* Attention

This my personal code repository. I haven't tested them fully. So I can't guarantee they works...


* Ancient README


* WebApp list:

1. CistromeDB

The CistromeDB website based on Django framework. Check
CistromeDB/INSTALL.txt for detail.

* Exectuables list:

1. motif_enrich.py 
Usage: motif_enrich.py [options]

Calculate the motif enrichment measured in foldchange and p-value for one BED
file and one reference BED file

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -s SPECIES, --species=SPECIES
                        species, must be "mm8" or "hg18"
  -i IFILE, --ifile=IFILE
                        input BED file, e.g. the ChIP regions
  -r RFILE, --rfile=RFILE
                        input reference BED file, e.g. the tiled regions.
                        [optional] if not set, use the whole genome as
                        reference
  -c CUTOFF, --cutoff=CUTOFF
                        cutoff for the motif scan score
  -d IDIR, --idir=IDIR  input directory for binary Motif Scan Results files
  -a, --all             If set, also show the depleted motifs. Default, not
                        show
  --minfc=MINFC         minimum foldchange for motif enrichment, default:0
  --maxp=MAXP           maximum p-value for motif enrichment, default:1
  --minpercent=MINPERCENT
                        minimum percentage of input BED regions containing
                        motif, default:5
  --maxpercent=MAXPERCENT
                        maximum percentage of input BED regions containing
                        motif, default:300
  --verbose=VERBOSE     Name of a directory. if set, save verbose information
                        in the direcotry.
  -o OFILE, --ofile=OFILE
                        output file
2. ceas.py
Usage: ceas.py [options]

CEAS -- Cis-regulatory Element Annotation System

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  --chip-res=CHIP_RES   ChIP resolution, default: 600 bp
  --bg-res=BG_RES       Genome BG resolution, default: 100 bp
  --promoter=PROMOTER   Promoter range size, default: 3000 bp
  --bipromoter=BIPROMOTER
                        Bidirectional-promoter range size, default: 5000 bp
  --downstream=DOWNSTREAM
                        Downstream range size, default: 3000 bp
  --nopf                No profiling is run and the options regarding
                        profiiling will not be effective if this switch is set
  --rel-dist=REL_DIST   Relative distance to TSS/TTS for gene profiling,
                        default: 3000 bp
  --metagene-size=METAGENE_SIZE
                        Metagene size, default: 3000 bp
  --pf-res=PF_RES       Profiling resolution, default: 50 bp
  --gn-groups=GN_GROUPS
                        Gene-group file names (eg, top10.txt,bottom10.txt),
                        default: all genes
  --gn-group-names=GN_NAMES
                        Gene-group names for profiling (eg, top 10%,bottom
                        10%), default: None
  -a, --alt-gn-name     'name2' in refGene table is used if set. This flag is
                        meaningful only if --gn-groups is set.
  -i IFILE, --ifile=IFILE
                        input BED file, e.g. the ChIP regions
  -w WFILE, --wfile=WFILE
                        input wiggle file.
  -n NCBED, --ncbed=NCBED
                        noncoding region BED file, default: None
  -g GDB, --gene-db=GDB
                        Gene annotation database file from Cistrome website
  --gt=GT               optional genome table. default: None
  -o OFILE, --ofile=OFILE
                        output R script. default: stdout
  --verbose=VERBOSE     Name of a directory. if set, save verbose information
                        in the direcotry.

3. qc_chIP.py 
Usage: qc_chIP.py [options]

QC for two replicates of ChIP-chip experiment. Do both peak level and
probe level calculations.

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -p PEAK1, --peak1=PEAK1
                        peak file in xls format for #1 replicate
  -q PEAK2, --peak2=PEAK2
                        peak file in xls format for #2 replicate
  -x WIG1, --wig1=WIG1  wiggle file for #1 replicate
  -y WIG2, --wig2=WIG2  wiggle file for #2 replicate
  -r RFILE, --rfile=RFILE
                        R output file
  -f FORMAT, --format=FORMAT
                        ma2c, mat or macs, default: ma2c
  -s STEP, --step=STEP  number of steps to calculate cor based on some score
                        ranges, default: 5

4. qc_chIP2.py 
Usage: qc_chIP2.py [options]

QC for two replicates of ChIP-chip experiment. Only for naive overall
probe level calculation.

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -x WIG1, --wig1=WIG1  wiggle file for #1 replicate
  -y WIG2, --wig2=WIG2  wiggle file for #2 replicate
  -r RFILE, --rfile=RFILE
                        R output file. If not set, do not save R file.
  -s STEP, --step=STEP  probe step, default: 100
  -f FORMAT, --format=FORMAT
                        ma2c, mat or macs, default: ma2c

5. count_probes_in_peaks.py 
Usage: count_probes_in_peaks.py [options]

Summarize ChIP-chip experiment. Calculate how many probes are included
in peak regions.

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -p PEAK1, --peak1=PEAK1
                        peak file in xls format for #1 replicate
  -x WIG1, --wig1=WIG1  wiggle file for #1 replicate
  -o OFILE, --ofile=OFILE
                        output file
  -f FORMAT, --format=FORMAT
                        ma2c, mat or macs, default: ma2c

6. count_probes_in_ranges.py 
Usage: count_probes_in_ranges.py [options]

Summarize ChIP-chip experiment. Calculate how many probes fall into
certain score ranges '(-inf,-1],(-1,0],(0,+1],(+1,+inf)'.

Options:
  --version             show program's version number and exit
  -h, --help            Show this help message and exit.
  -x WIG1, --wig1=WIG1  wiggle file for #1 replicate
  -o OFILE, --ofile=OFILE
                        output file

7. xyz2image.py 

Restore the microarray image.

 need 1 parameter: xyz2image.py <X-Y-Value-file>

 X-Y-Value-file is a tab-delimited file with 1st column as
 X-corrdinates, 2nd column as Y, and 3rd column as log-ratio value