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script update py3 #2

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64 changes: 32 additions & 32 deletions biotiger/index.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -139,40 +139,40 @@ def gen_prefix(input):
return o

def die_with_help():
print """
****************
TIGER v2.0 Help:
****************

tiger index Options:

-i|input Specify input file. File must be in FastA format and must be aligned prior.
Datasets with uneven sequence lengths will return an error.

-s|split Split dataset across multiple files to run simultaneously. Takes int argument.

-o|output Specify the prefix name of output files.

-u|unknowns Specify unknown characters in the alignment. Unknown characters are omitted from
site patterns and so are not considered in the analysis.
-u ?,-,*: defines ?, - and * as unknown characters. (*Be sure to put only a comma
between characters, NO SPACE!!)

Default is ? only

Examples:
1. Generate a .tgr file for complete sequence named full_seq.tgr & set unknowns to ? and - :
tiger index -i my_file.aln -o full_seq -u ?,-

2. Generate 10 subsets of the data with an output prefix of tiger_split and a reference:
tiger index -i my_file.aln -o tiger_split -s 10
** Results in files named tiger_split.1.tgr, tiger_split.2,tgr, and so on, along with
tiger_split.ref.tgr

"""
print("""
****************
TIGER v2.0 Help:
****************
tiger index Options:
-i|input Specify input file. File must be in FastA format and must be aligned prior.
Datasets with uneven sequence lengths will return an error.
-s|split Split dataset across multiple files to run simultaneously. Takes int argument.
-o|output Specify the prefix name of output files.
-u|unknowns Specify unknown characters in the alignment. Unknown characters are omitted from
site patterns and so are not considered in the analysis.
-u ?,-,*: defines ?, - and * as unknown characters. (*Be sure to put only a comma
between characters, NO SPACE!!)
Default is ? only
Examples:
1. Generate a .tgr file for complete sequence named full_seq.tgr & set unknowns to ? and - :
tiger index -i my_file.aln -o full_seq -u ?,-
2. Generate 10 subsets of the data with an output prefix of tiger_split and a reference:
tiger index -i my_file.aln -o tiger_split -s 10
** Results in files named tiger_split.1.tgr, tiger_split.2,tgr, and so on, along with
tiger_split.ref.tgr
""")
sys.exit(1)

def die_with_message(message):
print message
print(message)
sys.exit(1)

90 changes: 45 additions & 45 deletions biotiger/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,56 +295,56 @@ def run(opts):
except IOError:
die_with_message("Cannot open outfile %s%s" % (opts.output, suffix))
else:
print output_str
print(output_str)


def die_with_help():
print """
****************
TIGER v2.0 Help:
****************

tiger output Options:
print("""
****************
TIGER v2.0 Help:
****************

-i|input Specify input file. Must be in .gr format.

-c|combine Specify input file. This file should contain a list of .gr files to be combined.

-fa|fasta Provide original .fa file for sequence data.

-o|output Specify prefix name for output files (prints to stdout if not provided)

-f|format Changes formatting options.
NEXUS, with comments:
-f 0: output bin numbers, sites unsorted (default)
-f 1: output bin number, sites sorted on rank
-f 2: displays rank values rather than bin numbers
-f 3: displays rank values and sites sorted on rank
FastA:
-f 4

-inc|include_only Give list of bins to include (only) in output
-inc 3,4,5,6 (Note: No spaces, just commas)

-exc|exclude_only Give list of bins to exclude from output
-exc 1,2,9,10

-m|mask Mask -inc/-exc sites. (Default is to remove them)

-b|bins Set the number of bins to be used.
-b <int>: Sites will be placed into <int> number of bins. <int> is a whole number.

Default is 10.
Examples:
1. Write a FastA file, masking site that fall into Bin1, Bin2, Bin9 and Bin10 of 10 bins:
tiger output -i sample.gr -fa my_data.fa -f 4 -exc 1,2,9,10 -b 10 --mask

2. Write a NEXUS file combining test.0.gr, test.1.gr, test.2.gr with sites sorted on rank
tiger output -c list_of_gr_files.txt -fa my_data.fa -f 3

"""
tiger output Options:

-i|input Specify input file. Must be in .gr format.

-c|combine Specify input file. This file should contain a list of .gr files to be combined.

-fa|fasta Provide original .fa file for sequence data.

