ngsutils_bam_filter: filter.py annotate

annotate filter.py @ 1:8187a729d9f4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841

author	iuc
date	Sun, 06 Dec 2015 05:03:12 -0500
parents	4e4e4093d65d
children	7a68005de299

rev	line source
0 4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	1 #!/usr/bin/env python
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	2 ## category General
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	3 ## desc Removes reads from a BAM file based on criteria
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	4 """
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	5 Removes reads from a BAM file based on criteria
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	6
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	7 Given a BAM file, this script will only allow reads that meet filtering
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	8 criteria to be written to output. The output is another BAM file with the
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	9 reads not matching the criteria removed.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	10
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	11 Note: this does not adjust tag values reflecting any filtering. (for example:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	12 if a read mapped to two locations (IH:i:2), and one was removed by
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	13 filtering, the IH:i tag would still read IH:i:2).
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	14
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	15 Currently, the available filters are:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	16 -minlen val Remove reads that are smaller than {val}
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	17 -maxlen val Remove reads that are larger than {val}
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	18 -mapped Keep only mapped reads
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	19 -unmapped Keep only unmapped reads
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	20 -properpair Keep only properly paired reads (both mapped,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	21 correct orientation, flag set in BAM)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	22 -noproperpair Keep only not-properly paired reads
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	23
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	24 -mask bitmask Remove reads that match the mask (base 10/hex)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	25 -uniq {length} Remove reads that are have the same sequence
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	26 Note: BAM file should be sorted
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	27 (up to an optional length)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	28 -uniq_start Remove reads that start at the same position
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	29 Note: BAM file should be sorted
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	30 (Use only for low-coverage samples)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	31
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	32 -mismatch num # mismatches or indels
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	33 indel always counts as 1 regardless of length
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	34 (requires NM tag in reads)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	35
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	36 -mismatch_dbsnp num dbsnp.txt.bgz
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	37 # mismatches or indels - not in dbSNP.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	38 Variations are called using the MD tag.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	39 Variations that are found in the dbSNP list are
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	40 not counted as mismatches. The dbSNP list is a
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	41 Tabix-indexed dump of dbSNP (from UCSC Genome
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	42 Browser). Indels in dbSNP are also counted.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	43 Adds a 'ZS:i' tag with the number of found SNPs
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	44 in the read.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	45 (requires NM and MD tags)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	46
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	47 Example command for indexing:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	48 ngsutils tabixindex snp.txt.gz -s 2 -b 3 -e 4 -0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	49
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	50 -mismatch_ref num ref.fa # mismatches or indel - looks up mismatches
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	51 directly in a reference FASTA file
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	52 (use if NM tag not present)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	53
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	54 -mismatch_ref_dbsnp num ref.fa dbsnp.txt.bgz
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	55 # mismatches or indels - looks up mismatches
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	56 directly from a reference FASTA file. (See
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	57 -mismatch_dbsnp for dbSNP matching)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	58 (use if NM or MD tag not present)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	59
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	60 -nosecondary Remove reads that have the 0x100 flag set
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	61 -noqcfail Remove reads that have the 0x200 flag set
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	62 -nopcrdup Remove reads that have the 0x400 flag set
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	63
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	64
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	65 -exclude ref:start-end Remove reads in this region (1-based start)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	66 -excludebed file.bed {nostrand}
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	67 Remove reads that are in any of the regions
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	68 from the given BED file. If 'nostrand' is given,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	69 strand information from the BED file is ignored.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	70
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	71 -include ref:start-end Remove reads NOT in the region (can only be one)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	72 -includebed file.bed {nostrand}
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	73 Remove reads that are NOT any of the regions
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	74 from the given BED file. If 'nostrand' is given,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	75 strand information from the BED file is ignored.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	76
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	77 Note: If this is a large dataset, use
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	78 "bamutils extract" instead.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	79
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	80 -includeref refname Exclude reads NOT mapped to a reference
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	81 -excluderef refname Exclude reads mapped to a particular reference
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	82 (e.g. chrM, or _dup chromosomes)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	83
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	84 -whitelist fname Remove reads that aren't on this list (by name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	85 -blacklist fname Remove reads that are on this list (by name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	86 These lists can be whitespace-delimited with
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	87 the read name as the first column.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	88 -maximum_mismatch_ratio val
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	89 Filter by maximum mismatch ratio (fraction of length)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	90
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	91 -eq tag_name value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	92 -lt tag_name value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	93 -lte tag_name value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	94 -gt tag_name value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	95 -gte tag_name value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	96
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	97 As a special case, "MAPQ" can be used as the tag_name and the SAM MAPQ
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	98 value will be used.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	99
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	100 Common tags to filter by:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	101 AS Alignment score
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	102 IH Number of alignments
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	103 NM Edit distance (each indel counts as many as its length)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	104
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	105 MAPQ Mapping quality (defined as part of SAM spec)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	106
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	107 The tag type (:i, :f, :Z) is optional.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	108
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	109 """
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	110
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	111 import os
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	112 import sys
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	113 import pysam
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	114 from ngsutils.bam import bam_iter
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	115 from ngsutils.support.dbsnp import DBSNP
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	116 from ngsutils.bam import read_calc_mismatches, read_calc_mismatches_ref, read_calc_mismatches_gen, read_calc_variations
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	117 from ngsutils.bed import BedFile
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	118
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	119
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	120 def usage():
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	121 print __doc__
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	122 print """
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	123 Usage: bamutils filter in.bam out.bam {-failed out.txt} criteria...
