tmhmm_and_signalp: tools/protein_analysis/psortb.py annotate

annotate tools/protein_analysis/psortb.py @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

author	peterjc
date	Thu, 21 Sep 2017 11:35:20 -0400
parents	f3ecd80850e2
children	238eae32483c

rev	line source
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	1 #!/usr/bin/env python
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	2 """Wrapper for psortb for use in Galaxy.
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	3
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	4 This script takes exactly six command line arguments - which includes the
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	5 number of threads, and the input protein FASTA filename and output
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	6 tabular filename. It then splits up the FASTA input and calls multiple
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	7 copies of the standalone psortb v3 program, then collates the output.
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	8 e.g. Rather than this,
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	9
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	10 psort $type -c $cutoff -d $divergent -o long $sequence > $outfile
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	11
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	12 Call this:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	13
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	14 psort $threads $type $cutoff $divergent $sequence $outfile
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	15
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	16 If ommitting -c or -d options, set $cutoff and $divergent to zero or blank.
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	17
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	18 Note that this is somewhat redundant with job-splitting available in Galaxy
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	19 itself (see the SignalP XML file for settings), but both can be applied.
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	20
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	21 Additionally it ensures the header line (with the column names) starts
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	22 with a # character as used elsewhere in Galaxy.
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	23 """
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	24
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	25 from __future__ import print_function
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	26
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	27 import os
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	28 import sys
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	29 import tempfile
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	30
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	31 from seq_analysis_utils import run_jobs, split_fasta, thread_count
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	32
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	33 FASTA_CHUNK = 500
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	34
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	35 if "-v" in sys.argv or "--version" in sys.argv:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	36 """Return underlying PSORTb's version"""
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	37 sys.exit(os.system("psort --version"))
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	38
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	39 if len(sys.argv) != 8:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	40 sys.exit("Require 7 arguments, number of threads (int), type (e.g. archaea), "
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	41 "output (e.g. terse/normal/long), cutoff, divergent, input protein "
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	42 "FASTA file & output tabular file")
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	43
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	44 num_threads = thread_count(sys.argv[1], default=4)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	45 org_type = sys.argv[2]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	46 out_type = sys.argv[3]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	47 cutoff = sys.argv[4]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	48 if cutoff.strip() and float(cutoff.strip()) != 0.0:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	49 cutoff = "-c %s" % cutoff
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	50 else:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	51 cutoff = ""
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	52 divergent = sys.argv[5]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	53 if divergent.strip() and float(divergent.strip()) != 0.0:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	54 divergent = "-d %s" % divergent
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	55 else:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	56 divergent = ""
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	57 fasta_file = sys.argv[6]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	58 tabular_file = sys.argv[7]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	59
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	60 if out_type == "terse":
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	61 header = ['SeqID', 'Localization', 'Score']
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	62 elif out_type == "normal":
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	63 sys.exit("Normal output not implemented yet, sorry.")
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	64 elif out_type == "long":
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	65 if org_type == "-n":
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	66 # Gram negative bacteria
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	67 header = ['SeqID', 'CMSVM-_Localization', 'CMSVM-_Details', 'CytoSVM-_Localization', 'CytoSVM-_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	68 'ECSVM-_Localization', 'ECSVM-_Details', 'ModHMM-_Localization', 'ModHMM-_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	69 'Motif-_Localization', 'Motif-_Details', 'OMPMotif-_Localization', 'OMPMotif-_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	70 'OMSVM-_Localization', 'OMSVM-_Details', 'PPSVM-_Localization', 'PPSVM-_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	71 'Profile-_Localization', 'Profile-_Details',
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	72 'SCL-BLAST-_Localization', 'SCL-BLAST-_Details',
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	73 'SCL-BLASTe-_Localization', 'SCL-BLASTe-_Details',
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	74 'Signal-_Localization', 'Signal-_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	75 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Periplasmic_Score', 'OuterMembrane_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	76 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	77 'Secondary_Localization', 'PSortb_Version']
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	78 elif org_type == "-p":
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	79 # Gram positive bacteria
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	80 header = ['SeqID', 'CMSVM+_Localization', 'CMSVM+_Details', 'CWSVM+_Localization', 'CWSVM+_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	81 'CytoSVM+_Localization', 'CytoSVM+_Details', 'ECSVM+_Localization', 'ECSVM+_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	82 'ModHMM+_Localization', 'ModHMM+_Details', 'Motif+_Localization', 'Motif+_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	83 'Profile+_Localization', 'Profile+_Details',
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	84 'SCL-BLAST+_Localization', 'SCL-BLAST+_Details',
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	85 'SCL-BLASTe+_Localization', 'SCL-BLASTe+_Details',
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	86 'Signal+_Localization', 'Signal+_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	87 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Cellwall_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	88 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	89 'Secondary_Localization', 'PSortb_Version']
