mycrobiota: mycrobiota.py annotate

annotate mycrobiota.py @ 0:607c5e7e0a64 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5

author	erasmus-medical-center
date	Wed, 13 Dec 2017 10:09:50 -0500
parents
children

rev	line source
0 607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	1 import argparse
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	2 import csv
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	3 import math
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	4 import os
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	5 from subprocess import call
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	6
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	7
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	8 def main():
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	9 print("Welcome to the MYcrobiota suite")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	10 parser = argparse.ArgumentParser()
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	11 parser.add_argument('-c', '--command', required=True,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	12 help="What action to perform")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	13 parser.add_argument('-ct', '--count_table', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	14 help="mothur count table")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	15 parser.add_argument('-cp', '--copies', help="copies of NC for samples")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	16 parser.add_argument('-nccp', '--nc_copies', help="copies of NC for itself")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	17 parser.add_argument('-t', '--taxonomy', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	18 help="mothur taxonomy file")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	19 parser.add_argument('-s', '--shared_file', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	20 help="mothur shared file")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	21 parser.add_argument('-otu', '--otutable', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	22 help="mothur OTU table")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	23 parser.add_argument('-f', '--fasta', action='append', help="fasta")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	24 parser.add_argument('-sl', '--summary_log', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	25 help="mothur summary log file")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	26 parser.add_argument('-o', '--outfile', help="output file")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	27 parser.add_argument('-od', '--outdir', help="output directory", default="")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	28 parser.add_argument('-lv', '--level', help="taxonomy level")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	29 parser.add_argument('-nc', '--negative_control',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	30 help="sample name of the negative control")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	31 parser.add_argument('-ncs', '--negative_control_species',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	32 help="species name of the negative control",
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	33 default="Oscillatoria")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	34 parser.add_argument('-r', '--replicate_suffix',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	35 help="suffix to identify replicates")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	36 parser.add_argument('-l', '--label', action='append',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	37 help="label for count table")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	38 parser.add_argument('--with-otu', dest='with_otu', action='store_true',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	39 default=False)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	40 args = parser.parse_args()
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	41
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	42 try:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	43 os.mkdir(args.outdir)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	44 except OSError:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	45 pass
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	46
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	47 print("Running command: "+args.command)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	48
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	49 if args.command == 'counttable_totals':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	50 count_table_totals(args.count_table[0], args.outdir, args.outfile)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	51
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	52 elif args.command == 'qc_report':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	53 if args.count_table:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	54 qc_report(args.count_table, args.label, 'counttables', args.outdir)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	55 elif args.summary_log:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	56 qc_report(args.summary_log, args.label, 'summarylogs', args.outdir)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	57
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	58 elif args.command == 'create_krona_plot':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	59 create_krona_plot(args.taxonomy, args.outdir, args.with_otu)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	60
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	61 elif args.command == 'create_krona_plot_multisample':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	62 create_krona_plot_multisample(args.taxonomy, args.shared_file,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	63 args.level, args.outdir, args.with_otu)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	64
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	65 elif args.command == 'correct_replicates':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	66 correct_replicates(args.shared_file, args.taxonomy, args.outdir,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	67 args.replicate_suffix, args.copies,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	68 args.negative_control, args.nc_copies,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	69 args.negative_control_species)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	70
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	71 elif args.command == 'make_multi_otutable':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	72 make_multi_otutable(args.taxonomy, args.shared_file, args.level,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	73 args.outdir)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	74
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	75 elif args.command == 'otutable_add_blast_links':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	76 otutable_add_blast_links(args.otutable, args.fasta)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	77
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	78 elif args.command == 'split_multi_otutable':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	79 split_multi_otutable(args.otutable)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	80
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	81 else:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	82 print("unknown command. exiting")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	83
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	84
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	85 def make_url(seq, baseurl):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	86 return baseurl+"?DATABASE=nr&PERC_IDENT=97&EXCLUDE_SEQ_UNCULT=on&" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	87 "HITLIST_SIZE=10&FILTER=L&FILTER=m&FILTER=R&EXPECT=10&" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	88 "FORMAT_TYPE=HTML&PROGRAM=blastn&CLIENT=web&" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	89 "SERVICE=megablast&PAGE=Nucleotides&CMD=Put&QUERY=" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	90 + seq.lower()
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	91
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	92
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	93 def make_RIDlink(RID, baseurl):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	94 return "<a target=\"_blank\" href=\""+baseurl+"?CMD=Get&RID="\
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	95 + RID + "\">view results</a>"
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	96
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	97
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	98 def make_rerun_link(seq, baseurl):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	99 return "<a target=\"_blank\" href=\"" + baseurl +\
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	100 "?DATABASE=nr&EXCLUDE_SEQ_UNCULT=yes&FILTER=L&FORMAT_TYPE=HTML" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	101 "&PROGRAM=blastn&CLIENT=web&SERVICE=megablast&PAGE=Nucleotides&" \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	102 "CMD=Web&QUERY=" + seq.lower() + "\">send to BLAST</a>"
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	103
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	104