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	124
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	125 Options:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	126 -failed fname A text file containing the read names of all reads
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	127 that were removed with filtering
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	128
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	129 Example:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	130 bamutils filter filename.bam output.bam -mapped -gte AS:i 1000
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	131
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	132 This will remove all unmapped reads, as well as any reads that have an AS:i
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	133 value less than 1000.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	134 """
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	135 sys.exit(1)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	136
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	137
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	138 class Unique(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	139 def __init__(self, length=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	140 if length:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	141 self.length = int(length)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	142 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	143 self.length = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	144
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	145 self.last_pos = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	146 self.pos_reads = set()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	147
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	148 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	149 return "uniq"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	150
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	151 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	152 if self.last_pos != (read.tid, read.pos):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	153 self.last_pos = (read.tid, read.pos)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	154 self.pos_reads = set()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	155
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	156 if read.is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	157 seq = read.seq[::-1] # ignore revcomp for now, it isn't needed, just need to compare in the proper order
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	158 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	159 seq = read.seq
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	160
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	161 if self.length:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	162 seq = seq[:self.length]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	163
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	164 if seq in self.pos_reads:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	165 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	166
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	167 self.pos_reads.add(seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	168 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	169
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	170 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	171 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	172
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	173
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	174 class UniqueStart(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	175 def __init__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	176 self.last_tid = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	177 self.last_fwd_pos = -1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	178 self.rev_pos_list = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	179
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	180 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	181 return "uniq_start"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	182
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	183 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	184 if self.last_tid is None or self.last_tid != read.tid:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	185 self.last_tid = read.tid
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	186 self.rev_pos = set()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	187 self.last_fwd_pos = -1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	188 self.last_rev_pos = -1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	189
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	190 if read.is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	191 # check reverse reads from their start (3' aend)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	192 # these aren't necessarily in the correct
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	193 # order in the file, so we have to track them in a set
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	194
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	195 start_pos = read.aend
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	196
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	197 # clean up hash if necesary
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	198 # Allow up to 100k over, to balance cleaning up the rev_pos hash
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	199 # and memory
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	200 if read.pos > (self.last_rev_pos + 100000):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	201 self.last_rev_pos = start_pos
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	202 del_list = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	203 for k in self.rev_pos:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	204 if k < read.pos:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	205 del_list.append(k)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	206
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	207 for k in del_list:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	208 self.rev_pos.remove(k)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	209
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	210 if not start_pos in self.rev_pos:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	211 self.rev_pos.add(start_pos)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	212 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	213 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	214 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	215 if read.pos != self.last_fwd_pos:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	216 self.last_fwd_pos = read.pos
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	217 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	218 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	219
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	220 # if self.last_pos != (read.tid, read.pos):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	221 # self.last_pos = (read.tid, read.pos)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	222 # return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	223 # return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	224
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	225 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	226 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	227
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	228
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	229 class Blacklist(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	230 def __init__(self, fname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	231 self.fname = fname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	232 self.notallowed = set()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	233 with open(fname) as f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	234 for line in f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	235 self.notallowed.add(line.strip().split()[0])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	236
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	237 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	238 return read.qname not in self.notallowed
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	239
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	240 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	241 return 'Blacklist: %s' % (self.fname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	242
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	243 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	244 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	245
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	246
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	247 class Whitelist(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	248 def __init__(self, fname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	249 self.fname = fname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	250 self.allowed = set()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	251 with open(fname) as f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	252 for line in f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	253 self.allowed.add(line.strip().split()[0])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	254
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	255 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	256 return read.qname in self.allowed
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	257
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	258 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	259 return 'Whitelist: %s' % (self.fname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	260
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	261 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	262 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	263
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	264
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	265 class IncludeRegion(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	266 _excludes = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	267 _last = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	268
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	269 def __init__(self, region):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	270 IncludeRegion._excludes.append(ExcludeRegion(region))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	271 # self.excl = ExcludeRegion(region)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	272
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	273 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	274 if read == IncludeRegion._last:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	275 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	276
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	277 IncludeRegion._last = read
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	278
