def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-string", dest="filein",
metavar="FILEIN",
help="Input file can be in format like <xls:a.xls,pdf:a.pdf,png:a.png,bw:a.bw,legend:a.legend (no , or : or ; allowed in legend);xls:b.xls,pdf:b.pdf;bw:c.bw,legend:c.legend>. <;> separates each sample which will be saved in one independent dict. <,> separates each file. <:> separate file type and file name which will be treated as a key-value pair.")
#parser.add_option("-t", "--type", dest="type",
# metavar="FILEIN", help="Type for each part of input file like <xls> or <xls;pdf> relative to different input format.")
parser.add_option("-T", "--title", dest="title",
help="Document title with well number at the beginning to specify the header level. Currently only first level header supported.")
parser.add_option("-d", "--description",
dest="description",
help="A paragraph in markdown format to describe this part of analysis.")
parser.add_option("-t", "--tag", dest="tag",
help="A unique string to label this part of analysis, only alphabets accepted.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="Any legal FASTA file.")
parser.add_option("-l",
"--max-len",
dest="max_len",
metavar="MAX_ALLOWED_LENGTH",
help="An integer number \
to set the maximum allowed length for each sequence line.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
desc = ""
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="A fasta file, all strings all > will \
be treated as sequence names.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--go-anno-file", dest="go",
metavar="go", help="The gene ontology file containing 3 columns. The first two columns will be used together and can be any annotation or any string when empty. The third column must be gene name with each one line.")
parser.add_option("-t", "--annoType", dest="annoType",
default="Anno", help="Any string like BP, MF, CC or KEGG, Reactome represents what type of annotation used.")
parser.add_option("-g", "--gene", dest="gene",
metavar="gene", help="One column gene list file or two columns with additional group column for each gene.")
parser.add_option("-p", "--pvalue", dest="pvalue",
default=0.05, metavar="pvalue", help="pvalue for enriched terms. Default 0.05.")
parser.add_option("-o", "--output", dest="output",
help="Prefix for output files. If there are 2 columns in gene list file, the second column will be used as a tag for output filename. If there are annotations from different databases (4 columsn in annotation file), db names will be used as a tag for output filename also.")
parser.add_option("-P", "--toptermsPlot", dest="topPlot",
default = 0, type="int",
help="Specify number of top items for enrichment plot. Default 0. Accept integers like 20.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.go != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--gtf-file",
dest="filein",
metavar="FILEIN",
help="GTF file")
parser.add_option("-b",
"--bed12",
dest="bed12",
help="GTF transfferred BED12 file")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
action="store_true",
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A network file containing at least \
two columns separated by tab with each represeent a list of paired genes.")
parser.add_option("-U", "--upstream-list", dest="up_file",
help="The file contains upstream genes .")
parser.add_option("-D", "--downstream-list", dest="dw_file",
help="The file contains downstream genes.")
parser.add_option("-u", "--upstream-col", dest="up_col",
help="The column contains upstream genes (1-based).")
parser.add_option("-d", "--downstream-col", dest="dw_col",
help="The column contains downstream genes (1-based).")
parser.add_option("-r", "--relationship-col", dest="re_col",
help="The column contains relationships (1-based). \
If not given, a '--' will be used to represent relationships.")
parser.add_option("-H", "--header", dest="header",
default=1, help="The number of header lines to skip, \
default 1.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A gff3 or gtf file with format specified above. Multiple genes can be included.")
parser.add_option("-c", "--coordinate", dest="coordinate",
help="Supply gene coordinate in format like <chr:start:end:strand:name>. \
Multiple coordinates separated by ';' are accepted. [The meaning of <start> and <end> ] \
is same as in gff file. 1-based, end not included.")
parser.add_option("-b", "--bamFiles", dest="bamFiles",
help="BAM files to be used in format like <samp1_1.bam,samp1_2.bam;samp2_1.bam;samp3_1.bam,samp3_2.bam,samp3_3.bam>. ")
parser.add_option("-l", "--bamLabels", dest="bamLabels",
help="Labels for BAM files given to -b in format like <samp1_1,samp1_2;samp2_1;samp3_1,samp3_2,samp3_3>. ")
parser.add_option("-r", "--total-mapped-reads-count", dest="readsCnt",
help="Total mapped reads count used for normalize BAM counts in format like <10000,10001;10010;10020,10021,10019>. ")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="go.obo")
#parser.add_option("-n", "--number", dest="number",
# type="int", help="Supply an int number")
#parser.add_option("-c", "--choice", dest="choice",
# type="choice", choices=["a", "b", "c"],
# default="a", help="Supply an int number")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
action="store_true",
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A matrix with first row as header and \
first column as row names. The results will be output to files.")
