span: span_wrapper.py annotate

annotate span_wrapper.py @ 3:4130e95bd6c8 draft

Batch processing mode supported

author	jetbrains
date	Mon, 19 Nov 2018 08:24:04 -0500
parents	5b99943c4627
children	70500fd87b60

rev	line source
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	1 #!/usr/bin/env python
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	2
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	3 import os
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	4 import shutil
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	5 import subprocess
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	6 import sys
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	7
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	8 argv = sys.argv[1:]
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	9 print 'Arguments {0}'.format(argv)
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	10
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	11 SPAN_JAR = os.environ.get("SPAN_JAR")
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	12 print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	13
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	14 # #if str($action.action_selector) == "model"
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	15 # #if str($control_file) != 'None':
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	16 # span_wrapper.py model_with_control
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	17 # "${genome_identifier}" "${genome_file}"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	18 # "${treatment_identifier}" "${treatment_file}"
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	19 # "${control_identifier}" "${control_file}"
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	20 # "${bin}"
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	21 #
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	22 # #else
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	23 # span_wrapper.py model without_control
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	24 # "${genome_identifier}" "${genome_file}"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	25 # "${treatment_identifier}" "${treatment_file}"
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	26 # "${bin}"
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	27 # #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	28 # #else
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	29 # #if str($control_file) != 'None':
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	30 # span_wrapper.py peaks_with_control
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	31 # "${genome_identifier}" "${genome_file}"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	32 # "${treatment_identifier}" "${treatment_file}"
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	33 # "${control_identifier}" "${control_file}"
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	34 # "${bin}"
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	35 # "${action.fdr}" "${action.gap}"
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	36 # #else
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	37 # span_wrapper.py peaks_without_control
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	38 # "${genome_identifier}" "${genome_file}"
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	39 # "${treatment_identifier}" "${treatment_file}"
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	40 # "${bin}"
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	41 # "${action.fdr}" "${action.gap}"
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	42 # #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	43 # #end if
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	44 action = argv[0]
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	45
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	46 working_dir = os.path.abspath('.')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	47 print 'WORKING DIRECTORY: {}'.format(working_dir)
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	48
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	49
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	50 def link(name, f):
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	51 """ SPAN uses file extension to detect input type, so original names are necessary, instead of Galaxy .dat files"""
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	52 result = os.path.join(working_dir, name)
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	53 if not os.path.exists(result):
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	54 os.symlink(f, result)
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	55 return result
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	56
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	57
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	58 if action == 'model_with_control':
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	59 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	60 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	61 control, control_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	62 bin) = argv[1:]
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	63 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} --bin {}'.format(
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	64 SPAN_JAR,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	65 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	66 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	67 link(control, control_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	68 bin)
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	69 elif action == 'model_without_control':
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	70 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	71 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	72 bin) = argv[1:]
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	73 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --bin {}'.format(
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	74 SPAN_JAR,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	75 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	76 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	77 bin)
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	78 elif action == "peaks_with_control":
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	79 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	80 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	81 control, control_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	82 bin,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	83 fdr, gap) = argv[1:]
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	84 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} --control {} ' \
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	85 '--bin {} --fdr {} --gap {} --peaks {}'.format(
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	86 SPAN_JAR,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	87 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	88 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	89 link(control, control_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	90 bin, fdr, gap,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	91 os.path.join(working_dir, 'result.peak'))
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	92 elif action == 'peaks_without_control':
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	93 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	94 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	95 bin,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	96 fdr, gap) = argv[1:]
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	97 cmd = 'java -jar {} analyze --chrom.sizes {} --treatment {} -' \
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	98 '-bin {} --fdr {} --gap {} --peaks {}'.format(
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	99 SPAN_JAR,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	100 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	101 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	102 bin, fdr, gap,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	103 os.path.join(working_dir, 'result.peak'))
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	104 else:
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	105 raise Exception("Unknown action command {}".format(action))
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	106
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	107 print 'Launching SPAN: {}'.format(cmd)
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	108 subprocess.check_call(cmd, cwd=None, shell=True)
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	109
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	110 # Move model to the the working dir with given name
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	111 fit_dir = os.path.join(working_dir, 'fit')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	112 model_original = os.path.join(fit_dir, os.listdir(fit_dir)[0])
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	113 shutil.move(model_original, os.path.join(working_dir, 'model.span'))
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	114
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	115 # Move log file
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	116 logs_dir = os.path.join(working_dir, 'logs')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	117 log_original = os.path.join(logs_dir, os.listdir(logs_dir)[0])
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	118 shutil.move(log_original, os.path.join(working_dir, "span.log"))

Mercurial > repos > jetbrains > span

annotate span_wrapper.py @ 3:4130e95bd6c8 draft