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	279 for excl in IncludeRegion._excludes:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	280 if not excl.filter(bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	281 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	282 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	283
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	284 # return not self.excl.filter(bam,read)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	285 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	286 return 'Including: %s' % (self.excl.region)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	287
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	288 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	289 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	290
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	291
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	292 class IncludeBED(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	293 def __init__(self, fname, nostrand=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	294 self.excl = ExcludeBED(fname, nostrand)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	295
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	296 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	297 return not self.excl.filter(bam, read)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	298
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	299 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	300 return 'Including from BED: %s%s' % (self.excl.fname, ' nostrand' if self.excl.nostrand else '')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	301
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	302 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	303 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	304
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	305
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	306 class ExcludeRegion(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	307 def __init__(self, region):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	308 self.region = region
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	309 spl = region.split(':')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	310 self.chrom = spl[0]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	311 se = [int(x) for x in spl[1].split('-')]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	312 self.start = se[0] - 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	313 self.end = se[1]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	314
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	315 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	316 if not read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	317 if bam.getrname(read.tid) == self.chrom:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	318 if self.start <= read.pos <= self.end:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	319 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	320 if self.start <= read.aend <= self.end:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	321 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	322 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	323
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	324 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	325 return 'Excluding: %s' % (self.region)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	326
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	327 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	328 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	329
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	330
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	331 class ExcludeRef(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	332 def __init__(self, ref):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	333 self.ref = ref
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	334
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	335 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	336 if not read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	337 if bam.getrname(read.tid) == self.ref:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	338 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	339 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	340
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	341 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	342 return 'Excluding: %s' % (self.ref)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	343
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	344 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	345 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	346
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	347 class IncludeRef(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	348 def __init__(self, ref):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	349 self.ref = ref
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	350
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	351 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	352 if not read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	353 if bam.getrname(read.tid) == self.ref:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	354 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	355 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	356
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	357 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	358 return 'Including: %s' % (self.ref)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	359
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	360 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	361 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	362
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	363
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	364 class ExcludeBED(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	365 def __init__(self, fname, nostrand=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	366 self.regions = {} # store BED regions as keyed bins (chrom, bin)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	367 self.fname = fname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	368 if nostrand == 'nostrand':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	369 self.nostrand = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	370 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	371 self.nostrand = False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	372
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	373 self.bed = BedFile(fname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	374 # with open(fname) as f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	375 # for line in f:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	376 # if not line:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	377 # continue
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	378 # if line[0] == '#':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	379 # continue
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	380 # cols = line.strip().split('\t')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	381
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	382 # chrom = cols[0]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	383 # start = int(cols[1])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	384 # end = int(cols[2])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	385 # if self.nostrand:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	386 # strand = '?'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	387 # else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	388 # strand = cols[5]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	389
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	390 # startbin = start / 100000
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	391 # endbin = end / 100000
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	392
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	393 # for bin in xrange(startbin, endbin + 1):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	394 # if not (chrom, bin) in self.regions:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	395 # self.regions[(chrom, bin)] = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	396 # self.regions[(chrom, bin)].append((start, end, strand))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	397
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	398 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	399 if not read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	400 if self.nostrand:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	401 strand = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	402 elif read.is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	403 strand = '-'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	404 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	405 strand = '+'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	406
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	407 for region in self.bed.fetch(bam.getrname(read.tid), read.pos, read.aend, strand):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	408 # region found, exclude read
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	409 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	410 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	411
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	412 # bin = read.pos / 100000
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	413 # ref = bam.getrname(read.tid)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	414
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	415 # if not (ref, bin) in self.regions:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	416 # return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	417
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	418 # for start, end, strand in self.regions[(ref, bin)]:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	419 # if not self.nostrand:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	420 # if strand == '+' and read.is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	421 # continue
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	422 # if strand == '-' and not read.is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	423 # continue
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	424 # if start <= read.pos <= end:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	425 # return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	426 # if start <= read.aend <= end:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	427 # return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	428 # return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	429
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	430 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	431 return 'Excluding from BED: %s%s' % (self.fname, ' nostrand' if self.nostrand else '')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	432