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	105 def otutable_add_blast_links(otutable, otureps):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	106 baseurl = "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi"
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	107
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	108 # for each otu create blast search of corresponding representative sequence
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	109 reps = [line for line in open(otureps[0], "r")]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	110
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	111 seqs = [r.rstrip('\n').replace('-', '') for r in reps if '>' not in r]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	112 seq_names = [r for r in reps if '>' in r]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	113 otulines = [line for line in open(otutable[0], "r")]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	114
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	115 # Add RID link and rerun link to table
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	116 with open("otutable_with_blast.tsv", "w+") as outfile, \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	117 open("filtered_otureps.fasta", "w+") as repsout:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	118 outfile.write(otulines[0].rstrip() + "\tBLAST\n")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	119
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	120 for otuline in otulines[1:]:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	121 otu = otuline.split('\t')[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	122 for i, seq in enumerate(seq_names):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	123 if otu in seq:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	124 outfile.write(otuline.rstrip() + "\t" +
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	125 make_rerun_link(seqs[i], baseurl) + "\n")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	126 # output otureps for these otus
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	127 for i, seq in enumerate(reps):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	128 if otu in seq:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	129 repsout.write(reps[i])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	130 repsout.write(reps[i+1])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	131
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	132
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	133 def summarylog_total(infile):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	134 with open(infile) as f:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	135 summarylog = f.readlines()
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	136 for line in summarylog:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	137 if line.startswith('# of Seqs:') \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	138 or line.startswith('total # of seqs:'):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	139 return int(line.split('\t')[-1])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	140 return None
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	141
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	142
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	143 def count_table_totals(infile, outdir='', outfile=''):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	144 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	145 Given a Mothur counttable, calculate the total number of sequences for each
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	146 sample. This can be appended as additional row in the count table by
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	147 providing a file name.
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	148
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	149 :param infile: Mothur count table.
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	150 :param outfile: Optional. Write the count table with an additional row with
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	151 totals to this file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	152 :param outdir: Optional. Write output do this directory
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	153 :return: A list with totals for all columns (samples) in the count table
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	154 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	155 # assume a single input file for now
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	156 out_rows = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	157 with open(infile) as f:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	158 count_table = csv.reader(f, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	159
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	160 header = next(count_table)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	161 totals = [0] * (len(header)-1)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	162
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	163 out_rows.append(header)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	164 for row in count_table:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	165 if row[0] != 'total':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	166 out_rows.append(row)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	167 for i in range(1, len(row)):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	168 totals[i-1] += int(row[i])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	169
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	170 out_rows.append(["total"] + map(str, totals))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	171
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	172 # write count table with totals to file if requested
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	173 if outfile:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	174 write_output(outdir, outfile, out_rows)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	175
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	176 return totals
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	177
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	178
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	179 def qc_report(infiles, label, inputtype, outdir=''):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	180 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	181 Construct QC table from multiple count files
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	182 - Report the number of sequences lost at each consecutive QC step
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	183 - Create a multi-sample report and a separate report for each sample
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	184
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	185 :param infiles: set of count tables
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	186 :param label: labels for each step
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	187 :param outdir: directory to place output files. Default: cwd
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	188 :return:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	189 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	190 assert len(infiles) == len(label), \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	191 "number of files and labels unequal, stopping"
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	192
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	193 print("qcreport")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	194 previous_totals = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	195 outlines = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	196 lasttotal = None
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	197
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	198 for (i, lab) in zip(infiles, label):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	199 with open(i, 'rb') as f:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	200 count_file = csv.reader(f, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	201
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	202 if inputtype == 'summarylogs':
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	203 print("summarylogs")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	204 if not outlines:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	205 outlines = [['Step', 'Total', 'Removed', 'Percentage']]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	206
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	207 # get total count
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	208 total = summarylog_total(i)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	209
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	210 # calculate difference with last
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	211 if not lasttotal:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	212 outlines.append([lab, total, None, None])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	213 else:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	214 diff = total - lasttotal
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	215 perc = float(diff)/float(lasttotal)*100.0
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	216 outlines.append([lab, total, diff, str("%.1f" % perc)+"%"])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	217
