179 lines
7.5 KiB
Text
179 lines
7.5 KiB
Text
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#------------------------------------------------------------------------------
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# $File: bioinformatics,v 1.5 2019/04/19 00:42:27 christos Exp $
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# bioinfomatics: file(1) magic for Bioinfomatics file formats
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###############################################################################
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# BGZF (Blocked GNU Zip Format) - gzip compatible, but also indexable
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# used by SAMtools bgzip/tabix (http://samtools.sourceforge.net/tabix.shtml)
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###############################################################################
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0 string \037\213
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>3 byte &0x04
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>>12 string BC
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>>>14 leshort &0x02 Blocked GNU Zip Format (BGZF; gzip compatible)
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>>>>16 leshort x \b, block length %d
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!:mime application/x-gzip
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###############################################################################
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# Tabix index file
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# used by SAMtools bgzip/tabix (http://samtools.sourceforge.net/tabix.shtml)
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###############################################################################
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0 string TBI\1 SAMtools TBI (Tabix index format)
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>0x04 lelong =1 \b, with %d reference sequence
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>0x04 lelong >1 \b, with %d reference sequences
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>0x08 lelong &0x10000 \b, using half-closed-half-open coordinates (BED style)
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>0x08 lelong ^0x10000
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>>0x08 lelong =0 \b, using closed and one based coordinates (GFF style)
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>>0x08 lelong =1 \b, using SAM format
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>>0x08 lelong =2 \b, using VCF format
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>0x0c lelong x \b, sequence name column: %d
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>0x10 lelong x \b, region start column: %d
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>0x08 lelong =0
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>>0x14 lelong x \b, region end column: %d
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>0x18 byte x \b, comment character: %c
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>0x1c lelong x \b, skip line count: %d
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###############################################################################
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# BAM (Binary Sequence Alignment/Map format)
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# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
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# data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
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###############################################################################
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0 string BAM\1 SAMtools BAM (Binary Sequence Alignment/Map)
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>0x04 lelong >0
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>>&0x00 regex =^[@]HD\t.*VN: \b, with SAM header
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>>>&0 regex =[0-9.]+ \b version %s
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>>&(0x04) lelong >0 \b, with %d reference sequences
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###############################################################################
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# BAI (BAM indexing format)
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# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
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###############################################################################
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0 string BAI\1 SAMtools BAI (BAM indexing format)
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>0x04 lelong >0 \b, with %d reference sequences
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###############################################################################
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# CRAM (Binary Sequence Alignment/Map format)
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###############################################################################
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0 string CRAM CRAM
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>0x04 byte >-1 version %d.
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>0x05 byte >-1 \b%d
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>0x06 string >\0 (identified as %s)
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###############################################################################
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# BCF (Binary Call Format), version 1
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# used by SAMtools & VCFtools (http://vcftools.sourceforge.net/bcf.pdf)
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# data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
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###############################################################################
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0 string BCF\4
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# length of seqnm data in bytes is positive
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>&0x00 lelong >0
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# length of smpl data in bytes is positive
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>>&(&-0x04) lelong >0 SAMtools BCF (Binary Call Format)
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# length of meta in bytes
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>>>&(&-0x04) lelong >0
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# have meta text string
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>>>>&0x00 search ##samtoolsVersion=
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>>>>>&0x00 string x \b, generated by SAMtools version %s
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###############################################################################
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# BCF (Binary Call Format), version 2.1
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# used by SAMtools (https://samtools.github.io/hts-specs/BCFv2_qref.pdf)
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# data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
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###############################################################################
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0 string BCF\2\1 Binary Call Format (BCF) version 2.1
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# length of header text
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>&0x00 lelong >0
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# have header string
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>>&0x00 search ##samtoolsVersion=
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>>>&0x00 string x \b, generated by SAMtools version %s
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###############################################################################
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# BCF (Binary Call Format), version 2.2
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# used by SAMtools (https://samtools.github.io/hts-specs/BCFv2_qref.pdf)
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# data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
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###############################################################################
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0 string BCF\2\2 Binary Call Format (BCF) version 2.2
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# length of header text
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>&0x00 lelong >0
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# have header string
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>>&0x00 search ##samtoolsVersion=
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>>>&0x00 string x \b, generated by SAMtools version %s
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###############################################################################
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# VCF (Variant Call Format)
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# used by VCFtools (http://vcftools.sourceforge.net/)
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###############################################################################
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0 search ##fileformat=VCFv Variant Call Format (VCF)
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>&0 string x \b version %s
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###############################################################################
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# FASTQ
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# used by MAQ (http://maq.sourceforge.net/fastq.shtml)
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###############################################################################
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# XXX Broken?