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	433 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	434 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	435
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	436
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	437 class Mismatch(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	438 def __init__(self, num):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	439 self.num = int(num)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	440
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	441 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	442 if read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	443 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	444
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	445 if read_calc_mismatches(read) > self.num:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	446 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	447
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	448 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	449
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	450 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	451 return '>%s mismatch%s' % (self.num, '' if self.num == 1 else 'es')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	452
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	453 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	454 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	455
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	456
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	457 class MismatchRef(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	458 def __init__(self, num, refname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	459 self.num = int(num)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	460 self.refname = refname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	461
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	462 if not os.path.exists('%s.fai' % refname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	463 pysam.faidx(refname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	464
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	465 self.ref = pysam.Fastafile(refname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	466
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	467 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	468 if read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	469 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	470
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	471 chrom = bam.getrname(read.tid)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	472 if read_calc_mismatches_ref(self.ref, read, chrom) > self.num:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	473 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	474
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	475 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	476
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	477 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	478 return '>%s mismatch%s in %s' % (self.num, '' if self.num == 1 else 'es', os.path.basename(self.refname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	479
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	480 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	481 self.ref.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	482
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	483
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	484 class MismatchDbSNP(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	485 def __init__(self, num, fname, verbose=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	486 sys.stderr.write('Note: MismatchDbSNP is considered experimental\n')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	487
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	488 self.num = int(num)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	489 self.fname = fname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	490 self.dbsnp = DBSNP(fname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	491 if verbose == 'verbose':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	492 self.verbose = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	493 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	494 self.verbose = False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	495
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	496 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	497 if read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	498 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	499
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	500 if read_calc_mismatches(read) <= self.num:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	501 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	502
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	503 chrom = bam.getrname(read.tid)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	504
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	505 mm = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	506 snps = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	507
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	508 for op, pos, seq in read_calc_variations(read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	509 if not self.dbsnp.is_valid_variation(chrom, op, pos, seq, self.verbose):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	510 mm += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	511 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	512 snps += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	513
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	514 if mm > self.num:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	515 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	516
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	517 if snps:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	518 read.tags = read.tags + [('ZS', snps)]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	519
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	520 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	521
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	522 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	523 return '>%s mismatch%s using %s' % (self.num, '' if self.num == 1 else 'es', os.path.basename(self.fname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	524
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	525 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	526 self.dbsnp.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	527
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	528
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	529 class MismatchRefDbSNP(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	530 def __init__(self, num, refname, dbsnpname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	531 sys.stderr.write('Note: MismatchRefDbSNP is considered experimental\n')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	532 self.num = int(num)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	533 self.refname = refname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	534 self.dbsnp = DBSNP(dbsnpname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	535
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	536 if not os.path.exists('%s.fai' % refname):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	537 pysam.faidx(refname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	538
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	539 self.ref = pysam.Fastafile(refname)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	540
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	541 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	542 if read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	543 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	544
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	545 chrom = bam.getrname(read.tid)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	546
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	547 mm = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	548 snps = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	549
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	550 for op, pos, seq in read_calc_mismatches_gen(self.ref, read, chrom):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	551 if not self.dbsnp.is_valid_variation(chrom, op, pos, seq):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	552 mm += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	553 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	554 snps += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	555
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	556 if mm > self.num:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	557 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	558
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	559 if snps:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	560 read.tags = read.tags + [('ZS', snps)]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	561
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	562 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	563
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	564 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	565 return '>%s mismatch%s using %s/%s' % (self.num, '' if self.num == 1 else 'es', os.path.basename(self.dbsnpname), os.path.basename(self.refname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	566
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	567 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	568 self.ref.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	569 self.dbsnp.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	570
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	571
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	572 class Mapped(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	573 def __init__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	574 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	575
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	576 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	577 if read.is_paired and (read.is_unmapped or read.mate_is_unmapped):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	578 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	579 elif read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	580 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	581 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	582
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	583 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	584 return 'is mapped'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	585
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	586 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	587 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	588
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	589
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	590 class Unmapped(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	591 def __init__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	592 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	593