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	218 lasttotal = total
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	219
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	220 else:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	221 # add header line to output
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	222 if not outlines:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	223 outlines = [['step'] + next(count_file)[1:]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	224
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	225 # calculate totals of each column in the count file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	226 totals = count_table_totals(i)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	227
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	228 # calculate difference with previous count file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	229 if not previous_totals:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	230 diffs = [""] * len(totals)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	231 else:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	232 diffs = [" (" + str(t1-t2)+"; "
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	233 + str("%.1f" % (float(t1-t2)/float(t2)*100.0)) +
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	234 "%)" for t1, t2 in zip(totals, previous_totals)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	235
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	236 outlines.append([lab] +
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	237 [str(a)+b for a, b in zip(totals, diffs)])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	238 previous_totals = totals
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	239
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	240 # write multi-sample output file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	241 write_output(outdir, 'all_qctable.tsv', outlines)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	242
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	243 # write per-sample output files
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	244 for j in range(2, len(outlines[0])):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	245 sample = outlines[0][j]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	246 sample_outlines = [[outlines_line[0], outlines_line[j]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	247 for outlines_line in outlines]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	248 write_output(outdir, 'persample_qctable_'+sample+'.tsv',
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	249 sample_outlines)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	250
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	251
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	252 def column(matrix, i):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	253 return [row[i] for row in matrix]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	254
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	255
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	256 def mean(data):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	257 return sum(data) / float(len(data))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	258
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	259
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	260 def stdev(data):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	261 c = mean(data)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	262 ss = sum((x-c)**2 for x in data)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	263 n = len(data)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	264 return math.sqrt(ss/(n-1))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	265
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	266
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	267 def write_output(outdir, filename, outlines):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	268 with open(os.path.join(outdir, filename), 'wb') as of:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	269 out_table = csv.writer(of, delimiter='\t', lineterminator='\n')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	270 for row in outlines:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	271 out_table.writerow(row)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	272
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	273
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	274 def correct_replicates(shared, taxonomy, outdir, replicate_suffix,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	275 sample_copies, negative_control='', nc_copies=-1,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	276 negative_control_species='Oscillatoria'):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	277 with open(shared[0], 'rb') as f, open(taxonomy[0], 'rb') as f2:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	278 shared_file = csv.reader(f, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	279 taxonomy_file = csv.reader(f2, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	280
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	281 # determine which OTU number is the control, Oscillatoria by default
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	282 # (Bacteria;Cyanobacteria;Cyanobacteria;..;Oscillatoria)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	283 try:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	284 line = next(taxonomy_file)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	285 while negative_control_species not in line[2]:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	286 line = next(taxonomy_file)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	287 otu = line[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	288 except StopIteration:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	289 print("negative control species not found in taxonomy, Exiting")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	290 return 1
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	291
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	292 ''' Calculate Copies '''
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	293 # per replicate of sample and NC, determine correction factor,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	294 # (number Oscillatoria seqs/known copies of it)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	295 # correct all sequence counts with that
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	296 myshared = [row for row in shared_file if row]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	297 newshared = [myshared[0]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	298 newshared2 = [myshared[0]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	299 newshared3 = [myshared[0]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	300 newshared4 = [myshared[0]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	301 oscil_column = myshared[0].index(otu)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	302
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	303 for row in myshared[1:]:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	304 if row[1].startswith(negative_control):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	305 copies = nc_copies
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	306 else:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	307 copies = sample_copies
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	308
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	309 correction_factor = float(row[oscil_column]) / float(copies)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	310
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	311 new_row = row[0:3]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	312 for count in row[3:]:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	313 try:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	314 newval = float(count) / correction_factor
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	315 except ZeroDivisionError:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	316 newval = float(count)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	317 new_row.append(newval)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	318 newshared.append(new_row)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	319
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	320 ''' Average copy counts across replicates '''
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	321 levels = set([row[0] for row in newshared[1:]])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	322 samples = set([row[1].split(replicate_suffix)[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	323 for row in newshared[1:]])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	324
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	325 for level in levels:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	326 for sample in samples:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	327 neg = True if sample.startswith(negative_control) else False
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	328 replicates = [row for row in newshared if row[0] == level
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	329 and row[1].startswith(sample)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	330 num_otus = int(replicates[0][2])+3