parser.add_option("-r", "--row", dest="row_correlation",
default=False, action="store_true", help="Default perform column correlation. \Specify to compute row correlation.")
parser.add_option("-l", "--log2-transform", dest="log2_trans",
default=False, action="store_true",
help="Perform log2 transform before computing pearson correlation value. A pseudo count 1 will be added before log2 transform.")
parser.add_option("-m", "--method", dest="method",
default="pearson", help="pearson (default), kendall, spearman")
#parser.add_option("-s", "--scale", dest="scale",
# default=False, action="store_true" help="Specify to scale data before correlation analysis. For row_correlation, scale will be perfomed on columns. For column correlation, scale will be performed on rows.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="A FASTA file.")
parser.add_option("-o",
"--order-file",
dest="order_file",
metavar="ORDER_FILE",
help="Only given when you want to sort \
FASTA file as this order. This file contains the names of FATSA \
sequence in files given to -i. ")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file_fastqc.html"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="The HTML output of fastqc.")
parser.add_option(
"-a",
"--adaptor",
dest="adaptor",
default="/MPATHB/soft/FastQC/Configuration/fastqc_adaptor.fa",
help="A two column file containing the adaptor sequences used \
by fastq. Default: /MPATHB/soft/FastQC/Configuration/fastqc_adaptor.fa")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A text file containing blog text")
parser.add_option("-s", "--stopwords", dest="stopwords",
default="/home/ct/blog/tong-chen.github.com/_posts/stopwords",
help="A file containing words to be ignored. One each row. Default system default.")
parser.add_option("-p", "--pic", dest="pic",
default="~/blog/tong-chen.github.com/_posts/logo_mode.png",
help="A picture to be moded on. Default system default.")
parser.add_option("-w", "--words-extra", dest="words",
help="SPecial words to be added to input file to weight it. In format like <airflow:30;docker:40> meaning add 30 airflow words and 40 docker words.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option(
"-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help=
"comma separated list of institutes. Currently support IGDB, IOZ, IB")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
action="store_true",
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="Gene expression matrix with first \
column representing gene names and first row as header lines.")
parser.add_option("-o", "--operation", dest="op",
default='average', help="The way to deal with \
duplicate expressions, default average meaning get the average \
expression of all probes. Accept <max> to keep the probe with the \
biggest difference, and <min> to keep the probe with the \
smalllest difference.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
desc = ""
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A standard bed file with \
six columns. Strand information will be considered. \
Extra columns will be ignored.")
parser.add_option("-n", "--number-bins", dest="nBins",
metavar="20", default="20",
help="The numbers bins in regions")
parser.add_option("-s", "--strand", dest="strand",
default=1, help="Consider strand information or not. \
Default TRUE. Strings or numbers that represent FALSE can turn \
off this parameter.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="File waiting for sort")
parser.add_option("-c", "--sort-col", dest="sort_col",
type="int", default=1, help="Specify the column to sort on. Default 1 meaning sort file on the first column.")
parser.add_option("-n", "--number-head", dest="num_head",
type="int", default=1, help="Specify the number of headlines to skip.")
parser.add_option("-o", "--order-file", dest="order_file",
help="The file containing ordered lists (one in each line).")
parser.add_option("-C", "--order-col", dest="order_col",
type="int", default=1, help="Specify the column in <order_file> used for sort <input-file>. Default 1 meaning used the first column.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print(desc, file=sys.stderr)
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="Short summary")
parser.add_option("-o",
"--output-file",
dest="op_prefix",
metavar="FILEIN",
help="Output file")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
action="store_true",
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="BLAST OUTPUT in JSON format.")
parser.add_option("-o",
"--output",
dest="output_fmt",
default='ACCESSION',
help="Output accession (default, ACCESSION) \
or FASTA sequences (FASTA).")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="Output of compareMotifs.pl")
parser.add_option("-n",
"--number-motif",
dest="number",
metavar="NUM",
help="The number of motifs you generated \
for each simulation. Since generated motifs will be done similarity \
check between each other, you may not get so many motifs sometimes.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="The output of s-plot heatmapS or kmeans.test.sh. \
Generally a data matrix with the first column as rownames and \
the last column as cluster info is acceptable.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="Cuffcompare or cufflink GTF. \
Any type of GTF would suitable. The GTF should be sorted by \
transcript name.")
