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        "author_email": "developer@twlee.nz",
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        "description": "# filter_illumina_index\n## Filter a Illumina FASTQ file based on index sequence.\n\nReads a Illumina FASTQ file and compares the sequence index in the\n`sample number` position of the sequence identifier to a supplied sequence\nindex. Entries that match the sequence index are filtered into the *filtered\nfile* (if any) and entries that don't match are filtered into the *unfiltered\nfile* (if any). Displays the count of total, filtered and unfiltered reads,\nas well as the number of mismatches found across all reads. Matching tolerating\na certain number of mismatches (`-m` parameter), and gzip compression for input\n(detected on the basis of file extension) and output (specified using `-c`\nparameter) are supported.\n\nFor 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\n\n### Usage details\n\n```\nusage: filter_illumina_index [-h] [--version] [-f FILTERED] [-u UNFILTERED] -i\n                             INDEX [-m MISMATCHES] [-c] [-v]\n                             inputfile\n\npositional arguments:\n  inputfile             Input FASTQ file, compression supported\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --version             show program's version number and exit\n  -f FILTERED, --filtered FILTERED\n                        Output FASTQ file containing filtered (positive) reads\n                        (default: None)\n  -u UNFILTERED, --unfiltered UNFILTERED\n                        Output FASTQ file containing unfiltered (negative)\n                        reads (default: None)\n  -m MISMATCHES, --mismatches MISMATCHES\n                        Maximum number of mismatches to accept (default: 0)\n  -c, --compressed      Compress output files (note: file extension not\n                        modified) (default: False)\n  -v, --verbose         Show verbose output (default: False)\n\nrequired named arguments:\n  -i INDEX, --index INDEX\n                        Sequence index to filter for (default: None)\n```\n\n### Example usage\n\nThe directory `srv` contains example reads in FASTQ and compressed FASTQ format with index `GATCGTGT` and one read with a mismatch.\n\nTo test, run:\n\n`filter_illumina_index srv/example_reads.fastq --index GATCGTGT --filtered var/filtered_reads.fastq --unfiltered var/unfiltered_reads.fastq`\n\nThis 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:\n\n```\nTotal reads: 30\nFiltered reads: 29\nUnfiltered reads: 1\n Reads with 0 mismatches: 29\n Reads with 1 mismatches: 1\n Reads with 2 mismatches: 0\n Reads with 3 mismatches: 0\n Reads with 4 mismatches: 0\n Reads with 5 mismatches: 0\n Reads with 6 mismatches: 0\n Reads with 7 mismatches: 0\n Reads with 8 mismatches: 0\n```\n\n---\n\n### Additional details\n\n* Author:       Tet Woo Lee\n* Copyright:    \u00a9 2018 Tet Woo Lee\n* Licence:      GPLv3\n* Dependencies: Biopython, tested on v1.72\n\n### Change log\n\nversion 1.0.2 2018-12-19\n: Shows statistics on number of mismatches found\n\nversion 1.0.1 2018-12-19\n: Speed up number of mismatches calculation\n\nversion 1.0 2018-12-14\n: Minor updates for PyPi and conda packaging\n\nversion 1.0.dev1 2018-12-13\n: First working version\n\n\n",
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