Index

Symbols

-b, --bamfile <bamfile> metacov-pileup command line option -b, --out-basehist <out_basehist> metacov-scan command line option -bo, --boffset <boffset> metacov-scan command line option -f, --reference-fasta <reference_fasta> metacov-pileup command line option metacov-scan command line option -g, --group-by <group_by> metacov-scan command line option -I, --out-isizehist <out_isizehist> metacov-scan command line option -k <k> metacov-scan command line option -k, --khist <khist> metacov-simulate command line option -K, --klen <klen> metacov-simulate command line option -k, --kmer-histogram <kmer_histogram> metacov-pileup command line option -K, --kmer-length <kmer_length> metacov-pileup command line option -l, --len <rlen> metacov-simulate command line option -m, --max-reads <max_reads> metacov-scan command line option -m, --mflen <mflen> metacov-simulate command line option -M, --out-mirrorhist <out_mirrorhist> metacov-scan command line option -Ml, --mirror-length <mirror_length> metacov-scan command line option

-MO, --mirror-offset <mirror_offset> metacov-scan command line option -n, --num-reads <num_reads> metacov-simulate command line option -n, --number <number> metacov-scan command line option -O, --offset <offset> metacov-scan command line option -o, --out <fwd_outfn> metacov-simulate command line option -o, --out-kmerhist <out_kmerhist> metacov-scan command line option -o, --outfile <outfile> metacov-pileup command line option -o2, --out2 <rev_outfn> metacov-simulate command line option -p, --proportions <proportions> metacov-simulate command line option -rb, --regionfile-blast7 <regionfile_blast7> metacov-pileup command line option -rc, --regionfile-csv <regionfile_csv> metacov-pileup command line option -rs, --rndSeed <rndseed> metacov-simulate command line option -s, --sdev <sdev> metacov-simulate command line option -s, --step <step> metacov-scan command line option -ss, --seqSys <seqsys> metacov-simulate command line option -t, --readfile-type <readfile_type> metacov-scan command line option

A

AlignmentFileIterator (class in metacov.scan)

B

blast_parser (class in metacov.blast)

ByFlag (class in metacov.scan)

F

FastQFile (class in metacov.pyfq) FastQFileIterator (class in metacov.scan) FastQFilePair (class in metacov.pyfq) FastQWriter (class in metacov.pyfq)

FILE [FILE...] metacov-simulate command line option filename (metacov.pyfq.FastQFile attribute) fmt7_parser (class in metacov.blast)

G

get_regions_from_bam() (in module metacov.util) get_regions_from_blast7() (in module metacov.util)

get_regions_from_csv() (in module metacov.util) get_rows() (metacov.scan.ByFlag method) (metacov.scan.ReadProcessorList method)

K

kmer_base2_to_ascii() (in module metacov.scan)

M

metacov (module) metacov-pileup command line option -K, --kmer-length <kmer_length> -b, --bamfile <bamfile> -f, --reference-fasta <reference_fasta> -k, --kmer-histogram <kmer_histogram> -o, --outfile <outfile> -rb, --regionfile-blast7 <regionfile_blast7> -rc, --regionfile-csv <regionfile_csv> metacov-scan command line option -I, --out-isizehist <out_isizehist> -M, --out-mirrorhist <out_mirrorhist> -MO, --mirror-offset <mirror_offset> -Ml, --mirror-length <mirror_length> -O, --offset <offset> -b, --out-basehist <out_basehist> -bo, --boffset <boffset> -f, --reference-fasta <reference_fasta> -g, --group-by <group_by> -k <k> -m, --max-reads <max_reads> -n, --number <number> -o, --out-kmerhist <out_kmerhist> -s, --step <step> -t, --readfile-type <readfile_type> READFILE

metacov-simulate command line option -K, --klen <klen> -k, --khist <khist> -l, --len <rlen> -m, --mflen <mflen> -n, --num-reads <num_reads> -o, --out <fwd_outfn> -o2, --out2 <rev_outfn> -p, --proportions <proportions> -rs, --rndSeed <rndseed> -s, --sdev <sdev> -ss, --seqSys <seqsys> FILE [FILE...] metacov.blast (module) metacov.cli (module) metacov.compat (module) metacov.pileup (module) metacov.pyfq (module) metacov.scan (module) metacov.simulate (module) metacov.util (module)

P

pos (metacov.pyfq.FastQFile attribute)

Q

qacc (metacov.util.Region attribute)

R

read1 (metacov.pyfq.FastQFilePair attribute) read2 (metacov.pyfq.FastQFilePair attribute) READFILE metacov-scan command line option

ReadIterator (class in metacov.scan) ReadProcessor (class in metacov.scan) ReadProcessorList (class in metacov.scan) Region (class in metacov.util) rlen (metacov.pyfq.FastQFile attribute)

S

sacc (metacov.util.Region attribute) scan_reads() (in module metacov.scan) send (metacov.util.Region attribute) seq (metacov.pyfq.FastQFile attribute)

set_max_readlen() (metacov.scan.ReadProcessor method) (metacov.scan.ReadProcessorList method) size (metacov.pyfq.FastQFile attribute) sstart (metacov.util.Region attribute)

W

write() (metacov.pyfq.FastQWriter method)