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	594 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	595 if read.is_paired and (read.is_unmapped or read.mate_is_unmapped):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	596 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	597 elif read.is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	598 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	599 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	600
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	601 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	602 return 'is unmapped'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	603
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	604 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	605 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	606
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	607
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	608 class ProperPair(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	609 def __init__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	610 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	611
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	612 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	613 if not read.is_paired:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	614 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	615
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	616 if read.is_unmapped or read.mate_is_unmapped:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	617 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	618
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	619 if read.is_reverse == read.mate_is_reverse:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	620 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	621
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	622 return read.is_proper_pair
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	623
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	624 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	625 return 'proper pair'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	626
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	627 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	628 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	629
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	630
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	631 class NoProperPair(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	632 def __init__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	633 self.proper = ProperPair()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	634 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	635
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	636 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	637 return not self.proper.filter(bam, read)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	638
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	639 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	640 return 'not proper pairs'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	641
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	642 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	643 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	644
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	645
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	646 class MaskFlag(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	647 def __init__(self, value):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	648 if type(value) == type(1):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	649 self.flag = value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	650 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	651 if value[0:2] == '0x':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	652 self.flag = int(value, 16)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	653 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	654 self.flag = int(value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	655
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	656 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	657 return "Doesn't match flag: %s" % self.flag
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	658
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	659 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	660 return (read.flag & self.flag) == 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	661
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	662 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	663 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	664
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	665
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	666 class SecondaryFlag(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	667 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	668 return "no 0x100 (secondary) flag"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	669
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	670 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	671 return not read.is_secondary
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	672
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	673 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	674 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	675
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	676
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	677 class ReadMinLength(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	678 def __init__(self, minval):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	679 self.minval = int(minval)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	680
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	681 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	682 return "read length min: %s" % self.minval
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	683
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	684 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	685 return len(read.seq) >= self.minval
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	686
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	687 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	688 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	689
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	690
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	691 class ReadMaxLength(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	692 def __init__(self, val):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	693 self.val = int(val)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	694
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	695 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	696 return "read length max: %s" % self.val
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	697
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	698 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	699 return len(read.seq) <= self.val
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	700
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	701 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	702 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	703
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	704
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	705 class MaximumMismatchRatio(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	706 def __init__(self, ratio):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	707 self.ratio = float(ratio)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	708
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	709 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	710 return "maximum mismatch ratio: %s" % self.val
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	711
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	712 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	713 return read_calc_mismatches(read) <= self.ratio*len(read.seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	714
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	715 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	716 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	717
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	718
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	719 class QCFailFlag(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	720 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	721 return "no 0x200 (qcfail) flag"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	722
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	723 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	724 return not read.is_qcfail
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	725
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	726 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	727 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	728
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	729
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	730 class PCRDupFlag(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	731 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	732 return "no 0x400 (pcrdup) flag"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	733
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	734 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	735 return not read.is_duplicate
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	736
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	737 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	738 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	739
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	740
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	741 class _TagCompare(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	742 def __init__(self, tag, value):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	743 self.args = '%s %s' % (tag, value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	744
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	745 if ':' in tag:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	746 self.tag = tag.split(':')[0]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	747 tagtype = tag.split(':')[1]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	748 if tagtype == 'i':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	749 self.value = int(value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	750 elif tagtype == 'f':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	751 self.value = float(value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	752 elif tagtype == 'H':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	753 self.value = int(value) # not sure about this
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	754 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	755 self.value = value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	756 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	757 self.tag = tag
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	758
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	759 # guess at type...
