Difference between revisions of "SHORE Subprograms"

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=shore tagstats=
 
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Gather read statistics for multiple samples. This is mainly intended for small RNA sequencing when no reference is available.
 
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'''Usage:''' shore tagstats [OPTIONS] [PATHS]
 
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{|
 
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| colspan=2 | '''Allowed options'''
 
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|----
 
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| ''-i'', ''--readpaths=<arg[:...][,...]>''  ||                              || SHORE directories or read file paths
 
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|----
 
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| ''-o'', ''--outdir=<arg>''                || (Default: ''ReadAnalysis'')  || Output directory
 
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|----
 
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| ''-r'', ''--report=<arg>''                || (Default: ''1'')            || Only report a sequence if it's represented at least <arg> times
 
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|----
 
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| ''-p'', ''--pseudo=<arg>''                || (Default: ''0'')            || Add a pseudocount of <arg> to each read count
 
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|----
 
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|}
 
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=shore binom_test=
 
=shore binom_test=
  

Revision as of 14:31, 23 September 2011

shore binom_test

shore binom_test can be used to evaluate two sets of count data agaist each other using a binomial test.


Usage: shore binom_test [OPTIONS]

Allowed options
-i, --input-file=<arg> (Default: stdin) Read count input file
-o, --output-file=<arg> (Default: stdout) Output file
-p, --distribution-p=<arg> (Default: 0.5) Parameter p of the binomial distribution
-n, --normalization-file=<arg> File with scaling factors for each column (overrides '-p')
-a, --alternative=<arg> (Default: less) Specifies the alternative hypothesis for the test (less or greater or twosided)
-1, --first-column=<arg> Name of the first read count column
-2, --2nd-column=<arg> Name of the second read count column (tested vs. column 1)
--global-scaling=<arg> (Default: 1) Scaling constant with wich all read counts are multiplied
-j, --input-header=<arg[,...]> Specify header for input file, if not available
-f, --fold-change Report fold enrichment values
--fdr-bh Calculate Benjamini-Hochberg FDR
--sort Sort output

shore mtc

The subprogram shore mtc implements various multiple testing correction methods. The expected input is a tab-delimited text file with a header, and the column containing the p-values to be adjusted must be named raw_p.

Implemented methods include

  • Benjamini-Hochberg false discovery rate control (fdr_bh)
  • Bonferroni familywise error rate control (fwer_bonferroni)
  • Holm familywise error rate control (fwer_holm)
  • Hochberg familywise error rate control (fwer_hochberg)
  • Sidak singlestep familywise error rate control (fwer_sidak_ss)
  • Sidak stepdown familywise error rate control (fwer_sidak_sd)
  • Benjamini-Yekutieli false discovery rate control (fdr_by).


Usage: shore mtc [OPTIONS]

Mandatory
-m, --method=<arg[,...]> Select correction method(s), out of: fdr_bh, fwer_bonferroni, fwer_holm, fwer_hochberg, fwer_sidak_ss, fwer_sidak_sd, fdr_by
-i, --input-file=<arg> (Default: stdin) The file the raw p-values are read from (expects a column 'raw_p')
-o, --output-file=<arg> (Default: stdout) Output file
Output
-u, --fdr-max=<arg> (Default: 1) Maximum q-value to report
-e, --echo-comments Echo all comments read from input files to stdout
-q, --quiet Do not print input, only report the q-values
Other
-j, --input-header=<arg[,...]> Use arg as input file header

shore annotate_region

shore annotate_region can be used to annotate previously defined genomic regions with the overlapping or nearest genes present in an annotation file. Only the central base of each region will be annotated. The annotation file must be in standard GFF format.


Usage: shore annotate_region [OPTIONS]

Mandatory
-a, --annotation-file=<arg> Annotation file
-f, --feature-file=<arg> File with the features to be annotated. This file must contain a header specifying the columns 'chr', 'pos' and optionally 'size' or 'end'
-o, --outfile=<arg> (Default: stdout) Output file
Optional
--header=<arg[,...]> Header for the feature file
--range Use the real regions and not just the central base
--gff Write output in GFF format
--so-filter=<arg[,...]> (Default: gene,transposable_element_gene) Only parse toplevel features of the given Sequence Ontology (SO) types
--print Just print the annotation tree
--query-pos=<arg> Query annotation for the given position

shore convert

Convert SHORE files into common file formats, and vice versa.

Available converters:

  • Alignment2ALN
  • Alignment2BED
  • Alignment2GFF
  • Alignment2Maplist
  • Alignment2SAM
  • ColorFlat2Fastq
  • Contig2AFG
  • Eland2Maplist
  • ExpandTabs
  • FlatPair2Fastq
  • Maplist2Eland
  • Reads2Fasta
  • Reads2Fastq
  • Reads2Flat
  • Reads2Qual
  • Solid2Fastq
  • Solid2Flat
  • Variant2GFF
  • Variant2VCF

Alignment2... converters can convert

  • SHORE map.list files (default)
  • SAM files (*.sam)
  • BAM files (*.bam)

Reads2... converters can convert

  • SHORE reads_0.fl files (default)
  • FastQ files (*.fq, *.fastq)
  • 454 Standard Flowgram Format SFF (*.sff)
  • Illumina QSEQ files (*.qseq, *_qseq.txt)
  • SHORE map.list files (*.list) (discards alignment information and only keeps the read information; input files must be sorted by read ID) 
By default, the SHORE file formats (map.list and reads_0.fl, respectively) are expected as input.
All other file types must have the correct file extensions to be recognized (an additional .gz is allowed for compressed files).