parser.add_option("-t", "--translate-gtf", dest="trans",
help="Normally GTFs generated by transdecoder. Each transcript \
will be treated as a scaffold.")
parser.add_option("-c", "--correct", dest="correct",
default=1, help="Correct the pep file, cds file (fasta format) generated \
by Transdecoder according to the strand of transcripts. \
Since come transcripts assembled using cufflinks have no direction \
information, we run Transdecoder in non-strand mode. \
Here we only select direct translation of transcripts \
which direction is known in cufflink GTFs. \
Default 1 meaning execute correction. Accept 0 to turn this off.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="The FASTA file")
parser.add_option("-s", "--separator", dest="sep",
default="IdoNotThinkThisWillAppear, DoyouThinkSo",
metavar="SEPARATOR", help="The separator used to get ID names. \
Default full line except leading > and trailing '\n' is \
used as ID names.")
parser.add_option("-F", "--first-x-words", dest="count",
default=1, help="Default 1 means extracting the first \
word before separator. Accept other number (x) to extract the \
first x words.")
parser.add_option("-n", "--name-list", dest="name",
help="One column file contains ID lists.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-c", "--compare-summary", dest="compare_summary",
default="binC0304YCnt.merge/SCX.binC0304YCnt.merge.all.DE.summary.xls",
help="File name for summary.xls output by multipleSampleCompare_summary.py. One special symbol <C0304Y> should be put at the bin-size position. For example, file <bin10000Cnt.merge/SCX.bin10000Cnt.merge.all.DE.summary.xls> should be <binC0304YCnt.merge/SCX.binC0304YCnt.merge.all.DE.summary.xls> (which is default). The program will replace <C0304Y> with given bin sizes.")
parser.add_option("-m", "--meltBinRegion", dest="meltBinRegion",
default="binC0304YCnt.merge/binC0304YCnt.merge.norm.chr_distrib.summary.xls",
help="File name for summary.xls output by meltRegionBinMatrix.py. One special symbol <C0304Y> should be put at the bin-size position. For example, file <bin10000Cnt.merge/bin10000Cnt.merge.norm.chr_distrib.summary.xls> should be <binC0304YCnt.merge/binC0304YCnt.merge.norm.chr_distrib.summary.xls> (which is default). The program will replace <C0304Y> with given bin sizes. Specifally giving <no> to ignore this part analysis.")
parser.add_option("-b", "--bin-size", dest="bin_size",
help="Bin size. Multiple sizes can be separated by < > or <,>.")
parser.add_option("-t", "--tag", dest="tag",
help="An unique string with only alohabets to label all labels in output Rmd.")
#parser.add_option("-o", "--output-prefix", dest="out_prefix",
# help="The prefix of output files.")
parser.add_option("-r", "--report-dir", dest="report_dir",
default='report', help="Directory for report files. Default 'report'.")
parser.add_option("-R", "--report-sub-dir", dest="report_sub_dir",
default='4_genome_bin_difference', help="Directory for saving report figures and tables. This dir will put under <report_dir>, so only dir name is needed. Default '4_genome_bin_difference'.")
#parser.add_option("-d", "--doc-only", dest="doc_only",
# default=False, action="store_true", help="Specify to only generate doc.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.bin_size != None, "A string needed for -b"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-n", "--nafold-det", dest="det",
metavar="NAFOLD.DET", help="The det file outputed from nafold. \
Normaly you can run nafold through wrapped nafold.pl.")
parser.add_option("-m", "--map-file", dest="map",
metavar="DAT.MAP", help="The parsed miRNA.dat file though \
parsemirBase.py. This is used to map miRNAs to pre-miRNAs.")
parser.add_option("-s", "--subset-file", dest="sub",
metavar="SUB", help="A file containing only part of \
miRNAs.[Unsupported]")
parser.add_option("-a", "--all-pos-status", dest="all_status",
metavar="TRUE", help="Return the pairing status of all \
positions. Default FALSE")
parser.add_option("-p", "--position", dest="pos",
metavar="POS", help="The positions you want to check. \
Accept discrete numbers like '1,2,4,6' or a range '1-5' or both. \
All mentioned numbers and internal numbers will be included and \
treated as 1-based from 5' end of miRNAs.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.det != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="The FASTA file")
parser.add_option("-s", "--separator", dest="sep",
default="IdoNotThinkThisWillAppear, DoyouThinkSo",
metavar="SEPARATOR", help="The separator used to get ID names. \
Default full line (no splitting) except leading > and trailing '\\n' is \
used as ID names. Please use <tab> to specify '\\t' as separtor.")