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	760 try:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	761 self.value = int(value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	762 except:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	763 try:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	764 self.value = float(value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	765 except:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	766 self.value = value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	767
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	768 def get_value(self, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	769 if self.tag == 'MAPQ':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	770 return read.mapq
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	771
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	772 for name, value in read.tags:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	773 if name == self.tag:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	774 return value
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	775
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	776 return None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	777
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	778 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	779 return "%s %s %s" % (self.tag, self.__class__.op, self.value)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	780
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	781 def close(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	782 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	783
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	784
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	785 class TagLessThan(_TagCompare):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	786 op = '<'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	787
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	788 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	789 if self.get_value(read) < self.value:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	790 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	791 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	792
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	793
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	794 class TagLessThanEqual(_TagCompare):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	795 op = '<='
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	796
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	797 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	798 if self.get_value(read) <= self.value:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	799 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	800 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	801
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	802
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	803 class TagGreaterThan(_TagCompare):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	804 op = '>'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	805
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	806 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	807 if self.get_value(read) > self.value:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	808 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	809 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	810
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	811
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	812 class TagGreaterThanEqual(_TagCompare):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	813 op = '>='
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	814
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	815 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	816 if self.get_value(read) >= self.value:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	817 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	818 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	819
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	820
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	821 class TagEqual(_TagCompare):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	822 op = '='
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	823
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	824 def filter(self, bam, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	825 if self.get_value(read) == self.value:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	826 return True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	827 return False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	828
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	829 _criteria = {
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	830 'mapped': Mapped,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	831 'unmapped': Unmapped,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	832 'properpair': ProperPair,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	833 'noproperpair': NoProperPair,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	834 'noqcfail': QCFailFlag,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	835 'nosecondary': SecondaryFlag,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	836 'nopcrdup': PCRDupFlag,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	837 'mask': MaskFlag,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	838 'lt': TagLessThan,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	839 'gt': TagGreaterThan,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	840 'lte': TagLessThanEqual,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	841 'gte': TagGreaterThanEqual,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	842 'eq': TagEqual,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	843 'mismatch': Mismatch,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	844 'mismatch_ref': MismatchRef,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	845 'mismatch_dbsnp': MismatchDbSNP,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	846 'mismatch_ref_dbsnp': MismatchRefDbSNP,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	847 'exclude': ExcludeRegion,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	848 'excludebed': ExcludeBED,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	849 'excluderef': ExcludeRef,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	850 'includeref': IncludeRef,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	851 'include': IncludeRegion,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	852 'includebed': IncludeBED,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	853 'whitelist': Whitelist,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	854 'blacklist': Blacklist,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	855 'length': ReadMinLength, # deprecated
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	856 'minlen': ReadMinLength,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	857 'maxlen': ReadMaxLength,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	858 'uniq': Unique,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	859 'maximum_mismatch_ratio': MaximumMismatchRatio
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	860 }
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	861
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	862
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	863 def bam_filter(infile, outfile, criteria, failedfile=None, verbose=False):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	864 if verbose:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	865 sys.stderr.write('Input file : %s\n' % infile)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	866 sys.stderr.write('Output file : %s\n' % outfile)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	867 if failedfile:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	868 sys.stderr.write('Failed reads: %s\n' % failedfile)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	869 sys.stderr.write('Criteria:\n')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	870 for criterion in criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	871 sys.stderr.write(' %s\n' % criterion)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	872
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	873 sys.stderr.write('\n')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	874
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	875 bamfile = pysam.Samfile(infile, "rb")
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	876 outfile = pysam.Samfile(outfile, "wb", template=bamfile)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	877