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# @<seqname>
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#0 regex =^@[A-Za-z0-9_.:-]+\?\n
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# <seq>
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#>&1 regex =^[A-Za-z\n.~]++
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# +[<seqname>]
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#>>&1 regex =^[A-Za-z0-9_.:-]*\?\n
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# <qual>
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#>>>&1 regex =^[!-~\n]+\n FASTQ
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###############################################################################
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# FASTA
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# used by FASTA (https://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf)
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###############################################################################
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#0 byte 0x3e
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# q>0 regex =^[>][!-~\t\ ]+$
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# Amino Acid codes: [A-IK-Z*-]+
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#>>1 regex !=[!-'Jj;:=?@^`|~\\] FASTA
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# IUPAC codes/gaps: [ACGTURYKMSWBDHVNX-]+
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# not in IUPAC codes/gaps: [EFIJLOPQZ]
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#>>>1 regex !=[EFIJLOPQZefijlopqz] \b, with IUPAC nucleotide codes
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#>>>1 regex =^[EFIJLOPQZefijlopqz]+$ \b, with Amino Acid codes
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###############################################################################
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# SAM (Sequence Alignment/Map format)
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# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
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###############################################################################
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# Short-cut version to recognise SAM files with (optional) header at beginning
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###############################################################################
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0 string @HD\t
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>4 search VN: Sequence Alignment/Map (SAM), with header
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>>&0 regex [0-9.]+ \b version %s
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###############################################################################
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# Longer version to recognise SAM alignment lines using (many) regexes
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###############################################################################
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# SAM Alignment QNAME
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0 regex =^[!-?A-~]{1,255}(\t[^\t]+){11}
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# SAM Alignment FLAG
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>0 regex =^([^\t]+\t){1}[0-9]{1,5}\t
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# SAM Alignment RNAME
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>>0 regex =^([^\t]+\t){2}\\*|[^*=]*\t
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# SAM Alignment POS
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>>>0 regex =^([^\t]+\t){3}[0-9]{1,9}\t
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# SAM Alignment MAPQ
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>>>>0 regex =^([^\t]+\t){4}[0-9]{1,3}\t
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# SAM Alignment CIGAR
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>>>>>0 regex =\t(\\*|([0-9]+[MIDNSHPX=])+)\t
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# SAM Alignment RNEXT
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>>>>>>0 regex =\t(\\*|=|[!-()+->?-~][!-~]*)\t
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# SAM Alignment PNEXT
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>>>>>>>0 regex =^([^\t]+\t){7}[0-9]{1,9}\t
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# SAM Alignment TLEN
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>>>>>>>>0 regex =\t[+-]{0,1}[0-9]{1,9}\t.*\t
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# SAM Alignment SEQ
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>>>>>>>>>0 regex =^([^\t]+\t){9}(\\*|[A-Za-z=.]+)\t
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# SAM Alignment QUAL
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>>>>>>>>>>0 regex =^([^\t]+\t){10}[!-~]+ Sequence Alignment/Map (SAM)
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>>>>>>>>>>>0 regex =^[@]HD\t.*VN: \b, with header
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>>>>>>>>>>>>&0 regex =[0-9.]+ \b version %s
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