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	90 elif org_type == "-a":
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	91 # Archaea
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	92 header = ['SeqID', 'CMSVM_a_Localization', 'CMSVM_a_Details', 'CWSVM_a_Localization', 'CWSVM_a_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	93 'CytoSVM_a_Localization', 'CytoSVM_a_Details', 'ECSVM_a_Localization', 'ECSVM_a_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	94 'ModHMM_a_Localization', 'ModHMM_a_Details', 'Motif_a_Localization', 'Motif_a_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	95 'Profile_a_Localization', 'Profile_a_Details',
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	96 'SCL-BLAST_a_Localization', 'SCL-BLAST_a_Details',
a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	97 'SCL-BLASTe_a_Localization', 'SCL-BLASTe_a_Details',
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	98 'Signal_a_Localization', 'Signal_a_Details',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	99 'Cytoplasmic_Score', 'CytoplasmicMembrane_Score', 'Cellwall_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	100 'Extracellular_Score', 'Final_Localization', 'Final_Localization_Details', 'Final_Score',
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	101 'Secondary_Localization', 'PSortb_Version']
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	102 else:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	103 sys.exit("Expected -n, -p or -a for the organism type, not %r" % org_type)
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	104 else:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	105 sys.exit("Expected terse, normal or long for the output type, not %r" % out_type)
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	106
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	107 tmp_dir = tempfile.mkdtemp()
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	108
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	109
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	110 def clean_tabular(raw_handle, out_handle):
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	111 """Clean up tabular TMHMM output, returns output line count."""
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	112 global header
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	113 count = 0
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	114 for line in raw_handle:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	115 if not line.strip() or line.startswith("#"):
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	116 # Ignore any blank lines or comment lines
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	117 continue
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	118 parts = [x.strip() for x in line.rstrip("\r\n").split("\t")]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	119 if parts == header:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	120 # Ignore the header line
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	121 continue
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	122 if not parts[-1] and len(parts) == len(header) + 1:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	123 # Ignore dummy blank extra column, e.g.
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	124 # "...2.0\t\tPSORTb version 3.0\t\n"
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	125 parts = parts[:-1]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	126 assert len(parts) == len(header), \
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	127 "%i fields, not %i, in line:\n%r" % (len(line), len(header), line)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	128 out_handle.write(line)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	129 count += 1
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	130 return count
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	131
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	132
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	133 # Note that if the input FASTA file contains no sequences,
f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	134 # split_fasta returns an empty list (i.e. zero temp files).
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	135 fasta_files = split_fasta(fasta_file, os.path.join(tmp_dir, "tmhmm"), FASTA_CHUNK)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	136 temp_files = [f + ".out" for f in fasta_files]
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	137 jobs = ["psort %s %s %s -o %s %s > %s" % (org_type, cutoff, divergent, out_type, fasta, temp)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	138 for fasta, temp in zip(fasta_files, temp_files)]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	139
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	140
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	141 def clean_up(file_list):
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	142 for f in file_list:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	143 if os.path.isfile(f):
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	144 os.remove(f)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	145 try:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	146 os.rmdir(tmp_dir)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	147 except Exception:
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	148 pass
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	149
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	150
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	151 if len(jobs) > 1 and num_threads > 1:
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	152 # A small "info" message for Galaxy to show the user.
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	153 print("Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs)))
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	154 results = run_jobs(jobs, num_threads)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	155 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	156 error_level = results[cmd]
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	157 if error_level:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	158 try:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	159 output = open(temp).readline()
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	160 except IOError:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	161 output = ""
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	162 clean_up(fasta_files + temp_files)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	163 sys.exit("One or more tasks failed, e.g. %i from %r gave:\n%s" % (error_level, cmd, output),
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	164 error_level)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	165 del results
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	166 del jobs
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	167
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	168 out_handle = open(tabular_file, "w")
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	169 out_handle.write("#%s\n" % "\t".join(header))
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	170 count = 0
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	171 for temp in temp_files:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	172 data_handle = open(temp)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	173 count += clean_tabular(data_handle, out_handle)
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	174 data_handle.close()
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	175 if not count:
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	176 clean_up(fasta_files + temp_files)
19 f3ecd80850e2 v0.2.9 Python style improvements peterjc parents: 18 diff changeset	177 sys.exit("No output from psortb")
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	178 out_handle.close()
20 a19b3ded8f33 v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 19 diff changeset	179 print("%i records" % count)
11 99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	180
99b82a2b1272 Uploaded v0.2.0 which added PSORTb wrapper (written with Konrad Paszkiewicz) peterjc parents: diff changeset	181 clean_up(fasta_files + temp_files)

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/psortb.py @ 20:a19b3ded8f33 draft