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	878 if failedfile:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	879 failed_out = open(failedfile, 'w')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	880 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	881 failed_out = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	882
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	883 passed = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	884 failed = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	885
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	886 def _callback(read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	887 return "%s \| %s kept,%s failed" % ('%s:%s' % (bamfile.getrname(read.tid), read.pos) if read.tid > -1 else 'unk', passed, failed)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	888
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	889 for read in bam_iter(bamfile, quiet=True):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	890 p = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	891
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	892 for criterion in criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	893 if not criterion.filter(bamfile, read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	894 p = False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	895 failed += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	896 if failed_out:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	897 failed_out.write('%s\t%s\n' % (read.qname, criterion))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	898 #outfile.write(read_to_unmapped(read))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	899 break
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	900 if p:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	901 passed += 1
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	902 outfile.write(read)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	903
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	904 bamfile.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	905 outfile.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	906 if failed_out:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	907 failed_out.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	908 sys.stdout.write("%s kept\n%s failed\n" % (passed, failed))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	909
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	910 for criterion in criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	911 criterion.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	912
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	913
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	914 def read_to_unmapped(read):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	915 '''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	916 Example unmapped read
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	917 2358_2045_1839 \| 4 \| * \| 0 \| 0 \| * \| * \| 0 \| 0 \| GGACGAGAAGGAGTATTTCTCCGAGAACACATTCACGGAGAGTCTAACTC \| 0QT\VNO^IIRJKXTIHIKTY\STZZ[XOJKPWLHJQQQ^XPQYIIRQII \| PG:Z:bfast \| AS:i:- \| NH:i:0 \| IH:i:1 \| HI:i:1 \| CS:Z:T10213222020221330022203222011113021130222212230122 \| CQ:Z:019=2+><%@.'>52%)'15?90<7;:5+(-49('-7-<>5-@5%<.2%= \| CM:i:0 \| XA:i:4
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	918
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	919 Example mapped read:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	920 2216_1487_198 \| 16 \| chr11:19915291-19925392 \| 5531 \| 12 \| 24M2D26M \| * \| 0 \| 0 \| TCTGTCTGGGTGCAGTAGCTATACGTAATCCCAGCACTTTGGGAGGCCAA \| 1C8FZ`M""""""WZ""%"#\I;"`R@D]``ZZ``\QKX\Y]````IK^` \| PG:Z:bfast \| AS:i:1150 \| NM:i:2 \| NH:i:10 \| IH:i:1 \| HI:i:1 \| MD:Z:24^CT26 \| CS:Z:T00103022001002113210023031213331122121223321221122 \| CQ:Z:A8=%;AB<;97<3/9:>>3>@?5&18@-%;866:94=14:=?,%?:7&)1 \| CM:i:9 \| XA:i:4 \| XE:Z:-------23322---2-11----2----------------------------
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	921
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	922 '''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	923 # TODO: rewrite read properties to unmapped state
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	924 # if colorspace: convert CS to NT directly
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	925 # remove excess tags
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	926
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	927 read.is_unmapped = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	928 read.tid = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	929 read.pos = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	930 read.mapq = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	931 return read
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	932
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	933 if __name__ == '__main__':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	934 infile = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	935 outfile = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	936 failed = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	937 criteria = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	938
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	939 crit_args = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	940 last = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	941 verbose = False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	942 fail = False
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	943
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	944 for arg in sys.argv[1:]:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	945 if last == '-failed':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	946 failed = arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	947 last = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	948 elif arg == '-h':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	949 usage()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	950 elif arg == '-failed':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	951 last = arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	952 elif arg == '-v':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	953 verbose = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	954 elif not infile and os.path.exists(arg):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	955 infile = arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	956 elif not outfile:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	957 outfile = arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	958 elif arg[0] == '-':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	959 if not arg[1:] in _criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	960 print "Unknown criterion: %s" % arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	961 fail = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	962 if crit_args:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	963 criteria.append(_criteria[crit_args[0][1:]](*crit_args[1:]))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	964 crit_args = [arg, ]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	965 elif crit_args:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	966 crit_args.append(arg)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	967 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	968 print "Unknown argument: %s" % arg
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	969 fail = True
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	970
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	971 if not fail and crit_args:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	972 criteria.append(_criteria[crit_args[0][1:]](*crit_args[1:]))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	973
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	974 if fail or not infile or not outfile or not criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	975 if not infile and not outfile and not criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	976 usage()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	977
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	978 if not infile:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	979 print "Missing: input bamfile"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	980 if not outfile:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	981 print "Missing: output bamfile"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	982 if not criteria:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	983 print "Missing: filtering criteria"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	984 usage()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	985 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068 iuc parents: diff changeset	986 bam_filter(infile, outfile, criteria, failed, verbose)

Mercurial > repos > iuc > ngsutils_bam_filter

annotate filter.py @ 1:8187a729d9f4 draft