Mercurial > repos > drosofff > msp_fasta_tabular_converter

annotate fasta_tabular_converter.py @ 3:36388b666bfc draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:24:13 -0500
parents 330dd8a8c31a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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1 #!/usr/bin/env python
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2 #
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36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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3 import argparse
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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4 import logging
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951cb6b3979b planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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5 import sys
951cb6b3979b planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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6 from collections import defaultdict
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7
3
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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9 def Parser():
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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10 the_parser = argparse.ArgumentParser()
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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11 the_parser.add_argument(
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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12 '--input', action="store", type=str, help="input file")
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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13 the_parser.add_argument(
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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14 '--output', action="store", type=str, help="output converted file")
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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15 the_parser.add_argument(
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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16 '--type', action="store", type=str, help="type of convertion")
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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17 args = the_parser.parse_args()
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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18 return args
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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1
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21 def readfasta_writetabular(fasta, tabular, mode="oneline"):
3
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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22 for line in fasta:
1
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23 if line[0] == ">":
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24 try:
3
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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25 seqdic["".join(stringlist)] += 1 # to dump the sequence of the previous item - try because of first missing stringlist variable
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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26 except NameError:
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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27 pass
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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28 stringlist = []
1
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29 else:
3
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30 try:
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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31 stringlist.append(line[:-1])
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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32 except UnboundLocalError: # if file went through filter and contains only empty lines
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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33 logging.info("first line is empty.")
2
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34 try:
3
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35 seqdic["".join(stringlist)] += 1 # for the last sequence
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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36 except NameError:
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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37 logging.info("input file has not fasta sequences.")
1
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38 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
3
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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39 tabular.write("%s\t%s\n" % (seq, seqdic[seq]))
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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40
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41
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42 def readtabular_writefasta(tabular, fasta):
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36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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43 counter = 0
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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44 for line in tabular:
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45 fields = line.split()
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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46 for i in range(int(fields[1])):
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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47 counter += 1
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48 fasta.write(">%s\n%s\n" % (counter, fields[0]))
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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49
0
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50
3
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51 def readtabular_writefastaweighted(tabular, fasta):
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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52 counter = 0
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53 for line in tabular:
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54 counter += 1
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55 fields = line[:-1].split()
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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56 fasta.write(">%s_%s\n%s\n" % (counter, fields[1], fields[0]))
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57
0
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58
3
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59 def readfastaweighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed):
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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60 number_reads = 0
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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61 for line in fastaweigthed_input:
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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62 if line[0] == ">":
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63 weigth = int(line[1:-1].split("_")[-1])
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64 number_reads += weigth
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65 else:
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66 seqdic[line[:-1]] += weigth
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67 n = 0
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68 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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69 n += 1
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70 fastaweigthed_reparsed.write(">%s_%s\n%s\n" % (n, seqdic[seq], seq))
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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71 log.info("%s reads collapsed" % number_reads)
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72
3
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73
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74 def readfastaweighted_writefasta(fastaweigthed, fasta):
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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75 counter = 0
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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76 for line in fastaweigthed:
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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77 if line[0] == ">":
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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78 weigth = int(line[1:-1].split("_")[-1])
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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79 else:
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80 seq = line[:-1]
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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81 for i in range(weigth):
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82 counter += 1
36388b666bfc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit b6de14061c479f0418cd89e26d6f5ac26e565a07
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83 fasta.write(">%s\n%s\n" % (counter, seq))
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84
0
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85
1
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86 def main(input, output, type):
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87 with open(input, "r") as input:
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88 with open(output, "w") as output:
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89 if type == "fasta2tabular":
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90 readfasta_writetabular(input, output)
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91 elif type == "tabular2fasta":
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92 readtabular_writefasta(input, output)
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93 elif type == "tabular2fastaweight":
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94 readtabular_writefastaweighted(input, output)
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95 elif type == "fastaweight2fastaweight":
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96 readfastaweighted_writefastaweighted(input, output)
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97 elif type == "fastaweight2fasta":
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98 readfastaweighted_writefasta(input, output)
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99
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100
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101 if __name__ == "__main__":
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102 seqdic = defaultdict(int)
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103 args = Parser()
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104 log = logging.getLogger(__name__)
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105 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
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106 main(args.input, args.output, args.type)