.converters.cat

Writes file(s) to stdout, decompress them if needed supports gzip, bzip2

Output is always to stdout (err goes to stderr, redirect it if you need to)

seriesoftubes.converters.cat.main()

what to do if we execute the module as a script

cat

seriesoftubes.converters.anytotab

Convert single-end or paired-end sequencing files to tab-format NAME SEQ1 QUAL1 (SEQ2 QUAL2)

Supports FASTQ (plaintext, gzip and bz2), SAM, BAM Output is always to stdout (err goes to stderr, redirect it if you need to)

seriesoftubes.converters.anytotab.main()

what to do if we execute the module as a script

seriesoftubes.converters.bamtofastq

Convert BAM/SAM to FASTQ format* @name sequence +name quality score (phred33)

files may be SAM or BAM (autodetected) If the file(s) contain paired-end sequences, we will write to two files (in the current working directory) If the files contain single end sequences, we will write to stdout by default Output is always to stdout (err goes to stderr, redirect it if you need to)

class seriesoftubes.converters.bamtofastq.UnpairedBAMToFastqConverter(file_, wd=None, stderr=None, logger=None)

Works with unpaired SAM/BAM file

seriesoftubes.converters.bamtofastq.main()

what to do if we execute the module as a script

bamtofastq can only convert files (not stdin) because of the paired-end problem

seriesoftubes.converters.bamtofastq.read_files(files=None, no_gzip=False, single_stdout=<open file '<stdout>', mode 'w' at 0x7f7ed30871e0>)

actually reads the SAM/BAM files

seriesoftubes.converters.bamtofastq2

Another module for converting bamtofastq, defaults to writing gzfiles Accepts only one input file

Includes class for converting paired-end sequencing files to two fastq pipes

Supports SAM, BAM

class seriesoftubes.converters.bamtofastq2.PairedBAMToFastqConverter(file_, wd=None, stderr=None, logger=None)

Works with any SAM/BAM file

seriesoftubes.converters.bamtofastq2.main()

what to do if we execute the module as a script (not intended for user by user)

seriesoftubes.converters.bamtotab

Convert BAM/SAM to tab-format

NAME SEQ1 QUAL1 SEQ2 QUAL2

files may be SAM or BAM (autodetected)

Output is always to stdout (err goes to stderr, redirect it if you need to)

seriesoftubes.converters.bamtotab.main()

what to do if we execute the module as a script bamtotab can only convert files because of the paired-end problem

seriesoftubes.converters.fastqtotab

Convert single or pairs of FASTQ files to tab-format

NAME SEQ1 QUAL1 (SEQ2 QUAL2)

Output is always to stdout (err goes to stderr, redirect it if you need to)

seriesoftubes.converters.fastqtotab.main()

what to do if we execute the module as a script

fastqtotab can only convert files because of the paired-end problem

seriesoftubes.converters.fastqtotab.read_files(file1, file2, open_func)

We do not validate records here