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	331 total = replicates[0][2]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	332 avg = [level, sample, total]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	333
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	334 for i in range(3, num_otus):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	335 counts = column(replicates, i)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	336 avg.append(mean(counts)) if 0 not in counts or neg \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	337 else avg.append(0)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	338
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	339 newshared2.append(avg)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	340
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	341 ''' Average sequence counts across replicates '''
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	342 levels = set([row[0] for row in myshared[1:]])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	343 samples = set([row[1].split(replicate_suffix)[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	344 for row in myshared[1:]])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	345
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	346 for level in levels:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	347 for sample in samples:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	348 replicates = [row for row in myshared if row[0] == level
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	349 and row[1].startswith(sample)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	350 num_otus = int(replicates[0][2]) + 3
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	351 total = replicates[0][2]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	352 avg = [level, sample, total]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	353
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	354 for i in range(3, num_otus):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	355 counts = map(int, column(replicates, i))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	356 avg.append(int(round(mean(counts))))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	357
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	358 newshared4.append(avg)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	359
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	360 ''' Correct for background '''
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	361 # for each otu, subtract 3 times the standard deviation of
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	362 # the negative control sample
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	363 for level in levels:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	364 NC = [row for row in newshared if row[0] == level
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	365 and row[1].startswith(negative_control)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	366 samples = [row for row in newshared2 if row[0] == level
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	367 and not row[1].startswith(negative_control)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	368 num_otus = int(samples[0][2])+3
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	369
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	370 for i in range(3, num_otus):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	371 m = mean(column(NC, i))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	372 sd = stdev(column(NC, i))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	373 corr = m + 3*sd
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	374
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	375 for s in samples:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	376 s[i] = max(0, int(round(s[i] - corr)))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	377
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	378 newshared3 += samples
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	379
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	380 # remove Negative control species otu from table
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	381 for i, row in enumerate(newshared3):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	382 del row[oscil_column]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	383 if i > 0:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	384 row[2] = int(row[2]) - 1
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	385
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	386 # sort file or other mothur tools may segfault :/
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	387 newshared3 = [newshared3[0]] + sorted(newshared3[1:],
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	388 key=lambda a_entry: a_entry[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	389 if a_entry[0] != 'unique' else 0)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	390
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	391 f2.seek(0)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	392 taxonomy_out = [row for row in taxonomy_file if row and row[0] != otu]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	393 write_output(outdir, 'taxonomy_corrected.tsv', taxonomy_out)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	394 write_output(outdir, 'shared_corrected.tsv', newshared3)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	395 write_output(outdir, 'shared_averaged.tsv', newshared4)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	396
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	397
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	398 def make_multi_otutable(taxonomy_file, shared_file, level, outdir):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	399 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	400 Create an otu table from shared file and taxonomy file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	401
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	402 example output:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	403
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	404 OTU sample1 sample2 .. sampleX Kingdom Phylum Class Order Family Genus
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	405 Otu001 13 8 .. 91 Bacteria Bacteroidetes Bacteroidia ..
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	406 ...
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	407
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	408 :param taxonomy_file:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	409 :param shared_file:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	410 :param level:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	411
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	412 :return:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	413 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	414
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	415 outlines = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	416 samples = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	417 # create multisample taxonomy from counts in shared file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	418 with open(taxonomy_file[0], 'r') as tax, open(shared_file[0]) as sh:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	419 taxonomy = csv.reader(tax, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	420 shared = csv.reader(sh, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	421 shared_header = next(shared)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	422 outlines.append(shared_header[3:])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	423
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	424 # get all taxonomies
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	425 taxonomies = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	426 for j, t in enumerate(taxonomy):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	427 if j > 0:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	428 taxonomies.append(filter(None, [x.split('(')[0]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	429 for x in t[2].split(';')]))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	430
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	431 for i, row in enumerate(shared):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	432 tax.seek(0) # make sure to start at beginning of file each time
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	433 if row[0] == level:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	434 samples.append(row[1])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	435 outlines.append(row[3:])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	436
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	437 transposed = map(list, zip(*outlines))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	438 header = ["OTU"] + samples + ["Kingdom", "Phylum", "Class", "Order",
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	439 "Family", "Genus"]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	440
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	441 writelines = [header] + [a + b for a, b in zip(transposed, taxonomies)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	442 if a[1:] != ['0'] * len(a[1:])]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	443