-o|output Specify prefix name for output files (prints to stdout if not provided)

-f|format Changes formatting options.
NEXUS, with comments:
-f 0: output bin numbers, sites unsorted (default)
-f 1: output bin number, sites sorted on rank
-f 2: displays rank values rather than bin numbers
-f 3: displays rank values and sites sorted on rank
FastA:
-f 4

-inc|include_only Give list of bins to include (only) in output
-inc 3,4,5,6 (Note: No spaces, just commas)

-exc|exclude_only Give list of bins to exclude from output
-exc 1,2,9,10

-m|mask Mask -inc/-exc sites. (Default is to remove them)

-b|bins Set the number of bins to be used.
-b <int>: Sites will be placed into <int> number of bins. <int> is a whole number.

Default is 10.
Examples:
1. Write a FastA file, masking site that fall into Bin1, Bin2, Bin9 and Bin10 of 10 bins:
tiger output -i sample.gr -fa my_data.fa -f 4 -exc 1,2,9,10 -b 10 --mask

2. Write a NEXUS file combining test.0.gr, test.1.gr, test.2.gr with sites sorted on rank
tiger output -c list_of_gr_files.txt -fa my_data.fa -f 3

""")
sys.exit(1)

def die_with_message(message):
print message
print(message)
sys.exit(1)
84 changes: 42 additions & 42 deletions biotiger/rate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def set_pattern(p):

def sort(rates, patterns):
if len(rates) != len(patterns):
print "Something's weird here. len(rates) != len(patterns)"
print("Something's weird here. len(rates) != len(patterns)")
sys.exit(1)

rate_d = {}
Expand Down Expand Up @@ -160,51 +160,51 @@ def gen_prefix(input):
return o

def die_with_help():
print """
****************
TIGER v2.0 Help:
****************

tiger rate Options:

-i|input Specify input file. File should be in .ti format.

-r|reference Specify reference sequence (.ti). -i file is used as default if none is provided.

-o|output Specify prefix name for output files.
print("""
****************
TIGER v2.0 Help:
****************

-rl|rate_list A list of the rate at each site may be optionally written to a specified
file.
-rl <file.txt> : writes list of the rates at each site to file.txt.

-ptp Specifies that a PTP test should be run.
* Note * this option has a huge effect on running time!

-z|randomisations Number of randomisations to be used for the PTP test.
-z <int>: each site will be randomised <int> times. <int> is a whole number.

Default is 100

-p|p_value Specify p-value which denotes significance in PTP test.
-p <float>: site will be denoted as significant if p-value is better than <float>.
<float> is a floating point number.

Default is 0.05

-pl|pval_list Write a list of p-values to a specified file.
-pl <file.txt>: writes list of p-values for each site to file.txt.

Examples:
1. Calculate rates for file test.ref.ti against itself, with a list of rates:
tiger rate -i test.ref.ti -rl
2. Calculate rates for file test.0.ti against test.ref.ti with a PTP test and a list of p values
tiger rate -i test.0.ti -r test.ref.ti -ptp -pl

"""
tiger rate Options:

-i|input Specify input file. File should be in .ti format.

-r|reference Specify reference sequence (.ti). -i file is used as default if none is provided.

-o|output Specify prefix name for output files.

-rl|rate_list A list of the rate at each site may be optionally written to a specified
file.
-rl <file.txt> : writes list of the rates at each site to file.txt.

-ptp Specifies that a PTP test should be run.
* Note * this option has a huge effect on running time!

-z|randomisations Number of randomisations to be used for the PTP test.
-z <int>: each site will be randomised <int> times. <int> is a whole number.

Default is 100

-p|p_value Specify p-value which denotes significance in PTP test.
-p <float>: site will be denoted as significant if p-value is better than <float>.
<float> is a floating point number.

Default is 0.05

-pl|pval_list Write a list of p-values to a specified file.
-pl <file.txt>: writes list of p-values for each site to file.txt.

Examples:
1. Calculate rates for file test.ref.ti against itself, with a list of rates:
tiger rate -i test.ref.ti -rl
2. Calculate rates for file test.0.ti against test.ref.ti with a PTP test and a list of p values
tiger rate -i test.0.ti -r test.ref.ti -ptp -pl

""")
sys.exit(1)

def die_with_message(message):
print message
print(message)
sys.exit(1)


Expand Down
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