Additionally, the special file names stdin and stdout may be used for reading from standard input and for writing to standard output, respectively.

For stdin, map.list format is expected for Alignment2... conversions and reads_0.fl format for Reads2... conversions. To convert different formats from standard input, use e.g. stdin.sam, stdin.fastq.gz, etc.

shore sort

Sort / merge tab-delimited text files


Usage: shore sort [OPTIONS] [TEXT_FILES]

Allowed options
-i, --infiles=<arg[,...]> A comma-separated list of plain-text input files
-o, --outfile=<arg> (Default: stdout) Output file
-p, --preset=<arg> Automatically select sort keys for the file type specified. Supported values: * maplist: map.list format sorted by genomic coordinate * maplist_id: map.list format sorted by read ID * reads0: reads flat file format sorted by read ID * gff: GFF format sorted by position
-k, --keystring=<arg> Concatenation of column ids (counted from 1) and key types. Valid key types: t (text), i (integer) and f (float); capital letters reverse the sort order - e.g. '-k 1i5t3i7I'.
-I, --inplace Output file is the same as the input file
-t, --tmpdir=<arg> Temporary file directory (defaults to $TMPDIR or /tmp)
-B, --blocksize=<arg> (Default: 2048) Block size in megabytes
-m, --nur-merge Merge already sorted files
-u, --unique Output only the first of an equal run
-c, --check Only test if the files are sorted
-b, --upper-bound=<arg[,...]> Returns byte offset (counted from 0) and text of the first line in a sorted file that compares greater than the keys given in <arg> (provide comma-separated values in order of key priority)
-T, --tail=<arg[,...]> Print all lines in a sorted file that compare greater than the keys given in <arg> (provide comma-separated values in order of key priority)
-C, --no-comments Do not treat line comments and empty lines specially
-v, --verbose Be more verbose

shore compress

Compress files to indexed gzip format


Usage: shore compress [OPTIONS] FILES

Allowed options
--outfile=<arg> Write to the file <arg> instead of <infile>.gz
--replace Remove original files after compression. If the input file is already compressed it will be recompressed and replaced
--tail=<arg> Instead of compressing files, dump the last <arg> bytes of a seekable file
--dumpgzx Print out the index for each file

shore 2dex

Range-indexing and query for tab-delimited text files


Usage: shore 2dex [OPTIONS] [TEXT_FILES]

Mandatory
-i, --infiles=<arg[,...]> A comma-separated list of tab-delimited plain-text input files (can also be any SHORE directory when -f MAPLIST is set)
Format Options
-f, --format=<arg> Provide file type for automatic settings, valid file types: MAPLIST, GFF, SAM
-c, --chr-column=<arg> Column w. chromosome or sequence name, provide the column name or @<column_number>
-p, --pos-column=<arg> Column w. start position, provide the column name or @<column_number>
-s, --size-column=<arg> Column w. feature size, provide the column name or @<column_number>
-e, --end-column=<arg> Column w. end position (inclusive), provide the column name or @<column_number>
-x, --xend-column=<arg> Column w. end position (exclusive), provide the column name or @<column_number>
-C, --commentchar=<arg> Comment line symbol
Index Options
-B, --blocksize=<arg> (Default: 131072) Block size determining the index resolution in bytes
-G, --maxgap=<arg> (Default: 131072) Maximum sequence gap in a block
Query Options
-q, --query=<arg> A range to query; prints all overlapping records. Valid ranges: 'SEQ:POS~SIZE', 'SEQ:POS..END', 'SEQ1:POS..SEQ2:END', 'SEQ:POS...XEND', 'SEQ1:POS...SEQ2:XEND' (END: inclusive, XEND: exclusive)
Other
-v, --verbose Be more verbose
-Q, --quiet Be less verbose

shore idtrans

SHORE uses numerical identifiers for all sequences of the reference. shore idtrans simplifies translating these numbers in some of the result files back into chromosome names as specified in the reference fasta file (and vice versa).

Required is either a *.trans file which is stored in the IndexFolder by shore preprocess, or a ref.txt file generated by shore mapflowcell.


Usage: shore idtrans [OPTIONS] FILES

Allowed options
-t, --transfile=<arg> *.trans file from IndexFolder
-r, --reffile=<arg> ref.txt file generated by mapflowcell
-o, --outfile=<arg> Output file (default: <infile>.idtrans)
-c, --columns=<arg[,...]> (Default: chr) Columns to be translated (column names or @<column_number>)
--name2id Translate names to IDs (default: translate IDs to names)
--nocompress Do not compress output files
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