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	444 # sort sample columns by name
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	445 lst = map(list, zip(*[w[1:-6] for w in writelines]))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	446 lst.sort(key=lambda x: x[0])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	447 lst = map(list, zip(*lst))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	448 writelines2 = [[writelines[i][0]] + lst[i] + writelines[i][-6:]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	449 for i in range(0, len(writelines))]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	450
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	451 # output corrected shared file
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	452 write_output(outdir, "multi_otutable.tsv", writelines2)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	453
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	454
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	455 def split_multi_otutable(otutable, with_avg=True):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	456 fulltable = [line.strip().split('\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	457 for line in open(otutable[0], 'r') if line]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	458 samples = [s.split('_')[0] for s in fulltable[0][1:-6]]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	459 numcols = len(fulltable[0])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	460 numreplicates = (numcols - 7) / len(set(samples))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	461
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	462 for sample in set(samples):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	463 outlines = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	464 cols = [0] + [i+1 for i, s in enumerate(samples) if sample in s] \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	465 + [i for i in range(numcols-6, numcols)]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	466 for i, line in enumerate(fulltable):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	467 out = [line[j] for j in cols]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	468 if out[1:-6] != ['0'] * numreplicates:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	469 out.insert(-6, 'mean' if i == 0
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	470 else int(round(mean(map(int, out[1:-6])))))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	471 outlines.append(out)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	472
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	473 write_output('.', sample+'.otutable', outlines)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	474
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	475
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	476 def create_krona_plot_multisample(taxonomy_file, shared_file, level, outdir,
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	477 with_otu):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	478 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	479 Create krona plots from a multisample taxonomy plot and a shared file.
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	480 Create one multisample plot and a plot per individual sample
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	481
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	482 :param taxonomy_file:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	483 :param shared_file:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	484 :param level: which level to use, e.g. unique/0.03/..
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	485 :param with_otu:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	486 :return:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	487 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	488
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	489 taxonomies = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	490
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	491 # create taxonomy file per sample
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	492 with open(taxonomy_file[0], 'r') as tax, open(shared_file[0]) as sh:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	493 taxonomy = csv.reader(tax, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	494 shared = csv.reader(sh, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	495 shared_header = next(shared)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	496
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	497 for i, row in enumerate(shared):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	498 tax.seek(0) # make sure to start at beginning of file each time
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	499 if row[0] == level:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	500 sample = row[1]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	501
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	502 outfile = os.path.join(outdir, sample+".tsv")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	503 taxonomies.append(outfile)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	504 with open(outfile, 'w+') as of:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	505 out_table = csv.writer(of, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	506 out_table.writerow(next(taxonomy)) # header line
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	507 for j, t in enumerate(taxonomy):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	508 assert t[0] == shared_header[j+3], \
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	509 "OTU mismatch between taxonomy and shared file"
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	510 t[1] = row[j+3]
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	511 out_table.writerow(t + [shared_header[j+3]])
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	512
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	513 # make krona plot
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	514 create_krona_plot(taxonomies, outdir, with_otu)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	515
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	516
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	517 def create_krona_plot(taxonomy_files, outdir, with_otu):
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	518 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	519 Create a krona plot from one or more mothur taxonomy files
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	520
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	521 :param taxonomy_files: mothur taxonomy file (output from classify.otu)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	522 :param outdir: directory to store krona-formatted outputs. Default=cwd
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	523 :param with_otu: add OTU number as a level in the Krona plot? Default=True
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	524 :return:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	525 """
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	526 krona_input_files = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	527
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	528 # convert taxonomy files to krona input.
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	529 for tax in taxonomy_files:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	530 with open(tax, 'r') as f:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	531 taxonomy = csv.reader(f, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	532 out_rows = []
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	533
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	534 next(taxonomy) # skip header line
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	535 for row in taxonomy:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	536 out_rows.append(
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	537 filter(None, [row[1]] + row[2].rstrip(";\n").split(';') +
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	538 [row[0] if with_otu else None]))
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	539
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	540 outfile = os.path.join(outdir, tax.split("/")[-1]+"krona")
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	541 krona_input_files.append(outfile)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	542
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	543 with open(outfile, 'w+') as f2:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	544 out_table = csv.writer(f2, delimiter='\t')
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	545 for row in out_rows:
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	546 out_table.writerow(row)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	547
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	548 # execute krona command
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	549 call(["ktImportText"] + krona_input_files)
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	550
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	551
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	552 if __name__ == "__main__":
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5 erasmus-medical-center parents: diff changeset	553 main()

Mercurial > repos > erasmus-medical-center > mycrobiota

annotate mycrobiota.py @ 0:607c5e7e0a64 draft