filter-illumina-index 1.0.3

Filter a Illumina FASTQ file based on index sequence

filter_illumina_index

Filter a Illumina FASTQ file based on index sequence.

Reads a Illumina FASTQ file and compares the sequence index in the sample number position of the sequence identifier to a supplied sequence index. Entries that match the sequence index are filtered into the filtered file (if any) and entries that don't match are filtered into the unfiltered file (if any). Displays the count of total, filtered and unfiltered reads, as well as the number of mismatches found across all reads. Matching tolerating a certain number of mismatches (-m parameter), and gzip compression for input (detected on the basis of file extension) and output (specified using -c parameter) are supported.

Specifying an empty index, (-i "") enables 'passthrough' mode where all reads are directed to the output filtered file with no processing. Passthrough mode is useful if this program is part of a workflow that needs to be adapted to files that do not have a valid Illumina index, as it allows any processing of this program to be skipped.

For information on Illumina sequence identifiers in FASTQ files, see: http://support.illumina.com/content/dam/illumina-support/help/BaseSpaceHelp_v2/Content/Vault/Informatics/Sequencing_Analysis/BS/swSEQ_mBS_FASTQFiles.htm

Usage details

usage: filter_illumina_index [-h] [--version] [-f FILTERED] [-u UNFILTERED] -i
                             INDEX [-m MISMATCHES] [-c] [-v]
                             inputfile

positional arguments:
  inputfile             Input FASTQ file, compression supported

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -f FILTERED, --filtered FILTERED
                        Output FASTQ file containing filtered (positive) reads
                        (default: None)
  -u UNFILTERED, --unfiltered UNFILTERED
                        Output FASTQ file containing unfiltered (negative)
                        reads (default: None)
  -m MISMATCHES, --mismatches MISMATCHES
                        Maximum number of mismatches to tolerate (default: 0)
  -c, --compressed      Compress output files (note: file extension not
                        modified) (default: False)
  -v, --verbose         Show verbose output (default: False)

required named arguments:
  -i INDEX, --index INDEX
                        Sequence index to filter for; if empty (i.e. "") then
                        program will run in "passthrough" mode with all reads
                        directed to filtered file with no processing (default:
                        None)

Example usage

The directory srv contains example reads in FASTQ and compressed FASTQ format with index GATCGTGT and one read with a mismatch.

To test, run:

filter_illumina_index srv/example_reads.fastq --index GATCGTGT --filtered var/filtered_reads.fastq --unfiltered var/unfiltered_reads.fastq

This will process srv/example_reads.fastq, matching to index GATCGTGT with no mismatches allowed (default). Reads matching this index will be saved to var/filtered_reads.fastq and those not matching this index will be saved to var/unfiltered_reads.fastq. In addition, the following output will be displayed:

Total reads: 30
Filtered reads: 29
Unfiltered reads: 1
 Reads with 0 mismatches: 29
 Reads with 1 mismatches: 1
 Reads with 2 mismatches: 0
 Reads with 3 mismatches: 0
 Reads with 4 mismatches: 0
 Reads with 5 mismatches: 0
 Reads with 6 mismatches: 0
 Reads with 7 mismatches: 0
 Reads with 8 mismatches: 0

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Additional details

• Author: Tet Woo Lee
• Copyright: © 2018 Tet Woo Lee
• Licence: GPLv3
• Dependencies: Biopython, tested on v1.72

Change log

version 1.0.3 2020-01-04 : Added passthrough mode with empty index.

version 1.0.2 2018-12-19 : Shows statistics on number of mismatches found

version 1.0.1 2018-12-19 : Speed up number of mismatches calculation

version 1.0 2018-12-14 : Minor updates for PyPi and conda packaging

version 1.0.dev1 2018-12-13 : First working version