Mercurial > repos > drosofff > msp_fasta_tabular_converter

annotate fasta_tabular_converter.py @ 2:330dd8a8c31a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 030207144f0811822dbdda9a10e036ff8e794d7c
author drosofff
date Fri, 25 Mar 2016 19:29:40 -0400
parents 2f7278120be9
children 36388b666bfc
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1 #!/usr/bin/python
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2 #
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3 import sys
1
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4 import string
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5 import argparse
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6 from collections import defaultdict
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7
1
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8 def Parser():
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9 the_parser = argparse.ArgumentParser()
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10 the_parser.add_argument(
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11 '--input', action="store", type=str, help="input file")
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12 the_parser.add_argument(
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13 '--output', action="store", type=str, help="output converted file")
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14 the_parser.add_argument(
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15 '--type', action="store", type=str, help="type of convertion")
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16 args = the_parser.parse_args()
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17 return args
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18
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19 def readfasta_writetabular(fasta, tabular, mode="oneline"):
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20 F = open(fasta, "r")
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21 for line in F:
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22 if line[0] == ">":
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23 try:
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24 seqdic["".join(stringlist)] += 1 # to dump the sequence of the previous item - try because of first missing stringlist variable
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25 except: pass
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26 stringlist=[]
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27 else:
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28 stringlist.append(line[:-1])
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29 try:
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30 seqdic["".join(stringlist)] += 1 # for the last sequence
330dd8a8c31a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 030207144f0811822dbdda9a10e036ff8e794d7c
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31 except: pass # in case file to convert is empty
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32 F.close()
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33 F = open(tabular, "w")
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34 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
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35 print >> F, "%s\t%s" % (seq, seqdic[seq])
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36 F.close()
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37
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38
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39 def readtabular_writefasta(tabular, fasta):
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40 F = open(tabular, "r")
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41 Fw = open(fasta, "w")
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42 counter = 0
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43 for line in F:
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44 fields = line.split()
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45 for i in range(int(fields[1])):
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46 counter += 1
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47 print >> Fw, ">%s\n%s" % (counter, fields[0])
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48 F.close()
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49 Fw.close()
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50
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51 def readtabular_writefastaweighted (tabular, fasta):
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52 F = open(tabular, "r")
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53 Fw = open(fasta, "w")
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54 counter = 0
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55 for line in F:
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56 counter += 1
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57 fields = line[:-1].split()
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58 print >> Fw, ">%s_%s\n%s" % (counter, fields[1], fields[0])
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59 F.close()
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60 Fw.close()
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61
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62 def readfastaeighted_writefastaweighted(fastaweigthed_input, fastaweigthed_reparsed):
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63 F = open(fastaweigthed_input, "r")
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64 number_reads = 0
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65 for line in F:
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66 if line[0] == ">":
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67 weigth = int(line[1:-1].split("_")[-1])
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68 number_reads += weigth
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69 else:
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70 seqdic[line[:-1]] += weigth
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71 F.close()
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72 F = open(fastaweigthed_reparsed, "w")
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73 n=0
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74 for seq in sorted(seqdic, key=seqdic.get, reverse=True):
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75 n += 1
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76 print >> F, ">%s_%s\n%s" % (n, seqdic[seq], seq)
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77 F.close()
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78 print "%s reads collapsed" % number_reads
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79
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80 def readfastaeighted_writefasta(fastaweigthed, fasta):
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81 F = open(fastaweigthed, "r")
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82 Fw = open(fasta, "w")
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83 counter = 0
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84 for line in F:
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85 if line[0] == ">":
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86 weigth = int(line[1:-1].split("_")[-1])
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87 else:
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88 seq = line[:-1]
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89 for i in range (weigth):
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90 counter += 1
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91 print >> Fw, ">%s\n%s" % (counter, seq)
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92 F.close()
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93 Fw.close()
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94
1
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95 def main(input, output, type):
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96 if type == "fasta2tabular":
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97 readfasta_writetabular(input, output)
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98 elif type == "tabular2fasta":
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99 readtabular_writefasta(input, output)
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100 elif type == "tabular2fastaweight":
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101 readtabular_writefastaweighted (input, output)
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102 elif type == "fastaweight2fastaweight":
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103 readfastaeighted_writefastaweighted(input, output)
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104 elif type == "fastaweight2fasta":
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105 readfastaeighted_writefasta(input, output)
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106
1
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107 if __name__ == "__main__":
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108 seqdic = defaultdict(int)
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109 args = Parser()
2
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110 main (args.input, args.output, args.type)