Filter a Illumina FASTQ file based on index sequence
Project description
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 ""
or -i
with no argumenent) 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 all 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. no
argument or "") 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:
filter_illumina_index 1.0.3.post2
Input file: srv/example_reads.fastq
Filtering for sequence index: GATCGTGT
Max mismatches tolerated: 0
Output filtered file: var/filtered_reads.fastq
Output unfiltered file: var/unfiltered_reads.fastq
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
Additional details
- Author: Tet Woo Lee
- Copyright: © 2018-2020 Tet Woo Lee
- Licence: GPLv3
- Dependencies: Biopython, tested on v1.72
Change log
version 1.0.3.post2 2020-01-04
Improved output
- Add version number to output
- Show parameters in output
- Allow no argument for passthrough mode
version 1.0.3.post1 2020-01-04
Minor bugfix
- Bugfix: Bump version number in script
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
Project details
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