parser.add_option("-F", "--first-x-words", dest="count",
default=1, help="Default 1 means extracting the first \
word before separator. Accept other number (x) to extract the \
first x words.")
parser.add_option("-n", "--name-list", dest="name",
help="One or several columns file containing ID lists in one column.")
parser.add_option("-c", "--name-col-index", dest="name_col_ix",
default=1, type='int',
help="Specify the columns containing IDs. Default 1 representing the first column.")
parser.add_option("-r", "--rename-col-index", dest="rename_col_ix",
default=0, type='int',
help="Specify the columns containing IDs. Default 0 representing no rename.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file -b bedfile"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="The input file should contain \
at least three columns with the first column as the name in \
the forth column given to -b.")
parser.add_option("-b",
"--bed",
dest="bed",
help="The bed file contains the coordinates of \
sequences used for short motif search. Six column file with \
strand information needed.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >> sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i",
"--input-file",
dest="filein",
metavar="FILEIN",
help="file given to clusterProfileGO.sh.")
parser.add_option("-v",
"--verbose",
dest="verbose",
default=0,
help="Show process information")
parser.add_option("-d",
"--debug",
dest="debug",
default=False,
help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-o", "--output-folder", dest="output",
metavar="FILEIN", help="The directory to save output files.")
parser.add_option("-t", "--title", dest="title",
metavar="TITLE", help="Title for document.")
parser.add_option("-a", "--author-list", dest="author",
metavar="AUTHOR", help="Author or affilication or other information. \
Multiple items separated by <;> can be given here.")
parser.add_option("-d", "--document-class", dest="doc_class", default="article",
help="Document class, article, book, report. Default [article]")
parser.add_option("-l", "--latex-template", dest="latex_temp", default="null",
help="A file to set latex output template. [Optional]")
parser.add_option("-b", "--bibliography", dest="bib",
help="Bibliography files for reference citation. Nomally these files can be got from EndNote or Zotero. Multiple files should be supplied as <1.bib, 2.bib>.")
parser.add_option("-B", "--biblio-style", dest="bib_style", default="apalike",
help="Bibliography style for reference citation. Default <apalike>.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-D", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.output != None, "A filename needed for -o"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
global desc
print >>sys.stderr, desc
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
usages = "%prog -i file"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="A multiple aignment FASTA file")
parser.add_option("-m", "--multiple-aligned-fasta", dest="msa",
default='phylip', help="Specify the type of given \
multiple alignment file.Currently <phylip>(default) or <fasta> \
is acccepted. ")
parser.add_option("-g", "--gap-keep", dest="gap_keep",
default=1, type='int', help="Keep sites with gaps (default).\
Accept <0> to delete sites with gaps.")
parser.add_option("-v", "--verbose", dest="verbose",
action="store_true", help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, action="store_true", help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
def cmdparameter(argv):
if len(argv) == 1:
cmd = 'python ' + argv[0] + ' -h'
os.system(cmd)
sys.exit(1)
desc = ""
usages = "%prog -i homer_out -b bed_used_for_findMotif -t RNA"
parser = OP(usage=usages)
parser.add_option("-i", "--input-file", dest="filein",
metavar="FILEIN", help="This is the output of \
findMotifsGenome.pl or findMotifs.pl when using -find. ")
parser.add_option("-b", "--bed-file", dest="bedin",
metavar="inputBed", help="The original bed file which has been given to \
findMotifsGenome.pl and used to get the file given to -i. If -t is \
RNA, an at least six-column file is needed. If -t is DNA, an at-leat \
four-column file is needed. Other columns will be ignored. \
If you run findMotifsGenome.pl using -size 200 or other parameters \
rather than <-size given>, you may need the real bed which \
findMotifsGenome.pl used. ")
parser.add_option("-t", "--type", dest="type",
default='RNA', help="The attribute of given bed file \
represented sequences. For <DNA>, the strand information of regions in \
output bed file is accordant with output file of findMotifsGenome.pl. \
For <RNA>, the strand information of one region is accordant with its \
strand information in file given to -b.")
parser.add_option("-H", "--header", dest="header",
default=1, help="The number of header lines to skip.")
parser.add_option("-v", "--verbose", dest="verbose",
default=0, help="Show process information")
parser.add_option("-d", "--debug", dest="debug",
default=False, help="Debug the program")
(options, args) = parser.parse_args(argv[1:])
assert options.filein != None, "A filename needed for -i"
return (options, args)
